Re: [gmx-users] WHAM
Hi Justin, Thanks a lot for the reply. Yes I have had a look at section 4.4.2. But section 5.3 tells that this WHAM can be used with the REMD data set as well. So my question is that how to present this REMD data of multiple trajectories as input to WHAM? Do I need to work around with the WHAM code or there is some other way? Any suggestion is welcome. Thanks again. Regards, Anirban On Thu, Sep 16, 2010 at 5:28 PM, Justin A. Lemkul wrote: > > > Anirban Ghosh wrote: > >> Hi ALL, >> >> I have carried out REMD simulation on a protein (20 replicas). Now I want >> to carry 2D PMF calculation using RMSD and Radius of gyration as the >> reaction coordinates using Grossfield Lab's WHAM package. For this what >> should be my input parameters to the WHAM program and in which format? >> Any suggestion in this regard is welcome. >> > > I would suggest you consult the documentation for the program (i.e. the > Grossfield WHAM manual, section 4.2.2). I don't know how you intend to pass > your data to a program that is designed for umbrella sampling, but I suppose > that's your task. > > -Justin > > >> >> Regards, >> >> >> Anirban >> >> > -- > > > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Extending REMD simulation
- Original Message - From: henri mone Date: Friday, September 17, 2010 9:36 Subject: [gmx-users] Extending REMD simulation To: gmx-users@gromacs.org, gpor...@gwdg.de > Dear Gromacs experts, > > I started a REMD simulation which terminated succesfully after 4830ps. > I now want to extend it to 50ns. > I'm using Gromacs 4.0.3 which supports checkpoint files. I > got now > around 40 files with the ending "*.cpt" and "*_prev.cpt". > I couldn't find any documentation on how to extend a REMD simulation > via checkpoint file. > The only mailinglist post I found was [1] but there was no reply > to it :( . You simply need an iterative approach on the same lines as for a normal simulation. See http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] about NPT run
zhongjin wrote: Hi, I want to run a NPT run,could I put some groups into position restraint, or make them frozened ? I find it is OK in NVT ensemble. But I am not sure whether it is proper. Frozen groups cannot have their coordinates scaled by pressure coupling. I believe this can lead to spurious contributions to the virial and pressure, so it is generally recommended that NPT not be combined with frozen groups. -Justin Thanks! Zhongjin He -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] about NPT run
Hi, I want to run a NPT run,could I put some groups into position restraint, or make them frozened ? I find it is OK in NVT ensemble. But I am not sure whether it is proper. Thanks!Zhongjin He -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Residue 'MOL' not found in residue topology database
http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9909 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. > -- Forwarded message -- > From: AJANI HARESH > Date: Thu, Sep 16, 2010 at 2:00 PM > Subject: Residue 'MOL' not found in residue topology database > To: tsje...@gmail.com > > > I am using gromacs 4.0. > Currently I am working on one prtein structure and ligand. > > when I use the following command:"pdb2gmx -f 1GT.pdb -p gr.top -o > gr.gro" > > There's a fatal error: > > Residue 'MOL' not found in residue topology database > Fatal error: Residue '' not found in residue topology database " > > Woud you be so glad to tell me how can I resolve this problem? > > Thank you for advice > > - > HARESH AJANI > 09925522578 > ajani_har...@yahoo.co.in -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Extending REMD simulation
Dear Gromacs experts, I started a REMD simulation which terminated succesfully after 4830ps. I now want to extend it to 50ns. I'm using Gromacs 4.0.3 which supports checkpoint files. I got now around 40 files with the ending "*.cpt" and "*_prev.cpt". I couldn't find any documentation on how to extend a REMD simulation via checkpoint file. The only mailinglist post I found was [1] but there was no reply to it :( . Any help is welcome. Thanks, Henri 1: http://lists.gromacs.org/pipermail/gmx-users/2008-September/036534.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] revive gmx-announce
