<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><br>Hi Mark,<br><br>Are there differences between functions 9 and 1? So can I implement these dihedrals in successive lines, just using function 9 or 1?<br><br>Amin<br>--- On <b>Tue, 2/11/10, gmx-users-request@gromacs.org <i><gmx-users-request@gromacs.org></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: gmx-users-request@gromacs.org <gmx-users-request@gromacs.org><br>Subject: gmx-users Digest, Vol 79, Issue 8<br>To: gmx-users@gromacs.org<br>Date: Tuesday, 2 November, 2010, 5:29<br><br><div class="plainMail">Send gmx-users mailing list submissions to<br> <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br> <a
href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>or, via email, send a message with subject or body 'help' to<br> <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br><br>You can reach the person managing the list at<br> <a ymailto="mailto:gmx-users-owner@gromacs.org" href="/mc/compose?to=gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of gmx-users digest..."<br><br><br>Today's Topics:<br><br> 1. Re: multiple torsions for one dihedral (Mark Abraham)<br> 2. questions about umbrella sampling (<a ymailto="mailto:mircial@sjtu.edu.cn"
href="/mc/compose?to=mircial@sjtu.edu.cn">mircial@sjtu.edu.cn</a>)<br> 3. RE: Reg:walls and pbc xy (Berk Hess)<br> 4. Re: Reg:walls and pbc xy (vinothkumar mohanakrishnan)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Tue, 02 Nov 2010 17:21:29 +1100<br>From: Mark Abraham <<a ymailto="mailto:mark.abraham@anu.edu.au" href="/mc/compose?to=mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>><br>Subject: Re: [gmx-users] multiple torsions for one dihedral<br>To: Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a ymailto="mailto:fbbaf7a444d7e.4cd04899@anu.edu.au" href="/mc/compose?to=fbbaf7a444d7e.4cd04899@anu.edu.au">fbbaf7a444d7e.4cd04899@anu.edu.au</a>><br>Content-Type: text/plain; charset="us-ascii"<br><br>Yes, multiple "type 1"
dihedrals for use with AMBER and CHARMM forcefields can be implemented, either as successive [dihedraltypes] of type 9 (since GROMACS 4.0, IIRC) or as multiple [dihedrals] of type 1 (since ages).<br><br>Mark<br><br>----- Original Message -----<br>From: Amin Arabbagheri <<a ymailto="mailto:amin_arab@yahoo.com" href="/mc/compose?to=amin_arab@yahoo.com">amin_arab@yahoo.com</a>><br>Date: Tuesday, November 2, 2010 17:06<br>Subject: [gmx-users] multiple torsions for one dihedral<br>To: <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><br>-----------------------------------------------------------<br>| > Hi all,<br>> <br>> I'm using AMBER99p force field in GROMACS. In the AMBER forcefield for some dihedrals, there are several values, in which n values are different. <br>> As an example, for C3-C3-N-C, I have<br>> C3-C3-N-C .50 180.0
-4<br>> C3-C3-N-C .15 180.0 -3<br>> C3-C3-N-C .53 0.0 1<br>> <br>> For the version 4, is there a convenient way to use these multiple dihedrals?<br>> Thanks,<br>> Amin<br>> <br> |<br>-----------------------------------------------------------<br>> <br> > -- <br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=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 <br>> <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 ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=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>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20101102/9d1f3ca5/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20101102/9d1f3ca5/attachment-0001.html</a><br><br>------------------------------<br><br>Message: 2<br>Date: Tue, 02 Nov 2010 15:16:55 +0800<br>From: <a ymailto="mailto:mircial@sjtu.edu.cn" href="/mc/compose?to=mircial@sjtu.edu.cn">mircial@sjtu.edu.cn</a><br>Subject: [gmx-users] questions about umbrella sampling<br>To: <a ymailto="mailto:gmx-users@gromacs.org"
href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID: <<a ymailto="mailto:20101102151655.msoayn0bno4gk40k@webmail.sjtu.edu.cn" href="/mc/compose?to=20101102151655.msoayn0bno4gk40k@webmail.sjtu.edu.cn">20101102151655.msoayn0bno4gk40k@webmail.sjtu.edu.cn</a>><br>Content-Type: text/plain; charset=GB2312; DelSp="Yes"; format="flowed"<br><br>Dear All:<br><br>I am using umbrella sampling method to calculate potential of mean<br>force and I encountered the following questions:<br>1, at the *.ppa file, I need to incorporate a parameter indicating the<br>"the position of the pull group will restraint to, relative to the<br>reference group" (i.e., the "pos1" parameter).<br><br>To my understanding, in the initial structure, the pull group is not<br>need to at the exact position defined by the aformationed parameter<br>("pos1" parameter) in the .ppa file. I just need to put
