<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><meta charset="utf-8"><span class="Apple-style-span" style="font-family: Times; "><pre><font class="Apple-style-span" face="Arial" size="4"><span class="Apple-style-span" style="font-size: 14px;">Dear Per:</span></font></pre><pre><font class="Apple-style-span" face="Arial" size="4"><span class="Apple-style-span" style="font-size: 14px;">Thanks for your reply. </span></font></pre><pre><font class="Apple-style-span" face="Arial" size="4"><span class="Apple-style-span" style="font-size: 14px;">I did start the simulation from an equilibrated structure. Instead of setting them to 0, if I simply use a large cut-off (say 1.6), everything works just fine. </span></font></pre><pre><font class="Apple-style-span" face="Arial" size="4"><span class="Apple-style-span" style="font-size: 14px;">Best,</span></font></pre><pre><font class="Apple-style-span" face="Arial" size="4"><span class="Apple-style-span" style="font-size: 14px;">Bin</span></font></pre><pre><font class="Apple-style-span" face="Arial" size="4"><span class="Apple-style-span" style="font-size: 14px;"><br></span></font></pre><pre><font class="Apple-style-span" face="Arial" size="4"><span class="Apple-style-span" style="font-size: 14px;"><br></span></font></pre><pre><font class="Apple-style-span" face="Arial" size="4"><span class="Apple-style-span" style="font-size: 14px;"><br></span></font></pre><pre><font class="Apple-style-span" face="Arial" size="4"><span class="Apple-style-span" style="font-size: 14px;">============</span></font></pre><pre><font class="Apple-style-span" face="Arial">Hi,
for implicit solvent, people generally use longer cut-offs, as you noted.
There can be many reasons for your seg. fault, however.
Did you do energy minimization before starting md?
Please also test the same system with using a cut-off to see if that works.
/Per
8 aug 2010 kl. 22.36 skrev BIN ZHANG:
></font><i><font class="Apple-style-span" face="Arial"> But the problem is with this set up, I will always get a "Segmentation fault" with gromacs VERSION 4.5-beta2.
</font></i><font class="Apple-style-span" face="Arial">></font><i><font class="Apple-style-span" face="Arial">
</font></i><font class="Apple-style-span" face="Arial">></font><i><font class="Apple-style-span" face="Arial"> Is this supposed to be a bug or for this version, I can only use a large cutoff?</font>
</i>
</pre></span><div><div>On Aug 8, 2010, at 10:56 PM, <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Send gmx-users mailing list submissions to<br><span class="Apple-tab-span" style="white-space:pre"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br><span class="Apple-tab-span" style="white-space:pre"> </span>http://lists.gromacs.org/mailman/listinfo/gmx-users<br>or, via email, send a message with subject or body 'help' to<br><span class="Apple-tab-span" style="white-space:pre"> </span>gmx-users-request@gromacs.org<br><br>You can reach the person managing the list at<br><span class="Apple-tab-span" style="white-space:pre"> </span>gmx-users-owner@gromacs.org<br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of gmx-users digest..."<br>Today's Topics:<br><br> 1. Best forcefield for DMPC - Protein system (Deniz KARASU)<br> 2. Best forcefield for DMPC - Protein system (Deniz KARASU)<br> 3. cutoff for implicit solvent in gromacs4.5 (BIN ZHANG)<br> 4. Large output files and limited disk space. How do I<span class="Apple-tab-span" style="white-space:pre"> </span>handle<br> them? (NG HUI WEN)<br> 5. Re: Large output files and limited disk space. How do I<br> handle them? (Mark Abraham)<br><br><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Deniz KARASU <karasudeniz@gmail.com><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">August 8, 2010 8:45:08 AM PDT<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">gmx-users@gromacs.org<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>[gmx-users] Best forcefield for DMPC - Protein system</b><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Reply-To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Discussion list for GROMACS users <gmx-users@gromacs.org><br></span></div><br><br>Hi,<br><br>I am planing to use 53a6 ff for my membrane protein system. And I can<br>use Kukol 2009 lipid or Roger 2010 lipid and topology so I wonder is there any<br>problem about 53a6 force field and what is the most suitable force<br>field for membrane protein systems?<br><br>I read from http://www.mail-archive.com/gmx-users@gromacs.org/msg27700.html<br>mail that there are some problems about 53a6 forcefield.<br><br><br>1) Kukol, A., 2009. Lipid models for united-atom molecular dynamics<br>simulations of proteins<br>2) D Poger, WF Van Gunsteren, 2010. A new force field for simulating<br>phosphatidylcholine bilayers.<br><br>Thanks.<br>Deniz.