Hi Inon, That's exactly what we talked about today at a developers' meeting. We'll be posting there announcements! Rossen On 2010-09-15 17.08, Inon Sharony wrote: Hi everyone! I saw that the recent proliferation of GROMACS 4.5 had a hiccup involved (hence 4.5.1), but I only caught this a couple of weeks after it happened (Jewish holidays...) I'm wondering if it would be possible to re-activate the gmx-announce mailing list (or better yet -- reform it as an RSS or atom feed) so that the really important announcements that come out only once-in-a-while could be disseminated without the need to get every post from the users' list. Thanks for your time, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] settle constraints for spc water model
David Rodríguez wrote: Hi all, I am in a similar situation like this one: http://lists.gromacs.org/pipermail/gmx-users/2010-January/048079.html I need two different groups for crystallographic and solvation waters (identical topologies, except for residue), with SPC model and SETTLE algorithm for both. But as expected (see link above), it complaints for having more than one settle (suggests to use 3 normal constraints instead) at EM. I was wondering if someone would kindly provide that constraints for SPC (since the referred thread deals with TIP4). The [settles] directives for both SPC and TIP4P are identical. The constraints in the above-quoted post are what you need. -Justin Thanks in advance. Best regards, -- David Rodríguez Díaz, PhD Student PFIS Grant (ISCIII, MICINN) Fundación Pública Galega de Medicina Xenómica (SERGAS) Hospital Clínico Universitario. Edificio de Consultas, Planta -2 Choupana s/n. E15706 - Santiago de Compostela (A Coruña) SPAIN E-mail: david.rodriguez.diaz at usc dot es Phone: +34 881813873 / Fax: +34 981528071 -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Phd positions
Dear all, since many people in our institute are gromacs users, this announcement could make some sense on the gmx mailing list. Please forward it to interested people. Best wishes, Giovanni Bussi # Dear colleague, we would like to remind the forthcoming deadline - September 23 - for the application for the "PHD IN PHYSICS AND CHEMISTRY OF BIOLOGICAL SYSTEMS" at SISSA, Trieste. This year we have 5 positions available, for Italian and foreigner students. The application should be filled exclusively online at the following address: www.sissa.it/applications/phd For further information about the available research lines, see the website http://www.sissa.it/sbp Notice that SISSA can partially cover the travel expense for students willing to participate to the entrance exam. Please forward this information to interested students and colleague. Best wishes, on behalf of the PhD faculty, C. Micheletti, A. Laio and G. Bussi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] settle constraints for spc water model
Hi all, I am in a similar situation like this one: http://lists.gromacs.org/pipermail/gmx-users/2010-January/048079.html I need two different groups for crystallographic and solvation waters (identical topologies, except for residue), with SPC model and SETTLE algorithm for both. But as expected (see link above), it complaints for having more than one settle (suggests to use 3 normal constraints instead) at EM. I was wondering if someone would kindly provide that constraints for SPC (since the referred thread deals with TIP4). Thanks in advance. Best regards, -- David Rodríguez Díaz, PhD Student PFIS Grant (ISCIII, MICINN) Fundación Pública Galega de Medicina Xenómica (SERGAS) Hospital Clínico Universitario. Edificio de Consultas, Planta -2 Choupana s/n. E15706 - Santiago de Compostela (A Coruña) SPAIN E-mail: david.rodriguez.diaz at usc dot es Phone: +34 881813873 / Fax: +34 981528071 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] potential energy in implicit solvent simulations
Dear GROMACS users, I am conducting energy minimization with an implicit solvent, using GROMACS version 4.5.1 at double precision. The minimization provides the minimal potential energy I'm interested in, but I also wanted to see the contributions to it. I therefore used g_energy_d and picked the potential energy itself (no. 10) together with what I thought are its constituents (no. 1-9). However, those contributions do not sum to the potential energy. There is also a term #Surf*SurfTen (no. 30) but it is printed as zero. Can you explain this situation? The relevant part of g_energy_d's output for a certain example is the following: # This file was created Thu Sep 16 16:51:26 2010 # by the following command: # g_energy_d -s em2.tpr -f em2.edr -o em2.potential_energy.xvg # # g_energy_d is part of G R O M A C S: # # GROningen Mixture of Alchemy and Childrens' Stories # @title "Gromacs Energies" @xaxis label "Time (ps)" @yaxis label "(kJ/mol), (bar nm)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Bond" @ s1 legend "Angle" @ s2 legend "Proper Dih." @ s3 legend "Ryckaert-Bell." @ s4 legend "GB Polarization" @ s5 legend "LJ-14" @ s6 legend "Coulomb-14" @ s7 legend "LJ (SR)" @ s8 legend "Coulomb (SR)" @ s9 legend "Potential" @ s10 legend "#Surf*SurfTen" 0.00 179.387112 1063.328043 64.818404 2220.374294 440.027560 3580.261354 12299.937527 -3164.489764 -44972.543752 -27990.3807600.00 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] problem adding H atoms
