[gmx-users] to visualise protein conformation after every 1ns
Hello All, Sorry for a dumb question,,but I have a query that I want to run a 5 ns simulation on one of the protein and I want to see protein's conformation after every 1 ns,i.e to have a pdb file, so how should I proceed or changes should I make in mdp file. Thanks -- Sonali Dhindwal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] to visualise protein conformation after every 1ns
On 7/16/10 9:02 AM, sonali dhindwal wrote: Hello All, Sorry for a dumb question,,but I have a query that I want to run a 5 ns simulation on one of the protein and I want to see protein's conformation after every 1 ns,i.e to have a pdb file, so how should I proceed or changes should I make in mdp file. Thanks -- Sonali Dhindwal trjconv -o koko.pdb -dt 1000 -s -f -sep -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Subject: [gmx-users] to visualise protein conformation after every 1ns
You can use the command trjconv to obtain them. trjconv -s md -f md -dt 1000 -o out.pdb For more information, please see the help of trjconv. Zhang Cun Message: 7 Date: Fri, 16 Jul 2010 12:32:36 +0530 (IST) From: sonali dhindwal sonali11dhind...@yahoo.co.in Subject: [gmx-users] to visualise protein conformation after every 1ns To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 707407.78411...@web94615.mail.in2.yahoo.com Content-Type: text/plain; charset=utf-8 Hello All, Sorry for a dumb question,,but I have a query that I want to run a 5 ns simulation on one of the protein and I want to see protein's conformation after every 1 ns,i.e to have a pdb file, so how should I proceed or changes should I make in mdp file. Thanks -- Sonali Dhindwal -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100716/d4991a77/attachment.html -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 75, Issue 88 * -- Blog: http://www.edwardpku.com/cun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] to visualise protein conformation after every 1ns
Hello Sir, Thanks for the reply, I tried to run this commad on a simuation which I started to ran for 10 ns,and has already completed around 3 ns I gave trjconv -o 1ns.pdb -dt 1000 -s topol.tpr -f traj.xtc -sep after this it asked for selecting which one I want among, System, protein,bacakbone,c-alpha etc, I selected system, and the output is three files, namely 1ns0.pdb 1ns1.pdb 1ns2.pdb 1ns3.pdb Am I doing it correct ? Thanks -- Sonali Dhindwal --- On Fri, 16/7/10, David van der Spoel sp...@xray.bmc.uu.se wrote: From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, 16 July, 2010, 12:34 PM On 7/16/10 9:02 AM, sonali dhindwal wrote: Hello All, Sorry for a dumb question,,but I have a query that I want to run a 5 ns simulation on one of the protein and I want to see protein's conformation after every 1 ns,i.e to have a pdb file, so how should I proceed or changes should I make in mdp file. Thanks -- Sonali Dhindwal trjconv -o koko.pdb -dt 1000 -s -f -sep -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] to visualise protein conformation after every 1ns
Sonali, Why wouldn't it be correct if you did just what David told you to do? And how would you be able to check yourself whether you were correct? We can't hold your hand here for every step you make. Have you already gone through the tutorial material linked on the Gromacs website? If not, please do so. In any case, try to feel more confident about yourself. You made it to academia already, didn't you? Cheers, Tsjerk On Fri, Jul 16, 2010 at 9:58 AM, sonali dhindwal sonali11dhind...@yahoo.co.in wrote: Hello Sir, Thanks for the reply, I tried to run this commad on a simuation which I started to ran for 10 ns,and has already completed around 3 ns I gave trjconv -o 1ns.pdb -dt 1000 -s topol.tpr -f traj.xtc -sep after this it asked for selecting which one I want among, System, protein,bacakbone,c-alpha etc, I selected system, and the output is three files, namely 1ns0.pdb 1ns1.pdb 1ns2.pdb 1ns3.pdb Am I doing it correct ? Thanks -- Sonali Dhindwal --- On *Fri, 16/7/10, David van der Spoel sp...@xray.bmc.uu.se* wrote: From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, 16 July, 2010, 12:34 PM On 7/16/10 9:02 AM, sonali dhindwal wrote: Hello All, Sorry for a dumb question,,but I have a query that I want to run a 5 ns simulation on one of the protein and I want to see protein's conformation after every 1 ns,i.e to have a pdb file, so how should I proceed or changes should I make in mdp file. Thanks -- Sonali Dhindwal trjconv -o koko.pdb -dt 1000 -s -f -sep -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone:46 18 471 4205fax: 46 18 511 755 sp...@xray.bmc.uu.se http://mc/compose?to=sp...@xray.bmc.uu.se sp...@gromacs.org http://mc/compose?to=sp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.orghttp://mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.orghttp://mc/compose?to=gmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to write a frames.ndx for -fr option of trjconv
