Dear Chris:<br><br>Thanks for you reply. You are right. The printf in gromacs 4.0.7 is very different from gromacs 4.5.3. and the output file in gromacs 4.5.3 is right. I think they fixed the bug :)<br><br>Thank you very much,<br>
Kun<br><br><div class="gmail_quote">On Mon, Apr 18, 2011 at 1:41 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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Today's Topics:<br>
<br>
1. Re: Re: energy group exclusions (Justin A. Lemkul)<br>
2. Re: diverging temperature with pressure coupling (Dommert Florian)<br>
3. Cylinder Pulling output file pullx.xvg wron<br>
(<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>)<br>
4. Simulation of CNT with Amber forcefield (majid hasan)<br>
5. Re: Simulation of CNT with Amber forcefield (Justin A. Lemkul)<br>
6. protein-ligand complex tutorial (ahmet y?ld?r?m)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 18 Apr 2011 07:27:27 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Re: energy group exclusions<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DAC201F.2010901@vt.edu">4DAC201F.2010901@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Sikandar Mashayak wrote:<br>
> Also, what about non-bonded interactions within the protein? Does<br>
> exclusion group only exclude the non-bonded interactions between two<br>
> different molecules and non-bonded interactions within the single<br>
> molecule atoms are still computed?<br>
><br>
<br>
Nonbonded interactions are excluded between each defined pair. Therefore, with<br>
<br>
energygrp_excl = Protein Protein SOL SOL<br>
<br>
you are excluding all nonbonded interactions between protein atoms (Protein<br>
Protein pair) and between solvent atoms (SOL SOL pair). Protein-solvent<br>
interactions are calculated. The use of energygrp_excl (as documented)<br>
indicates that only nonbonded interactions are affected. That is, bonded<br>
energies should still be calculated for all groups.<br>
<br>
-Justin<br>
<br>
> On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak<br>
> <<a href="mailto:symashayak@gmail.com">symashayak@gmail.com</a> <mailto:<a href="mailto:symashayak@gmail.com">symashayak@gmail.com</a>>> wrote:<br>
><br>
> Hi<br>
><br>
> When we define energy group exclusions e.g. like in manual energygrp<br>
> excl = Protein Protein SOL SOL<br>
> and do md rerun, then only non-bonded interactions between Protein<br>
> and SOL are computed. I am wondering what happens to bonded<br>
> interactions within the protein, do they contribute to energies even<br>
> though we have excluded protein-protein interactions?<br>
><br>
> thanks<br>
> sikandar<br>
><br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Mon, 18 Apr 2011 13:41:42 +0200<br>
From: Dommert Florian <<a href="mailto:dommert@icp.uni-stuttgart.de">dommert@icp.uni-stuttgart.de</a>><br>
Subject: Re: [gmx-users] diverging temperature with pressure coupling<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <1303126902.2464.107.camel@fermi><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
On Mon, 2011-04-18 at 11:42 +0200, David van der Spoel wrote:<br>
> On 2011-04-18 11.22, Dommert Florian wrote:<br>
> > Hello,<br>
> ><br>
> > oh this nasty ILs ;) I am currently investigating a similar problem,<br>
> > that deals with PR-coupling and my impression is that Leap-Frog is the<br>
> > problem and not PR. Currently I am running simulations with md-vv and<br>
> > MTTK to verify my ideas. On the other hand I am using two tc_groups for<br>
> > my ILs due their difference in size. Unfortunately you have not written<br>
> > which IL you deal with, but thinking about long chain ILs like<br>
> > [BMIM][Cl], or [BMIM][PF6], the degrees of freedom for the different<br>
> > molecules differ strongly. Here the big question is why does the<br>
> > barostat influence the thermostat. It seems one has to be very very<br>
> > careful, when choosing the coupling parameter for PR. I did a bunch of<br>
> > simulations just varying the coupling parameter and obtained large<br>
> > differences in the dynamics of my system, while static properties like<br>
> > RDF, density of mass, and pressure look quite fine. For example if I<br>
> > calculate the conductivity including correlation effects the values<br>
> > differ from 2 S/m up to 12 S/m. But so far I also have no idea why ???<br>
> > I am really happy when I finally got my results with vv and if you are<br>
> > interested I can report back to the list or off-list, just let me know.<br>
> ><br>