Stacey Meadley wrote: Hi, I am using pdb2gmx with amber ff and there is a problem adding the H atom to the second residue of both chains of my protein? The residue at that location is repeated in later in the chain and has no problem with the hydrogens so I don't understand why it gives me the error? Can you post some more complete information? For example: 1. Your Gromacs version 2. Your exact command line 3. The error message you receive (copy and paste, please) 4. A snippet of your coordinate file containing the first two or three residues (for testing purposes) -Justin I relatively new to this and this is the first time I'm using amber ff in gromacs so thanks for all the previous posts which help me quite a bit so far. Stacey -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] problem adding H atoms
Hi, I am using pdb2gmx with amber ff and there is a problem adding the H atom to the second residue of both chains of my protein? The residue at that location is repeated in later in the chain and has no problem with the hydrogens so I don't understand why it gives me the error? I relatively new to this and this is the first time I'm using amber ff in gromacs so thanks for all the previous posts which help me quite a bit so far. Stacey -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Fwd: Residue 'MOL' not found in residue topology database
Probably I wasn't the only one who got this in a personal mail box, but I'll forward it anyway. And, no, I'm not a private tutor, unless I've explicitly indicated otherwise. Tsjerk -- Forwarded message -- From: AJANI HARESH Date: Thu, Sep 16, 2010 at 2:00 PM Subject: Residue 'MOL' not found in residue topology database To: tsje...@gmail.com I am using gromacs 4.0. Currently I am working on one prtein structure and ligand. when I use the following command:"pdb2gmx -f 1GT.pdb -p gr.top -o gr.gro" > There's a fatal error: > Residue 'MOL' not found in residue topology database Fatal error: Residue '' not found in residue topology database " Woud you be so glad to tell me how can I resolve this problem? Thank you for advice - HARESH AJANI 09925522578 ajani_har...@yahoo.co.in -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] trjconv -pbc
Carla Jamous wrote: Hi everyone, please I'm doing a simulation of a dimer with a ligand. When I want to visualize my trajectory, I have the problem that my dimer or my ligand or both diffuse out of the box and I don't have a continuous trajectory. I tried many options: 1)trjconv -center -pbc mol -ur compact (centering on protein) 2) trjconv -center -pbc mol (centering on the ligand) 3) trjconv -center -pbc atom (centering on ligand) and then, trjconv -pbc whole 4) trjconv -pbc nojump and then trjconv -fit rot+trans 5) trjconv -center -pbc mol (centering on protein) and then trjconv -fit rot+trans 6) trjconv -center -pbc mol -ur compact (centering on ligand) and then -fit rot+trans _all of these options didn't work_ I tried a last one: trjconv -center -pbc atom -ur compact (centering on ligand) and then trjconv -pbc nojump and then trjconv -fit rot+trans this one is the best one but I still have one part of my molecule that diffuses out of the box at one point in my trajectory. Please I'm out of ideas, can anyone give me a hint on how to get a fully continuous trajectory entirely centered in my box? Make a custom index group that corresponds to a residue (or several) at the dimer interface. Then use that group for centering. It still make take a couple of passes through trjconv, but I would think that trjconv -pbc mol -center would probably work in this case. -Justin Thank you Carla -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] WHAM
Anirban Ghosh wrote: Hi ALL, I have carried out REMD simulation on a protein (20 replicas). Now I want to carry 2D PMF calculation using RMSD and Radius of gyration as the reaction coordinates using Grossfield Lab's WHAM package. For this what should be my input parameters to the WHAM program and in which format? Any suggestion in this regard is welcome. I would suggest you consult the documentation for the program (i.e. the Grossfield WHAM manual, section 4.2.2). I don't know how you intend to pass your data to a program that is designed for umbrella sampling, but I suppose that's your task. -Justin Regards, Anirban -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] trjconv -pbc