Dear Gromacs users, I need trjconv to write me pdb files at a list of frames that are randomly chosen throughout the whole production trajectory (they belong to the least energetic 100 frames). I can use trjconv to write a pdb at each frame but this is gonna be time consuming, so I looked in the specifications of trjconv and found that there is an optional input -fr frames.ndx, I guess this might be useful for what I want but I am not quite sure how to write an index file for randomly distributed frames points not for atoms or residues, the command make_ndx doesn;t provide any options for frames of time points!! I tried to create an ndx file manually by writing the frames numbers in a txt file, calling it frames.ndx, feed this to the -fr option of trjconv, as I expected, trjconv dealt with the numbers as numbers of atoms not of frames! How can I tell trjconv that the numbers in frames.ndx file are actually numbers of specific time points not of residues. Any help or hint is very appreciated.. Thanks alot Hassan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_lie query
Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] inversion of lipid bilayer with water in the centre
Dear Gromacs Users, I have a lipid bilayer with me and I would like to simulate a system by keeping the water molecules with proteins in it and lipid surrounding the water on both sides, can any body suggest me please... Thanks Ram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] to visualise protein conformation after every 1ns
Thanks Tsjerk, I was confused, that why 3 files are generated as output. I will check it. I appreciate what you said, I will read more. Regards -- Sonali Dhindwal --- On Fri, 16/7/10, Tsjerk Wassenaar tsje...@gmail.com wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, 16 July, 2010, 1:43 PM Sonali, Why wouldn't it be correct if you did just what David told you to do? And how would you be able to check yourself whether you were correct? We can't hold your hand here for every step you make. Have you already gone through the tutorial material linked on the Gromacs website? If not, please do so. In any case, try to feel more confident about yourself. You made it to academia already, didn't you? Cheers, On Fri, Jul 16, 2010 at 9:58 AM, sonali dhindwal sonali11dhind...@yahoo.co.in wrote: Hello Sir, Thanks for the reply, I tried to run this commad on a simuation which I started to ran for 10 ns,and has already completed around 3 ns I gave trjconv -o 1ns.pdb -dt 1000 -s topol.tpr -f traj.xtc -sep after this it asked for selecting which one I want among, System, protein,bacakbone,c-alpha etc, I selected system, and the output is three files, namely 1ns0.pdb 1ns1.pdb 1ns2.pdb 1ns3.pdb Am I doing it correct ? Thanks -- Sonali Dhindwal --- On Fri, 16/7/10, David van der Spoel sp...@xray.bmc.uu.se wrote: From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, 16 July, 2010, 12:34 PM On 7/16/10 9:02 AM, sonali dhindwal wrote: Hello All, Sorry for a dumb question,,but I have a query that I want to run a 5 ns simulation on one of the protein and I want to see protein's conformation after every 1 ns,i.e to have a pdb file, so how should I proceed or changes should I make in mdp file. Thanks -- Sonali Dhindwal trjconv -o koko.pdb -dt 1000 -s -f -sep -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone:46 18 471 4205fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] scripting question
Dear Gromacs users, This question is much more of a unix/linux scripting issue. Let's say I have 10 pdb files named mt_1.pdb, mt_2.pdb, .mt_10.pdb. If I need to energy minimize the 10 pdb files using the same em.mdp and the same mt.top file, how can I create a script for minimizing the 10 files without me specifying each file for grommp and mdrun on an individual basis, for 10 files it could be fine, but for more files like 100 or 200, this is quite time consuming and liable for errors? Any help of hint is very appreciated Hassan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] to visualise protein conformation after every 1ns