> > On the other hand I do not know if the force field could be a problem.<br>
> > PR changes the box size according to a Lagrangian equation of motion in<br>
> > contrast to Berendsen, which just does size rescaling. I do not know how<br>
> > sensible this equations of motions are in respect to the motion of the<br>
> > atoms. Perhaps one can try to perform simulation with a higher accuracy<br>
> > for the electrostatic interactions. I realized that the standard PME<br>
> > settings are quite poor for ILs. Perhaps the Berendsen pressure coupling<br>
> > can deal with this, because it forces the box to scale. PR follows its<br>
> > equations of motions and PERHAPS introduces artefacts if the integration<br>
> > of atomic trajectories is too inaccurate.<br>
> ><br>
> > So my PME settings are like this:<br>
> ><br>
> > rcut=1.3 ( here the force field tells you the number )<br>
> > pme_order=6<br>
> > fourierspacing=0.05<br>
> > rtol=1e-8<br>
> ><br>
> > This are just approximate values, exact numbers can be calculated by<br>
> > g_pme_error for your system.<br>
> ><br>
> Florian, these PME values are scary! Are you running in double precision<br>
> too, otherwise I guess it will be difficult to get the errors as low as<br>
> you want them.<br>
<br>
Hello David,<br>
<br>
these settings yield an accuracy of 10^-4 kJ/(mol nm), which should be<br>
captured by a single precision calculation, if I take into account that<br>
I have forces around 100kJ/(mol nm). Am I wrong ?<br>
<br>
> As regards the Temperature diversion (no pun intended), this is a known<br>
> issue also with Berendsen T,P coupling. The reason for this is lack of<br>
> interaction between the different subsystems. It is interesting to hear<br>
> the PR makes it worse though, because of the better ensemble properties.<br>
><br>
> If this also has an effect on dynamic properties all of us are in even<br>
> more trouble. I recently had problems reproducing dielectric constants.<br>
> I will now redo my simulation with Berendsen P-coupling instead of PR,<br>
> even though grompp tells me not to!<br>
><br>
<br>
So I assume the rerun with Berendsen will give you faster dynamics,<br>
which I had when using Berendsen. However as you mentioned you get into<br>
problems for creating a correct canonical ensemble.<br>
<br>
Cheers,<br>
<br>
Flo<br>
<br>
<br>
> > Cheers,<br>
> ><br>
> > Flo<br>
> ><br>
> ><br>
> > On Sun, 2011-04-17 at 03:10 -0400, Roland Schulz wrote:<br>
> >> Forwarding this email from my group colleague:<br>
> >><br>
> >><br>
> >> Dear Gromacs users,<br>
> >><br>
> >><br>
> >><br>
> >> I am trying to simulate a cellulose fiber in an ionic liquid solution<br>
> >> in the NPT ensemble. During the simulation, the entire system is<br>
> >> coupled to a thermostat. Yet, I observe an inhomogeneous temperature<br>
> >> distribution throughout my system (hot-solvent/cold-solute) when I use<br>
> >> Parrinello-Rahman pressure coupling but NOT when I employ Berendsen<br>
> >> pressure coupling. I have tested velocity-rescaling and the<br>
> >> Nose-Hoover scheme to keep the temperature constant and in both cases<br>
> >> Parrinello-Rahman pressure coupling seems to cause the solute’s<br>
> >> temperature to become significantly lower than the solvent’s (to<br>
> >> decompose temperatures, I am using “mdrun -rerun” with a run input<br>
> >> that defines tc_grps separately).<br>
> >><br>
> >><br>
> >><br>
> >> I was wondering whether there were any known algorithmic reasons for<br>
> >> this unphysical temperature gradient when using Parrinello-Rahman<br>
> >> pressure coupling.<br>
> >><br>
> >> Thank you.<br>
> >><br>
> >> Barmak<br>
> >><br>
> >><br>
> >> Comment from me: The effect is large. The ionic liquid is 5 degrees<br>
> >> higher and the cellulose is 50 degrees lower (after 50ps, after that<br>
> >> it stays constant). With Berendsen pressure both parts fluctuate<br>
> >> around the same target temperature (as one would expect). Any reason<br>
> >> why one doesn't get the correct temperature with rerun? Or is their a<br>
> >> better way to get the temperature for different groups(for a<br>
> >> simulation with just one tc-group)? Any reason why Parrinello-Rahman<br>
> >> pressure coupling would have this effect on the temperature?<br>
> >><br>
> >><br>
> >> Roland<br>
> >><br>
> >><br>
> >> --<br>
> >> ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br>
> >> <a href="tel:865-241-1537" value="+18652411537">865-241-1537</a>, ORNL PO BOX 2008 MS6309<br>
> >> --<br>