<br><br><br><br><br><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Deniz KARASU <karasudeniz@gmail.com><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">August 8, 2010 8:47:48 AM PDT<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">gmx-users@gromacs.org<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>[gmx-users] Best forcefield for DMPC - Protein system</b><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Reply-To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Discussion list for GROMACS users <gmx-users@gromacs.org><br></span></div><br><br>Hi,<br><br>I am planing to use 53a6 ff for my membrane protein system. And I can<br>use Kukol 2009 lipid or Roger 2010 lipid and topology so I wonder is there any<br>problem about 53a6 force field and what is the most suitable force<br>field for membrane protein systems?<br><br>I read from http://www.mail-archive.com/gmx-users@gromacs.org/msg27700.html<br>mail that there are some problems about 53a6 forcefield.<br><br><br>1) Kukol, A., 2009. Lipid models for united-atom molecular dynamics<br>simulations of proteins<br>2) D Poger, WF Van Gunsteren, 2010. A new force field for simulating<br>phosphatidylcholine bilayers.<br><br>Thanks.<br>Deniz.<br><br><br><br><br><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">BIN ZHANG <zhngbn@gmail.com><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">August 8, 2010 1:36:39 PM PDT<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Discussion list for GROMACS users <gmx-users@gromacs.org><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>[gmx-users] cutoff for implicit solvent in gromacs4.5</b><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Reply-To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Discussion list for GROMACS users <gmx-users@gromacs.org><br></span></div><br><br>Dear all:<br><br>I have a question about the appropriate cut-off usage in implicit solvent simulation. After googling for a while, I found most references mentioning using non cut-off for these type of simulations. For non cut-off, I assume in gromacs using the following parameters:<br><br>coulombtype = Cut-off<br>vdwtype = Cut-off<br>nstype = grid<br>nstlist = 0<br>rlist = 0<br>rcoulomb = 0<br>rvdw = 0<br><br>; implicit solvent options<br>implicit_solvent = GBSA<br>gb_epsilon_solvent = 80<br>gb_algorithm = OBC<br>rgbradii = 0 ; need to be equal to rlist<br><br>But the problem is with this set up, I will always get a "Segmentation fault" with gromacs VERSION 4.5-beta2.<br><br>Is this supposed to be a bug or for this version, I can only use a large cutoff?<br><br>Thanks,<br>Bin<br><br><br><br><br><br><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">"NG HUI WEN" <HuiWen.Ng@nottingham.edu.my><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">August 8, 2010 8:04:57 PM PDT<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><gmx-users@gromacs.org><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>[gmx-users] Large output files and limited disk space. How do I handle them?</b><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Reply-To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Discussion list for GROMACS users <gmx-users@gromacs.org><br></span></div><br><br><div> <div><font color="#000000" size="2" face="Arial">Dear gmxusers,</font></div> <div><font size="2" face="Arial"></font> </div> <div><font size="2" face="Arial">I have a very basic question here which I hope someone could help me with. I was running a couple of simulations over the weekend on a shared cluster and both came to a stop for the same reasons:</font></div> <div><font size="2" face="Arial"> <div dir="ltr"> </div> <div dir="ltr">Program mdrun_mpi, VERSION 4.0.7<br>Source code file: trnio.c, line: 252</div> <div dir="ltr">File input/output error:<br>Cannot write trajectory frame; maybe you are out of quota?</div> <div dir="ltr"> </div></font></div> <div><font size="2" face="Arial">Indeed there were quite a number of large files in my user directory (e.g. the .trr files and etc). I think the problems probably arise from the fact that (i) I am storing my trajectory as full precision .trr files and (ii) setting too small a value for nstxout and nstvout in .mdp. </font></div> <div><font size="2" face="Arial"></font> </div> <div><font size="2" face="Arial">I have seen some tutorials that suggested using "trjconv" to derive the reduced precision .xtc files from the .trr files and then discard the latter. My question is, would this be wise as I am not sure whether I would find myself needing these .trr files in the future.</font></div> <div><font size="2" face="Arial"></font> </div> <div><font size="2" face="Arial">Here's a snippet of my .mdp file. Am I saving my coordinates and velocities too frequently? If I were to increase this, are there any compelling factors that I need to take into considerations?<br>; Run parameters<br>integrator = md ; leap-frog integrator<br>nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns)<br>dt = 0.002 ; 2 fs<br>; Output control<br>nstxout = 100 ; save coordinates every 0.2 ps<br>nstvout = 100 ; save velocities every 0.2 ps<br>nstenergy = 100 ; save energies every 0.2 ps<br>nstlog = 100 ; update log file every 0.2 ps<br></font><font size="2" face="Arial"></font></div><font size="2" face="Arial"></font> <div><font size="2" face="Arial"></font> </div> <div><font size="2" face="Arial">Many thanks for your help!