0ns, 1ns, 2ns and 3ns gives four files. On 16 July 2010 10:47, sonali dhindwal sonali11dhind...@yahoo.co.in wrote: Thanks Tsjerk, I was confused, that why 3 files are generated as output. I will check it. I appreciate what you said, I will read more. Regards -- Sonali Dhindwal --- On *Fri, 16/7/10, Tsjerk Wassenaar tsje...@gmail.com* wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, 16 July, 2010, 1:43 PM Sonali, Why wouldn't it be correct if you did just what David told you to do? And how would you be able to check yourself whether you were correct? We can't hold your hand here for every step you make. Have you already gone through the tutorial material linked on the Gromacs website? If not, please do so. In any case, try to feel more confident about yourself. You made it to academia already, didn't you? Cheers, On Fri, Jul 16, 2010 at 9:58 AM, sonali dhindwal sonali11dhind...@yahoo.co.inhttp://mc/compose?to=sonali11dhind...@yahoo.co.in wrote: Hello Sir, Thanks for the reply, I tried to run this commad on a simuation which I started to ran for 10 ns,and has already completed around 3 ns I gave trjconv -o 1ns.pdb -dt 1000 -s topol.tpr -f traj.xtc -sep after this it asked for selecting which one I want among, System, protein,bacakbone,c-alpha etc, I selected system, and the output is three files, namely 1ns0.pdb 1ns1.pdb 1ns2.pdb 1ns3.pdb Am I doing it correct ? Thanks -- Sonali Dhindwal --- On *Fri, 16/7/10, David van der Spoel sp...@xray.bmc.uu.sehttp://mc/compose?to=sp...@xray.bmc.uu.se * wrote: From: David van der Spoel sp...@xray.bmc.uu.sehttp://mc/compose?to=sp...@xray.bmc.uu.se Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: Discussion list for GROMACS users gmx-users@gromacs.orghttp://mc/compose?to=gmx-us...@gromacs.org Date: Friday, 16 July, 2010, 12:34 PM On 7/16/10 9:02 AM, sonali dhindwal wrote: Hello All, Sorry for a dumb question,,but I have a query that I want to run a 5 ns simulation on one of the protein and I want to see protein's conformation after every 1 ns,i.e to have a pdb file, so how should I proceed or changes should I make in mdp file. Thanks -- Sonali Dhindwal trjconv -o koko.pdb -dt 1000 -s -f -sep -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.se http://mc/compose?to=sp...@xray.bmc.uu.se sp...@gromacs.org http://mc/compose?to=sp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.orghttp://mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.orghttp://mc/compose?to=gmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-users@gromacs.orghttp://mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.orghttp://mc/compose?to=gmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.orghttp://mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.orghttp://mc/compose?to=gmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list
Re: [gmx-users] scripting question
google: for loop bash On Fri, 16 Jul 2010 02:57:12 -0700, Hassan Shallal wrote Dear Gromacs users, This question is much more of a unix/linux scripting issue. Let's say I have 10 pdb files named mt_1.pdb, mt_2.pdb, .mt_10.pdb. If I need to energy minimize the 10 pdb files using the same em.mdp and the same mt.top file, how can I create a script for minimizing the 10 files without me specifying each file for grommp and mdrun on an individual basis, for 10 files it could be fine, but for more files like 100 or 200, this is quite time consuming and liable for errors? Any help of hint is very appreciated Hassan -- Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to write a frames.ndx for -fr option of trjconv
Hassan Shallal wrote: Dear Gromacs users, I need trjconv to write me pdb files at a list of frames that are randomly chosen throughout the whole production trajectory (they belong to the least energetic 100 frames). I can use trjconv to write a pdb at each frame but this is gonna be time consuming, so I looked in the specifications of trjconv and found that there is an optional input -fr frames.ndx, I guess this might be useful for what I want but I am not quite sure how to write an index file for randomly distributed frames points not for atoms or residues, the command make_ndx doesn;t provide any options for frames of time points!! I tried to create an ndx file manually by writing the frames numbers in a txt file, calling it frames.ndx, feed this to the -fr option of trjconv, as I expected, trjconv dealt with the numbers as numbers of atoms not of frames! How can I tell trjconv that the numbers in frames.ndx file are actually numbers of specific time points not of residues. That's what it's supposed to do, so I'd suspect that there's something wrong with your index file. If you want to write out frames 1 and 2, for instance, your frames.ndx file should be something like: [ frames ] 1 2 -Justin Any help or hint is very appreciated.. Thanks alot Hassan -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] inversion of lipid bilayer with water in the centre