Hi everyone, please I'm doing a simulation of a dimer with a ligand. When I want to visualize my trajectory, I have the problem that my dimer or my ligand or both diffuse out of the box and I don't have a continuous trajectory. I tried many options: 1)trjconv -center -pbc mol -ur compact (centering on protein) 2) trjconv -center -pbc mol (centering on the ligand) 3) trjconv -center -pbc atom (centering on ligand) and then, trjconv -pbc whole 4) trjconv -pbc nojump and then trjconv -fit rot+trans 5) trjconv -center -pbc mol (centering on protein) and then trjconv -fit rot+trans 6) trjconv -center -pbc mol -ur compact (centering on ligand) and then -fit rot+trans *all of these options didn't work* I tried a last one: trjconv -center -pbc atom -ur compact (centering on ligand) and then trjconv -pbc nojump and then trjconv -fit rot+trans this one is the best one but I still have one part of my molecule that diffuses out of the box at one point in my trajectory. Please I'm out of ideas, can anyone give me a hint on how to get a fully continuous trajectory entirely centered in my box? Thank you Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] WHAM
Hi ALL, I have carried out REMD simulation on a protein (20 replicas). Now I want to carry 2D PMF calculation using RMSD and Radius of gyration as the reaction coordinates using Grossfield Lab's WHAM package. For this what should be my input parameters to the WHAM program and in which format? Any suggestion in this regard is welcome. 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] #ifndef FLEXIBLE or #ifdef FLEXIBLE
- Original Message - From: zhongjin Date: Thursday, September 16, 2010 20:49 Subject: [gmx-users] #ifndef FLEXIBLE or #ifdef FLEXIBLE To: gmx-users@gromacs.org --- | > Hi,#ifndef FLEXIBLE means not #ifdef FLEXIBLE? That is to say #ifndef FLEXIBLE means if not define? Yes. In either GROMACS version, you can use grompp -pp to verify what the preprocessor is doing. Mark | --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: Tabulated potentials and normal nonbonded interaction at the same time
Hi, first, thank you for you're answers. I looked more into the stuff. I think i would use the following setup: Since the CG-solvent is uncharged, i can use the normal coulomb- interaction (PME) for the system. For the vdw-part, i would use 'vdw_type=user' and: energy_grps = CG Mol energygrp_tables = CG CG (CG self-interaction) CG Mol (CG- Molecule interaction) (CG = CG-solvent; Mol=Molecule) So i would need two tables (for each interaction one). With this i should get all the vdw-interaction where the CG- solvent is involved. But since i need normal vdw-interactions for the Molecule self- interaction, i would need in the .mdp-file 'vdw_type = user' AND 'vdw_type = cut-off' Or am i wrong (hope so)? Because the only way i can think of to solve the problem, would be that i make for every vdw-self- interaction of the Molecule an own table, which wouldn't be good (since i read somewhere that tables are slower then to calculated the interaction normally). So how could i solve the problem, or this there no problem because i didn't understand the whole stuff correctly (seems so because of Marks reply)? I haven't ever actually done it, but I'm expecting "vdw_type= cut-off" and "energygrp_tables = CG CG CG Mol" to work if you supply the two tables. What I can see in the manual neither confirms nor denies this, but it is cost-free to try :-) Mark Ok, i will try it and report back if it works. Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: RE: [gmx-users] rerun warning
- Original Message - From: "Poojari, Chetan" Date: Thursday, September 16, 2010 20:33 Subject: RE: [gmx-users] rerun warning To: Discussion list for GROMACS users > Hello Mark, > > Thank you very much for quick reply. > > I am looking for LJ and coul interactions, please can i know > what can be done to avoid these warnings if incase i want to > calculate kinetic quantities... These are not kinetic quantities. They depend on positions of atoms, not velocities. If you need velocity-dependent data then you have no option but to rerun the trajectory, saving velocity coordinates suitably. But it sounds to me like you don't need to. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] rerun warning