</font></div> <div> </div> << <p><font face="Arial" size="2"><a href="http://www.nottingham.edu.my">Email has been scanned for viruses by UNMC email management service</a></font></p> >> </div><br><br><br><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Mark Abraham <mark.abraham@anu.edu.au><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">August 8, 2010 10:55:50 PM PDT<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Discussion list for GROMACS users <gmx-users@gromacs.org><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>Re: [gmx-users] Large output files and limited disk space. How do I handle them?</b><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 0.5);"><b>Reply-To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Discussion list for GROMACS users <gmx-users@gromacs.org><br></span></div><br><br><br><br>----- Original Message -----<br>From: NG HUI WEN <HuiWen.Ng@nottingham.edu.my><br>Date: Monday, August 9, 2010 13:17<br>Subject: [gmx-users] Large output files and limited disk space. How do I handle them?<br>To: gmx-users@gromacs.org<br><br><span dir="ltr"><p> <table><tbody><tr><td><p> </p><div><font color="#000000" face="Arial" size="2"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Dear gmxusers,</font></div> <div><font face="Arial" size="2"></font><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </div> <div><font face="Arial" size="2"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I have a very basic question here which I hope someone could help me with. I was running a couple of simulations over the weekend on a shared cluster and both came to a stop for the same reasons:</font></div> <div><font face="Arial" size="2"> <div dir="ltr"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </div> <div dir="ltr"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Program mdrun_mpi, VERSION 4.0.7<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Source code file: trnio.c, line: 252</div> <div dir="ltr"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>File input/output error:<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Cannot write trajectory frame; maybe you are out of quota?</div> <div dir="ltr"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </div></font></div> <div><font face="Arial" size="2"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Indeed there were quite a number of large files in my user directory (e.g. the .trr files and etc). I think the problems probably arise from the fact that (i) I am storing my trajectory as full precision .trr files and (ii) setting too small a value for nstxout and nstvout in .mdp. </font></div> <div><font face="Arial" size="2"></font><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </div> <div><font face="Arial" size="2"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I have seen some tutorials that suggested using "trjconv" to derive the reduced precision .xtc files from the .trr files and then discard the latter. My question is, would this be wise as I am not sure whether I would find myself needing these .trr files in the future.</font></div> <div><font face="Arial" size="2"></font><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </div> <div><font face="Arial" size="2"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Here's a snippet of my .mdp file. Am I saving my coordinates and velocities too frequently? If I were to increase this, are there any compelling factors that I need to take into considerations?<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>; Run parameters<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>integrator = md ; leap-frog integrator<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns)<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>dt = 0.002 ; 2 fs<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>; Output control<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>nstxout = 100 ; save coordinates every 0.2 ps<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>nstvout = 100 ; save velocities every 0.2 ps<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>nstenergy = 100 ; save energies every 0.2 ps<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>nstlog = 100 ; update log file every 0.2 ps<br><br></font>See http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume<br><br>Unless you know you need full precision data for some expected analyses, I'd expect most people want nstxout/nstvout every few nanoseconds to enable restarts (possible, but unlikely to be needed). For most analyses, using nstxtcout with suitable output groups is at least an order of magnitude more space-efficient. Also consider how large nstenergy should be.<br><br>Mark</div></td></tr></tbody></table></p></span> <br><br>-- <br>gmx-users mailing list<br>gmx-users@gromacs.org<br>http://lists.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at http://www.gromacs.org/search before posting!</blockquote></div><br></body></html>