ram bio wrote: Dear Gromacs Users, I have a lipid bilayer with me and I would like to simulate a system by keeping the water molecules with proteins in it and lipid surrounding the water on both sides, can any body suggest me please... If you place the bilayer at the bottom of the unit cell, and the protein in water above the bilayer, then you indeed have a protein that is bounded by the leaflets of the membrane through PBC. If you want to render that in some way such that you have the protein sandwiched within the leaflets of the membrane, you can use trjconv -center to center the unit cell around the protein, or perhaps trjconv -trans. For the purposes of actually running the simulation, though, the PBC takes care of your issue fairly easily. -Justin Thanks Ram -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] scripting question
Thanks alot Rui for the hint From: gmx-users-boun...@gromacs.org on behalf of J. Rui Rodrigues Sent: Fri 7/16/2010 3:26 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] scripting question google: for loop bash On Fri, 16 Jul 2010 02:57:12 -0700, Hassan Shallal wrote Dear Gromacs users, This question is much more of a unix/linux scripting issue. Let's say I have 10 pdb files named mt_1.pdb, mt_2.pdb, .mt_10.pdb. If I need to energy minimize the 10 pdb files using the same em.mdp and the same mt.top file, how can I create a script for minimizing the 10 files without me specifying each file for grommp and mdrun on an individual basis, for 10 files it could be fine, but for more files like 100 or 200, this is quite time consuming and liable for errors? Any help of hint is very appreciated Hassan -- Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt http://webmail.estg.ipleiria.pt/ ) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] to visualise protein conformation after every 1ns
ok, 4 files, my mistake, I checked all the files and they have RMSD among themselves of 2-3 Angstrom, can you please explain it why it is so ? Thanks -- Sonali Dhindwal --- On Fri, 16/7/10, Oliver Grant olymacfoo...@gmail.com wrote: From: Oliver Grant olymacfoo...@gmail.com Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, 16 July, 2010, 3:36 PM 0ns, 1ns, 2ns and 3ns gives four files. On 16 July 2010 10:47, sonali dhindwal sonali11dhind...@yahoo.co.in wrote: Thanks Tsjerk, I was confused, that why 3 files are generated as output. I will check it. I appreciate what you said, I will read more. Regards -- Sonali Dhindwal --- On Fri, 16/7/10, Tsjerk Wassenaar tsje...@gmail.com wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, 16 July, 2010, 1:43 PM Sonali, Why wouldn't it be correct if you did just what David told you to do? And how would you be able to check yourself whether you were correct? We can't hold your hand here for every step you make. Have you already gone through the tutorial material linked on the Gromacs website? If not, please do so. In any case, try to feel more confident about yourself. You made it to academia already, didn't you? Cheers, On Fri, Jul 16, 2010 at 9:58 AM, sonali dhindwal sonali11dhind...@yahoo.co.in wrote: Hello Sir, Thanks for the reply, I tried to run this commad on a simuation which I started to ran for 10 ns,and has already completed around 3 ns I gave trjconv -o 1ns.pdb -dt 1000 -s topol.tpr -f traj.xtc -sep after this it asked for selecting which one I want among, System, protein,bacakbone,c-alpha etc, I selected system, and the output is three files, namely 1ns0.pdb 1ns1.pdb 1ns2.pdb 1ns3.pdb Am I doing it correct ? Thanks -- Sonali Dhindwal --- On Fri, 16/7/10, David van der Spoel sp...@xray.bmc.uu.se wrote: From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, 16 July, 2010, 12:34 PM On 7/16/10 9:02 AM, sonali dhindwal wrote: Hello All, Sorry for a dumb question,,but I have a query that I want to run a 5 ns simulation on one of the protein and I want to see protein's conformation after every 1 ns,i.e to have a pdb file, so how should I proceed or changes should I make in mdp file. Thanks -- Sonali Dhindwal trjconv -o koko.pdb -dt 1000 -s -f -sep -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone:46 18 471 4205fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -Inline Attachment Follows- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please
[gmx-users] Selecting a force field for dioxane