Poojari, Chetan wrote: Hi Justin, As I dont have velocities defined in my traj. file, please can I know if theres some possibility of including them to the traj. file If you're re-running from a .xtc file, then no, there is no way to store velocities in such a file. You need a .trr if you need to calculate anything related to velocities. -Justin cheers, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 16 September 2010 12:35 To: Discussion list for GROMACS users Subject: Re: [gmx-users] rerun warning Poojari, Chetan wrote: Hello Mark, Thank you very much for quick reply. I am looking for LJ and coul interactions, please can i know what can be done to avoid these warnings if incase i want to calculate kinetic quantities... You need velocities, and thus, a .trr file. -Justin cheers, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham [mark.abra...@anu.edu.au] Sent: 16 September 2010 12:12 To: Discussion list for GROMACS users Subject: Re: [gmx-users] rerun warning - Original Message - From: "Poojari, Chetan" Date: Thursday, September 16, 2010 20:04 Subject: [gmx-users] rerun warning To: "gmx-users@gromacs.org" Hi, I am doing rerun to calculate LJ-SR & coul-SR interactions and other energy terms for energygrps defined in mdp file. I have constrained all bonds with lincs algorithm in mdp file. While running rerun i get following warnings WARNING: Some frames do not contain velocities. Ekin, temperature and pressure are incorrect, the virial will be incorrect when constraints are present. Please can I Know if the energy values generated are they incorrectif so how can i recalculate correct energies as i dont have velocities in my file to use g_traj If you're not trying to calculate the kinds of *kinetic* quantities described in the warning, then you don't care. Your first sentence sounds like you're after *static* quantities. If you do want kinetic quantities, then you're in trouble. Mark Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] #ifndef FLEXIBLE or #ifdef FLEXIBLE
Hi,#ifndef FLEXIBLE means not #ifdef FLEXIBLE? That is to say #ifndef FLEXIBLE means if not define?in GMX4.0.7define = -DFLEXIBLE[ moleculetype ]; molname nrexclSOL 2 [ atoms ]; id at type res nr residu name at name cg nr charge#ifdef _FF_OPLS1 opls_111 1 SOL OW 1 -0.8342 opls_112 1 SOL HW1 1 0.4173 opls_112 1 SOL HW2 1 0.417#endif#ifdef _FF_CHARMM1 OT 1 SOL OW 1 -0.8342 HT 1 SOL HW1 1 0.4173 HT 1 SOL HW2 1 0.417#endif#ifdef _FF_GROMACS 1 OWT3 1 SOL OW 1 -0.8342 HW 1 SOL HW1 1 0.4173 HW 1 SOL HW2 1 0.417#endif#ifdef _FF_GROMOS961 OWT3 1 SOL OW 1 -0.8342 HW 1 SOL HW1 1 0.4173 HW 1 SOL HW2 1 0.417#endif #ifdef FLEXIBLE[ bonds ]; i j funct length force.c.1 2 1 0.09572 502416.0 0.09572502416.0 1 3 1 0.09572 502416.0 0.09572502416.0 [ angles ]; i j k funct angle force.c.2 1 3 1 104.52 628.02 104.52 628.02 #else[ settles ]; i j funct length1 1 0.09572 0.15139 [ exclusions ]1 2 32 1 33 1 2#endif BUT in GMX4.5.1[ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 OWT31 SOL OW 1 -0.834 2 HW 1 SOL HW1 10.417 3 HW 1 SOL HW2 10.417 #ifndef FLEXIBLE [ settles ] ; i j funct length 1 1 0.09572 0.15139 [ exclusions ] 1 2 3 2 1 3 3 1 2 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 502416.0 0.09572502416.0 1 3 1 0.09572 502416.0 0.09572502416.0 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.52 628.02 104.52 628.02 #endif I think they are the same. If I want to use FLEXIBLE water, I should add define = -DFLEXIBLE in .mdp file as in GMX4.0.7.Is it right? Thanks!Zhongjin He -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] rerun warning
Hi Justin, As I dont have velocities defined in my traj. file, please can I know if theres some possibility of including them to the traj. file cheers, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 16 September 2010 12:35 To: Discussion list for GROMACS users Subject: Re: [gmx-users] rerun warning Poojari, Chetan wrote: > Hello Mark, > > Thank you very much for quick reply. > > I am looking for LJ and coul interactions, please can i know what can be done > to avoid these warnings if incase i want to calculate kinetic quantities... > You need velocities, and thus, a .trr file. -Justin > > cheers, > chetan > > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf > Of Mark Abraham [mark.abra...