> >> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> >> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> >> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
> >> Please don't post (un)subscribe requests to the list. Use the<br>
> >> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> >> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
> ><br>
> ><br>
><br>
><br>
> --<br>
> David van der Spoel, Ph.D., Professor of Biology<br>
> Dept. of Cell & Molec. Biol., Uppsala University.<br>
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
> <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
<br>
<br>
--<br>
Florian Dommert<br>
Dipl. - Phys.<br>
<br>
Institute for Computational Physics<br>
University Stuttgart<br>
<br>
Pfaffenwaldring 27<br>
70569 Stuttgart<br>
<br>
EMail: <a href="mailto:dommert@icp.uni-stuttgart.de">dommert@icp.uni-stuttgart.de</a><br>
Homepage: <a href="http://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert" target="_blank">http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert</a><br>
<br>
Tel.: <a href="tel:%2B49%20-%20%280%29711%20-%2068563613" value="+4971168563613">+49 - (0)711 - 68563613</a><br>
Fax.: <a href="tel:%2B49%20-%20%280%29711%20-%2068563658" value="+4971168563658">+49 - (0)711 - 68563658</a><br>
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Message: 3<br>
Date: Mon, 18 Apr 2011 11:53:28 -0400<br>
From: <a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a><br>
Subject: [gmx-users] Cylinder Pulling output file pullx.xvg wron<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:20110418115328.1gv8f4f0asg04gw8@webmail.utoronto.ca">20110418115328.1gv8f4f0asg04gw8@webmail.utoronto.ca</a>><br>
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format="flowed"<br>
<br>
That part of the pull code has a different printf statement in version<br>
4.5.3. Can you test 4.0.7 output vs. 4.5.3 output and see if 4.5.3 is<br>
correct? You could simple use nsteps=0 genvel=no and load a .gro with<br>
no velocities in your mdrun.<br>
<br>
Chris.<br>
<br>
-- original message --<br>
<br>
I am trying cylinder pulling as an option of umbrella sampling using gromacs<br>
4.0.7. Things seem to work but I noticed that in the output file pullx.xvg,<br>
the referece group's postion is always 0. I don't think it is right. When I<br>
use position pulling, the reference position is never 0.<br>
<br>
Thanks for you help.<br>
Kun<br>
<br>
Below is my .mdp file<br>
pull = umbrella<br>
pull_geometry = cylinder<br>
pull_r1 = 1.0<br>
Pull_r0 = 1.0<br>
pull_dim = N N Y<br>
pull_start = yes<br>
pull_init1 = 0.0<br>
pull_ngroups = 1<br>
pull_group0 = group0<br>
pull_group1 = group1<br>
pull_rate1 = 0.01<br>
pull_vec1 = 0.0 0.0 -1.0<br>
pull_k1 = 3000 ; kJ mol^-1 nm^-2<br>
pull_nstxout = 1000<br>
pull_nstfout = 1000<br>
<br>
Here is the output:<br>
<br>
@ title "Pull COM"<br>
@ xaxis label "Time (ps)"<br>
@ yaxis label "Position (nm)"<br>
@TYPE xy<br>
@ view 0.15, 0.15, 0.75, 0.85<br>
@ legend on<br>
@ legend box on<br>
@ legend loctype view<br>
@ legend 0.78, 0.8<br>
@ legend length 2<br>
@ s0 legend "0 Z"<br>
@ s1 legend "1 dZ"<br>
0.0000 0 5.69818<br>
2.0000 0 5.67685<br>
4.0000 0 5.68564<br>
6.0000 0 5.65461<br>
8.0000 0 5.63482<br>
10.0000 0 5.61658<br>
12.0000 0 5.61679<br>
14.0000 0 5.54434<br>
16.0000 0 5.55352<br>
18.0000 0 5.4964<br>
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<br>
Message: 4<br>
Date: Mon, 18 Apr 2011 10:17:12 -0700 (PDT)<br>
From: majid hasan <<a href="mailto:pu_majidhasan@yahoo.com">pu_majidhasan@yahoo.com</a>><br>
Subject: [gmx-users] Simulation of CNT with Amber forcefield<br>
To: gms-users mailing list <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:674190.93212.qm@web38304.mail.mud.yahoo.com">674190.93212.qm@web38304.mail.mud.yahoo.com</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Dear All,<br>
<br>
I am doing a DNA-CNT simulation, and I am trying to generate a topology of CNT<br>
using Amber99, which has been used for such systems, and CNT atoms are modeled<br>
using sp2 carbon parameters.<br>
<br>
But when I try to create topology file using: pdb2gmx -f cnt.pdb -p cnt.top, and<br>
Amber99 forcefield, I get this error:<br>
Fatal Error:<br>
Atom C in residue C 1 was not found in rtp entry RCN with 30 atoms while sorting<br>
atoms.<br>
<br>
During the execution, it says "There are 1 chains and 0 blocks of water and 1<br>
residues with 168 atoms" after analyzing pdb file.<br>
<br>
So I suspect problem is that it reads carbon as a residue in my .pdb file.<br>
<br>