Hi, I would like to know if anybody has reproduced the physical properties of dioxane (like dielectric constant, dipole moment, etc) in GROMACS. If so, what force field was found to be optimum? If not, then anybody has any idea about which force field to start with? Thanking you, banskt -- --- Saikat Banerjee Integrated Ph.D student Solid State and Structural Chemistry Unit (SSCU) Indian Institute of Science Bangalore-560012 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] to visualise protein conformation after every 1ns
sonali dhindwal wrote: ok, 4 files, my mistake, I checked all the files and they have RMSD among themselves of 2-3 Angstrom, can you please explain it why it is so ? Why wouldn't they? Are you expecting them to be the same? You won't get much in the way of an explanation for most questions like these. Only you know the system you're studying, how flexible it might be, etc. -Justin Thanks -- Sonali Dhindwal --- On *Fri, 16/7/10, Oliver Grant /olymacfoo...@gmail.com/* wrote: From: Oliver Grant olymacfoo...@gmail.com Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, 16 July, 2010, 3:36 PM 0ns, 1ns, 2ns and 3ns gives four files. On 16 July 2010 10:47, sonali dhindwal sonali11dhind...@yahoo.co.in /mc/compose?to=sonali11dhind...@yahoo.co.in wrote: Thanks Tsjerk, I was confused, that why 3 files are generated as output. I will check it. I appreciate what you said, I will read more. Regards -- Sonali Dhindwal --- On *Fri, 16/7/10, Tsjerk Wassenaar /tsje...@gmail.com /mc/compose?to=tsje...@gmail.com/* wrote: From: Tsjerk Wassenaar tsje...@gmail.com /mc/compose?to=tsje...@gmail.com Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: Discussion list for GROMACS users gmx-users@gromacs.org /mc/compose?to=gmx-us...@gromacs.org Date: Friday, 16 July, 2010, 1:43 PM Sonali, Why wouldn't it be correct if you did just what David told you to do? And how would you be able to check yourself whether you were correct? We can't hold your hand here for every step you make. Have you already gone through the tutorial material linked on the Gromacs website? If not, please do so. In any case, try to feel more confident about yourself. You made it to academia already, didn't you? Cheers, On Fri, Jul 16, 2010 at 9:58 AM, sonali dhindwal sonali11dhind...@yahoo.co.in http://mc/compose?to=sonali11dhind...@yahoo.co.in wrote: Hello Sir, Thanks for the reply, I tried to run this commad on a simuation which I started to ran for 10 ns,and has already completed around 3 ns I gave trjconv -o 1ns.pdb -dt 1000 -s topol.tpr -f traj.xtc -sep after this it asked for selecting which one I want among, System, protein,bacakbone,c-alpha etc, I selected system, and the output is three files, namely 1ns0.pdb 1ns1.pdb 1ns2.pdb 1ns3.pdb Am I doing it correct ? Thanks -- Sonali Dhindwal --- On *Fri, 16/7/10, David van der Spoel /sp...@xray.bmc.uu.se http://mc/compose?to=sp...@xray.bmc.uu.se/* wrote: From: David van der Spoel sp...@xray.bmc.uu.se http://mc/compose?to=sp...@xray.bmc.uu.se Subject: Re: [gmx-users] to visualise protein conformation after every 1ns To: Discussion list for GROMACS users gmx-users@gromacs.org http://mc/compose?to=gmx-us...@gromacs.org Date: Friday, 16 July, 2010, 12:34 PM On 7/16/10 9:02 AM, sonali dhindwal wrote: Hello All, Sorry for a dumb question,,but I have a query that I want to run a 5 ns simulation on one of the protein and I want to see protein's conformation after every 1 ns,i.e to have a pdb file, so how should I proceed or changes should I make in mdp file. Thanks -- Sonali Dhindwal trjconv -o koko.pdb -dt 1000 -s -f -sep -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.se http://mc/compose?to=sp...@xray.bmc.uu.se sp...@gromacs.org
Re: [gmx-users] Selecting a force field for dioxane
Saikat Banerjee wrote: Hi, I would like to know if anybody has reproduced the physical properties of dioxane (like dielectric constant, dipole moment, etc) in GROMACS. If so, what force field was found to be optimum? If not, then anybody has any idea about which force field to start with? Surely some literature searching will serve you well. A simple Google search for dioxane md simulation (without the quotes) turns up over 5000 results. -Justin Thanking you, banskt -- --- Saikat Banerjee Integrated Ph.D student Solid State and Structural Chemistry Unit (SSCU) Indian Institute of Science Bangalore-560012 --- -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_lie query
Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Selecting a force field for dioxane