the pull group<br>near that position, am I right?<br><br>2, Since I need to define the position of the pull group relative to<br>the reference group. I need to calculate the mass center of the<br>reference group as well as that of the pull group. Does there any<br>tools in GROMACS to calculate their mass center?<br><br>Thank you very much for your time and your kindness!<br><br>Best Regards<br><br>R-X Gu<br><br><br><br>----- 完成转寄邮件 -----<br><br><br><br><br>------------------------------<br><br>Message: 3<br>Date: Tue, 2 Nov 2010 09:07:19 +0100<br>From: Berk Hess <<a ymailto="mailto:gmx3@hotmail.com" href="/mc/compose?to=gmx3@hotmail.com">gmx3@hotmail.com</a>><br>Subject: RE: [gmx-users] Reg:walls and pbc xy<br>To: Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a
ymailto="mailto:COL113-W21D35D03BE8961C73BD6188E490@phx.gbl" href="/mc/compose?to=COL113-W21D35D03BE8961C73BD6188E490@phx.gbl">COL113-W21D35D03BE8961C73BD6188E490@phx.gbl</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br><br>Hi,<br><br>With wall_r_linpot your wall potential is linear from 1 nm downwards.<br>Since the LJ force is negative at 1 nm, your atoms are attracted to the walls.<br><br>But why not simply use two interfaces? You get double the sampling for free<br>and you do not have to bother with complicated wall setups.<br><br>Berk<br><br>Date: Tue, 2 Nov 2010 11:49:48 +0530<br>From: <a ymailto="mailto:kmvinoth@gmail.com" href="/mc/compose?to=kmvinoth@gmail.com">kmvinoth@gmail.com</a><br>To: <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Subject: [gmx-users] Reg:walls and pbc xy<br><br>Hi Gromacians<br><br>I want to create a liquid-liquid interface and study its
properties. Hence i combined two boxes ( say water and DCE). The two boxes are well equilibrated before merging and i created an interface. Now i want to perform energy minimisation for the interface by appling pbc in the xy direction and using walls. ( If i apply pbc in all the directions i get two interfaces where as i need only one interface hence i am applying it only on the xy direction and removing the boundary condition in the Z direction.).When i performed the energy minimisation for the interfacial system but i found that my system is exploding (several PDB files are written while running mdrun is executed) and i dont know why?.There is no issue when i use pbc in all directions. below is my em.mdp file. any help is highly appreciated.<br><br><br>integrator = steep <br>emtol = 40.0 <br>emstep = 0.01<br>nsteps
= 10000 <br>nstxout = 100 <br>nstvout = 100 <br>nstfout = 100 <br>nstlog = 100 <br><br>nstenergy = 100 <br>nstlist = 5 <br>ns_type = grid <br>rlist = 1.0 <br>coulombtype = PME <br>rcoulomb = 1.0 <br>vdwtype = Cut-off <br>rvdw = 1.0 <br><br>ewald_geometry = 3dc<br>nwall = 2<br>wall_type =
9-3<br>wall_r_linpot = 1<br>wall_atomtype = opls_966 opls_968<br>wall_density = 9-3 9-3<br>wall_ewald_zfac = 3<br>pbc = xy <br>fourierspacing = 0.18 <br><br><br><br>Regards<br>Vinoth<br><br><br>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=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 ymailto="mailto:gmx-users-request@gromacs.org"
href="/mc/compose?to=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>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20101102/2914ee6c/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20101102/2914ee6c/attachment-0001.html</a><br><br>------------------------------<br><br>Message: 4<br>Date: Tue, 2 Nov 2010 14:59:31 +0530<br>From: vinothkumar mohanakrishnan <<a ymailto="mailto:kmvinoth@gmail.com" href="/mc/compose?to=kmvinoth@gmail.com">kmvinoth@gmail.com</a>><br>Subject: Re: [gmx-users] Reg:walls and pbc