If this is the problem, then how do I make sure that it reads carbon as an atom<br>
and not a residue?<br>
<br>
My .pdb file has entries of the form:<br>
ATOM 1 C C A 1 4.039 ....<br>
ATOM 2 C C A 1 3.97 ....<br>
<br>
Thanks for your help,<br>
Majid<br>
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Message: 5<br>
Date: Mon, 18 Apr 2011 13:25:39 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Simulation of CNT with Amber forcefield<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DAC7413.9090109@vt.edu">4DAC7413.9090109@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
majid hasan wrote:<br>
> Dear All,<br>
><br>
> I am doing a DNA-CNT simulation, and I am trying to generate a topology<br>
> of CNT using Amber99, which has been used for such systems, and CNT<br>
> atoms are modeled using sp2 carbon parameters.<br>
><br>
> But when I try to create topology file using: pdb2gmx -f cnt.pdb -p<br>
> cnt.top, and Amber99 forcefield, I get this error:<br>
<br>
Have you created an .rtp entry for your CNT? I doubt that it's even possible<br>
for cyclic molecules like this one. pdb2gmx is only useful for linear molecules<br>
composed of repeating building blocks, with limited support for branching. You<br>
may want to consult:<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube" target="_blank">http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube</a><br>
<br>
Some of that information is outdated, but there is a plethora of information in<br>
the list archive about proper CNT topology generation. Search for posts by<br>
Christopher Stiles.<br>
<br>
> Fatal Error:<br>
> Atom C in residue C 1 was not found in rtp entry RCN with 30 atoms while<br>
> sorting atoms.<br>
><br>
<br>
This answers my question above. Your structure is being interpreted as RNA.<br>
Without significant effort and perhaps code modification, pdb2gmx is not likely<br>
to be useful here.<br>
<br>
> During the execution, it says "There are 1 chains and 0 blocks of water<br>
> and 1 residues with 168 atoms" after analyzing pdb file.<br>
><br>
> So I suspect problem is that it reads carbon as a residue in my .pdb file.<br>
><br>
> If this is the problem, then how do I make sure that it reads carbon as<br>
> an atom and not a residue?<br>
><br>
> My .pdb file has entries of the form:<br>
> ATOM 1 C C A 1 4.039 ....<br>
> ATOM 2 C C A 1 3.97 ....<br>
><br>
<br>
Well, you've named your residues "C" and the component atoms "C" so there's no<br>
real confusion about anything. It's also not the source of your problems.<br>
<br>
g_x2top may be a useful program for generating a topology, or perhaps other<br>
software that is entirely unrelated to Gromacs.<br>
<br>
-Justin<br>
<br>
> Thanks for your help,<br>
> Majid<br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Mon, 18 Apr 2011 20:40:49 +0300<br>
From: ahmet y?ld?r?m <<a href="mailto:ahmedo047@gmail.com">ahmedo047@gmail.com</a>><br>
Subject: [gmx-users] protein-ligand complex tutorial<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <BANLkTi=<a href="mailto:QgPp3bc%2BegScOMvrUVR7Acfwo8g@mail.gmail.com">QgPp3bc+egScOMvrUVR7Acfwo8g@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear Justin,<br>
<br>
You prepared a useful tutorial. if you used PO4 ligand (which has 2<br>
molecule) instead of 1JZ4 ligand from 3HTB.pdb, Then, in the .itp and .gro<br>
files of ligand because of 2 molecule, what change?<br>
Can you give some hint?<br>
Thanks<br>
<br>
3HTB.pdb<br>
....<br>
<br>
TER 1365 ASN A 163<br>
HETATM 1366 P PO4 A 165 15.430 -26.507 12.040 0.70 13.01 P<br>
HETATM 1367 O1 PO4 A 165 16.899 -26.359 11.761 0.70 8.42 O<br>
HETATM 1368 O2 PO4 A 165 14.565 -25.571 11.281 0.70 12.47 O<br>
HETATM 1369 O3 PO4 A 165 15.071 -28.010 11.811 0.70 11.58 O<br>
HETATM 1370 O4 PO4 A 165 15.042 -26.318 13.543 0.70 11.36 O<br>
HETATM 1371 P PO4 A 166 21.741 0.620 -18.648 0.50 20.49 P<br>
HETATM 1372 O1 PO4 A 166 23.073 -0.065 -18.917 0.50 18.04 O<br>
HETATM 1373 O2 PO4 A 166 21.958 2.010 -19.153 0.50 19.25 O<br>
HETATM 1374 O3 PO4 A 166 20.616 -0.014 -19.484 0.50 14.22 O<br>
HETATM 1375 O4 PO4 A 166 21.425 0.662 -17.127 0.50 15.77 O<br>
HETATM 1376 C4 JZ4 A 167 24.294 -24.124 -0.071 1.00 16.39 C<br>
..<br>
<br>
<br>
<br>
--<br>
Ahmet YILDIRIM<br>
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End of gmx-users Digest, Vol 84, Issue 150<br>
******************************************<br>
</font></blockquote></div><br><br clear="all"><br>-- <br>Kun Huang<br>Department of Physics, Rensselaer Polytechnic Institute. <br>Troy, NY. 12180. <br><br>