Dear banskt: I would take the LJ(12,6) parameters from AMBER and calculate the electrostatic charges using RESP - http://q4md-forcefieldtools.org/RED/ . Just what I would start with personally. Dr. Vitaly Chaban I would like to know if anybody has reproduced the physical properties of dioxane (like dielectric constant, dipole moment, etc) in GROMACS. If so, what force field was found to be optimum? If not, then anybody has any idea about which force field to start with? Thanking you, banskt -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Avoid generation of angles, pairs and dihedrals from pdb2gmx
Dear all According to the manual, pdb2gmx generates all the angles, pairs and dihedrals automatically in a polymer chain. Because I need nothing of them do you know any fast way to avoid this generation? The only think I found in the manual is to add [ exclusions ] in the .rtp file for whatever I don't want to be generated, but I am wondering if there is any better way. Thanks in advance Chrysostomos -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Avoid generation of angles, pairs and dihedrals from pdb2gmx
You can just delete them in the generated top file. dawei On Fri, Jul 16, 2010 at 10:45 AM, C. Batistakis cbat...@yahoo.gr wrote: Dear all According to the manual, pdb2gmx generates all the angles, pairs and dihedrals automatically in a polymer chain. Because I need nothing of them do you know any fast way to avoid this generation? The only think I found in the manual is to add [ exclusions ] in the .rtp file for whatever I don't want to be generated, but I am wondering if there is any better way. Thanks in advance Chrysostomos -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Need For a Script
Dear All, I am a new GROMACS user. I have been able to solvate a protein in a water box and also to simulate it and unfold it by heating it. But I have facing problem with the script of AFM pulling. I want to unfold a protein by pulling the two ends of the protein. Can anyone give me a full script for that so that I can standardise my protocol? Suggestion is urgent. Thanks in advance Samrat Pal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] frezzing a bond
Hello, I am trying to freeze a bond (3.5 A) in my system. I used the index file to define group and I added this two lines in my .mdp file. freezegrps = PA NE freezedim = Y Y Y Y Y Y I used g_dist to verify the distance between the freezing atoms and it turned out 3.9 A. I checked my .itp also (distance is 3.5). How can I freeze a bond? Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Charge grps and cut-off
Hi, I am getting these notes when I run grompp: NOTE 3 [file Init/ffsb_init.top]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. initialising group options... processing index file... Analysing residue names: There are: 3484 OTHER residues There are:67PROTEIN residues There are: 0DNA residues There are: 0RNA residues Analysing Protein... Analysing Other... Making dummy/rest group for Acceleration containing 11343 elements Making dummy/rest group for Freeze containing 11343 elements Making dummy/rest group for VCM containing 11343 elements Number of degrees of freedom in T-Coupling group Protein is 1777.76 Number of degrees of freedom in T-Coupling group non-Protein is 20898.23 Making dummy/rest group for User1 containing 11343 elements Making dummy/rest group for User2 containing 11343 elements Making dummy/rest group for XTC containing 10450 elements Making dummy/rest group for Or. Res. Fit containing 11343 elements Making dummy/rest group for QMMM containing 11343 elements T-Coupling has 2 element(s): Protein non-Protein Energy Mon. has 2 element(s): Protein non-Protein Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 2 element(s): Protein rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... Largest charge group radii for Van der Waals: 0.288, 0.263 nm Largest charge group radii for Coulomb: 0.288, 0.263 nm NOTE 4 [file nvtp.mdp]: The sum of the two largest charge group radii (0.551009) is larger than rlist (2.00) - rvdw (2.00) Can someone tell me how to correct these? Pooja On Thu, Jul 15, 2010 at 7:06 PM, Sai Pooja saipo...@gmail.com wrote: Hi, NOTE 4 [file /fs/home/sm868/llamapooja/ffsb/Setup/nvt.mdp]: The sum of the two largest charge group radii (0.510406) is larger than rlist (2.00) - rvdw (2.00) NOTE 5 [file /fs/home/sm868/llamapooja/ffsb/Setup/nvt.mdp]: The sum of the two largest charge group radii (0.510406) is larger than rlist (2.00) - rcoulomb (1.80) How does this effect the simulation? Do these introduce errors? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Need For a Script