xy<br>To: Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID:<br> <AANLkTi=rKZv+<a ymailto="mailto:4nmS0O5htkMLZ4nr0yaWLARCH2VWgd6i@mail.gmail.com" href="/mc/compose?to=4nmS0O5htkMLZ4nr0yaWLARCH2VWgd6i@mail.gmail.com">4nmS0O5htkMLZ4nr0yaWLARCH2VWgd6i@mail.gmail.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Hi Berk<br><br>I need only one interface because if i have two interfaces the "capillary<br>waves from one interface disturb the other even though the distance between<br>the average positions of the two interfaces are larger than the potential<br>cut-off" (this was said in the literature).<br><br>Can anyone explain me why walls are used for interfaces? and what is the<br>purpose of using walls?.<br>suppose if i put nwall =2 where exactly are the walls created? can anyone<br>explain me with an
example?<br><br>i read the manual but it is not making any sense to me. if i know this i<br>know what correction i should make in my mdp file to make it work for pbc<br>xy. any help is highly appreciated.<br><br>Regards<br>Vinoth<br><br>On Tue, Nov 2, 2010 at 1:37 PM, Berk Hess <<a ymailto="mailto:gmx3@hotmail.com" href="/mc/compose?to=gmx3@hotmail.com">gmx3@hotmail.com</a>> wrote:<br><br>> Hi,<br>><br>> With wall_r_linpot your wall potential is linear from 1 nm downwards.<br>> Since the LJ force is negative at 1 nm, your atoms are attracted to the<br>> walls.<br>><br>> But why not simply use two interfaces? You get double the sampling for free<br>> and you do not have to bother with complicated wall setups.<br>><br>> Berk<br>><br>> ------------------------------<br>> Date: Tue, 2 Nov 2010 11:49:48 +0530<br>> From: <a ymailto="mailto:kmvinoth@gmail.com"
href="/mc/compose?to=kmvinoth@gmail.com">kmvinoth@gmail.com</a><br>> To: <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> Subject: [gmx-users] Reg:walls and pbc xy<br>><br>><br>> Hi Gromacians<br>><br>> I want to create a liquid-liquid interface and study its properties. Hence<br>> i combined two boxes ( say water and DCE). The two boxes are well<br>> equilibrated before merging and i created an interface. Now i want to<br>> perform energy minimisation for the interface by appling pbc in the xy<br>> direction and using walls. ( If i apply pbc in all the directions i get two<br>> interfaces where as i need only one interface hence i am applying it only on<br>> the xy direction and removing the boundary condition in the Z<br>> direction.).When i performed the energy minimisation for the interfacial<br>> system but i found that my system
is exploding (several PDB files are<br>> written while running mdrun is executed) and i dont know why?.There is no<br>> issue when i use pbc in all directions. below is my em.mdp file. any help is<br>> highly appreciated.<br>><br>> integrator = steep<br>> emtol = 40.0<br>> emstep = 0.01<br>> nsteps = 10000<br>> nstxout = 100<br>> nstvout = 100<br>> nstfout = 100<br>> nstlog = 100<br>> nstenergy = 100<br>> nstlist = 5<br>> ns_type = grid<br>> rlist = 1.0<br>> coulombtype = PME<br>> rcoulomb = 1.0<br>> vdwtype = Cut-off<br>> rvdw
= 1.0<br>> ewald_geometry = 3dc<br>> nwall = 2<br>> wall_type = 9-3<br>> wall_r_linpot = 1<br>> wall_atomtype = opls_966 opls_968<br>> wall_density = 9-3 9-3<br>> wall_ewald_zfac = 3<br>> pbc = xy<br>> fourierspacing = 0.18<br>><br>><br>> Regards<br>> Vinoth<br>><br>> -- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=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> Please search the<br>> archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before<br>> posting! Please don't post
(un)subscribe requests to the list. Use the www<br>> interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>. Can't post? Read<br>> <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>><br>> --<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=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<br>> <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 ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=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>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20101102/7fffaaa1/attachment.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20101102/7fffaaa1/attachment.html</a><br><br>------------------------------<br><br>-- <br>gmx-users mailing list<br><a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=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><br>End of gmx-users Digest, Vol 79, Issue 8<br>****************************************<br></div></blockquote></td></tr></table><br>