Samrat Pal wrote: Dear All, I am a new GROMACS user. I have been able to solvate a protein in a water box and also to simulate it and unfold it by heating it. But I have facing problem with the script of AFM pulling. I want to unfold a protein by pulling the two ends of the protein. Can anyone give me a full script for that so that I can standardise my protocol? Suggestion is urgent. http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling Also, as a bit of advice, don't use the word urgent when asking for free help. You're hoping someone else (who is busy) will find time to solve an issue for you. -Justin Thanks in advance Samrat Pal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] frezzing a bond
Nilesh Dhumal wrote: Hello, I am trying to freeze a bond (3.5 A) in my system. I used the index file to define group and I added this two lines in my .mdp file. freezegrps = PA NE freezedim = Y Y Y Y Y Y I used g_dist to verify the distance between the freezing atoms and it turned out 3.9 A. I checked my .itp also (distance is 3.5). How can I freeze a bond? How about distance restraints instead? Seems like an applicable situation. Or, just define the actual bond in your topology and use constraints. -Justin Nilesh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Charge grps and cut-off
Sai Pooja wrote: Hi, I am getting these notes when I run grompp: NOTE 3 [file Init/ffsb_init.top]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. initialising group options... processing index file... Analysing residue names: There are: 3484 OTHER residues There are:67PROTEIN residues There are: 0DNA residues There are: 0RNA residues Analysing Protein... Analysing Other... Making dummy/rest group for Acceleration containing 11343 elements Making dummy/rest group for Freeze containing 11343 elements Making dummy/rest group for VCM containing 11343 elements Number of degrees of freedom in T-Coupling group Protein is 1777.76 Number of degrees of freedom in T-Coupling group non-Protein is 20898.23 Making dummy/rest group for User1 containing 11343 elements Making dummy/rest group for User2 containing 11343 elements Making dummy/rest group for XTC containing 10450 elements Making dummy/rest group for Or. Res. Fit containing 11343 elements Making dummy/rest group for QMMM containing 11343 elements T-Coupling has 2 element(s): Protein non-Protein Energy Mon. has 2 element(s): Protein non-Protein Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 2 element(s): Protein rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... Largest charge group radii for Van der Waals: 0.288, 0.263 nm Largest charge group radii for Coulomb: 0.288, 0.263 nm NOTE 4 [file nvtp.mdp]: The sum of the two largest charge group radii (0.551009) is larger than rlist (2.00) - rvdw (2.00) Can someone tell me how to correct these? Note 3 is explained in detail in the error message. Beyond that, read about the group concept in the manual. I've never seen Note 4 before, but a 2-nm cutoff is a bit strange for a protein simulation. Any reason you're using such large cutoffs? You may also want to provide your whole .mdp file to see if anyone can spot the underlying issue. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Charge grps and cut-off
Hi, I am trying to reproduce results from a paper which uses this cutoff. The work is on loop-folding and they use implicit solvent. I am using explicit solvent with charmm 27. Below is my mdp file. I am not sure if there is any advantage in using a large cut-off. ; VARIOUS PREPROCESSING OPTIONS title= NVT simulation (constant number, pressure and temperature) cpp = /lib/cpp define =-DPOSRES ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 10 ; OUTPUT CONTROL OPTIONS nstxout = 1 nstvout = 0 nstfout = 0 nstlog = 1 nstenergy= 1 nstxtcout= 0 xtc_precision= 0 xtc-grps = System energygrps = Protein Non-Protein ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 1.8 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME fourierspacing = 0.12 rcoulomb = 1.8 epsilon_rf = 78 vdw-type = Cut-off rvdw = 1.8 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t= 0.2 0.2 ref_t= 300 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no; Assign velocities to particles by taking them randomly from a Maxwell distribution gen_temp = 300.0 ; Temperature to generate corresponding Maxwell distribution gen_seed = ; Seed for (semi) random number generation. ; OPTIONS constraints = all-bonds Pooja On Fri, Jul 16, 2010 at 8:22 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: Hi, I am getting these notes when I run grompp: NOTE 3 [file Init/ffsb_init.top]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. initialising group options... processing index file... Analysing residue names: There are: 3484 OTHER residues There are:67PROTEIN residues There are: 0DNA residues There are: 0RNA residues Analysing Protein... Analysing Other... Making dummy/rest group for Acceleration containing 11343 elements Making dummy/rest group for Freeze containing 11343 elements Making dummy/rest group for VCM containing 11343 elements Number of degrees of freedom in T-Coupling group Protein is 1777.76 Number of degrees of freedom in T-Coupling group non-Protein is 20898.23 Making dummy/rest group for User1 containing 11343 elements Making dummy/rest group for User2 containing 11343 elements Making dummy/rest group for XTC containing 10450 elements Making dummy/rest group for Or. Res. Fit containing 11343 elements Making dummy/rest group for QMMM containing 11343 elements T-Coupling has 2 element(s): Protein non-Protein Energy Mon. has 2 element(s): Protein non-Protein Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 2 element(s): Protein rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... Largest charge group radii for Van der Waals: 0.288, 0.263 nm Largest charge group radii for Coulomb: 0.288, 0.263 nm NOTE 4 [file nvtp.mdp]: The sum of the two largest charge group radii (0.551009) is larger than rlist (2.00) - rvdw (2.00) Can someone tell me how to correct these? Note 3 is explained in detail in the error message. Beyond that, read about the group concept in the manual. I've never seen Note 4 before, but a 2-nm cutoff is a bit strange for a protein simulation. Any reason you're using such large cutoffs? You may also want to provide your whole .mdp file to see if anyone can
Re: [gmx-users] Charge grps and cut-off
Sai Pooja wrote: Hi, I am trying to reproduce results from a paper which uses this cutoff. The work is on loop-folding and they use implicit solvent. I am using explicit solvent with charmm 27. Below is my mdp file. I am not sure if there is any advantage in using a large cut-off. Large cutoffs can cause artifacts. This .mdp file also does not match the error message you quoted before. If it is indeed accurate, then it looks like your .mdp file is being interpreted incorrectly (2.0-nm cutoffs instead of 1.8 nm). If there is a misinterpretation, file a bugzilla. If you've simply posted the wrong file, please post the correct file, if necessary. But I'd suggest you do some homework about the effects of long cutoffs, especially if they deviate from what the force field derivation requires. -Justin ; VARIOUS PREPROCESSING OPTIONS title= NVT simulation (constant number, pressure and temperature) cpp = /lib/cpp define =-DPOSRES ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 10 ; OUTPUT CONTROL OPTIONS nstxout = 1 nstvout = 0 nstfout = 0 nstlog = 1 nstenergy= 1 nstxtcout= 0 xtc_precision= 0 xtc-grps = System energygrps = Protein Non-Protein ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 1.8 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME fourierspacing = 0.12 rcoulomb = 1.8 epsilon_rf = 78 vdw-type = Cut-off rvdw = 1.8 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t= 0.2 0.2 ref_t= 300 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no; Assign velocities to particles by taking them randomly from a Maxwell distribution gen_temp = 300.0 ; Temperature to generate corresponding Maxwell distribution gen_seed = ; Seed for (semi) random number generation. ; OPTIONS constraints = all-bonds Pooja On Fri, Jul 16, 2010 at 8:22 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sai Pooja wrote: Hi, I am getting these notes when I run grompp: NOTE 3 [file Init/ffsb_init.top]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. initialising group options... processing index file... Analysing residue names: There are: 3484 OTHER residues There are:67PROTEIN residues There are: 0DNA residues There are: 0RNA residues Analysing Protein... Analysing Other... Making dummy/rest group for Acceleration containing 11343 elements Making dummy/rest group for Freeze containing 11343 elements Making dummy/rest group for VCM containing 11343 elements Number of degrees of freedom in T-Coupling group Protein is 1777.76 Number of degrees of freedom in T-Coupling group non-Protein is 20898.23 Making dummy/rest group for User1 containing 11343 elements Making dummy/rest group for User2 containing 11343 elements Making dummy/rest group for XTC containing 10450 elements Making dummy/rest group for Or. Res. Fit containing 11343 elements Making dummy/rest group for QMMM containing 11343 elements T-Coupling has 2 element(s): Protein non-Protein Energy Mon. has 2 element(s): Protein non-Protein Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1has 1 element(s): rest User2