@anu.edu.au] > Sent: 16 September 2010 12:12 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] rerun warning > > - Original Message - > From: "Poojari, Chetan" > Date: Thursday, September 16, 2010 20:04 > Subject: [gmx-users] rerun warning > To: "gmx-users@gromacs.org" > >> Hi, >> >> I am doing rerun to calculate LJ-SR & coul-SR >> interactions and other energy terms for energygrps defined >> in mdp file. >> >> I have constrained all bonds with lincs algorithm in mdp file. >> >> While running rerun i get following warnings >> >> WARNING: Some frames do not contain velocities. >> Ekin, >> temperature and pressure are incorrect, >> the virial will >> be incorrect when constraints are present. >> >> >> Please can I Know if the energy values generated are they >> incorrectif so how can i recalculate correct energies as >> i dont have velocities in my file to use g_traj > > If you're not trying to calculate the kinds of *kinetic* quantities described > in the warning, then you don't care. Your first sentence sounds like you're > after *static* quantities. If you do want kinetic quantities, then you're in > trouble. > > Mark > > > > Forschungszentrum Juelich GmbH > 52425 Juelich > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), > Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > > -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] rerun warning
Poojari, Chetan wrote: Hello Mark, Thank you very much for quick reply. I am looking for LJ and coul interactions, please can i know what can be done to avoid these warnings if incase i want to calculate kinetic quantities... You need velocities, and thus, a .trr file. -Justin cheers, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham [mark.abra...@anu.edu.au] Sent: 16 September 2010 12:12 To: Discussion list for GROMACS users Subject: Re: [gmx-users] rerun warning - Original Message - From: "Poojari, Chetan" Date: Thursday, September 16, 2010 20:04 Subject: [gmx-users] rerun warning To: "gmx-users@gromacs.org" Hi, I am doing rerun to calculate LJ-SR & coul-SR interactions and other energy terms for energygrps defined in mdp file. I have constrained all bonds with lincs algorithm in mdp file. While running rerun i get following warnings WARNING: Some frames do not contain velocities. Ekin, temperature and pressure are incorrect, the virial will be incorrect when constraints are present. Please can I Know if the energy values generated are they incorrectif so how can i recalculate correct energies as i dont have velocities in my file to use g_traj If you're not trying to calculate the kinds of *kinetic* quantities described in the warning, then you don't care. Your first sentence sounds like you're after *static* quantities. If you do want kinetic quantities, then you're in trouble. Mark Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] rerun warning
Hello Mark, Thank you very much for quick reply. I am looking for LJ and coul interactions, please can i know what can be done to avoid these warnings if incase i want to calculate kinetic quantities... cheers, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham [mark.abra...@anu.edu.au] Sent: 16 September 2010 12:12 To: Discussion list for GROMACS users Subject: Re: [gmx-users] rerun warning - Original Message - From: "Poojari, Chetan" Date: Thursday, September 16, 2010 20:04 Subject: [gmx-users] rerun warning To: "gmx-users@gromacs.org" > Hi, > > I am doing rerun to calculate LJ-SR & coul-SR > interactions and other energy terms for energygrps defined > in mdp file. > > I have constrained all bonds with lincs algorithm in mdp file. > > While running rerun i get following warnings > > WARNING: Some frames do not contain velocities. > Ekin, > temperature and pressure are incorrect, > the virial will > be incorrect when constraints are present. > > > Please can I Know if the energy values generated are they > incorrectif so how can i recalculate correct energies as > i dont have velocities in my file to use g_traj If you're not trying to calculate the kinds of *kinetic* quantities described in the warning, then you don't care. Your first sentence sounds like you're after *static* quantities. If you do want kinetic quantities, then you're in trouble. Mark Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] rerun warning
- Original Message - From: "Poojari, Chetan" Date: Thursday, September 16, 2010 20:04 Subject: [gmx-users] rerun warning To: "gmx-users@gromacs.org" > Hi, > > I am doing rerun to calculate LJ-SR & coul-SR > interactions and other energy terms for energygrps defined > in mdp file. > > I have constrained all bonds with lincs algorithm in mdp file. > > While running rerun i get following warnings > > WARNING: Some frames do not contain velocities. > Ekin, > temperature and pressure are incorrect, > the virial will > be incorrect when constraints are present. > > > Please can I Know if the energy values generated are they > incorrectif so how can i recalculate correct energies as > i dont have velocities in my file to use g_traj If you're not trying to calculate the kinds of *kinetic* quantities described in the warning, then you don't care. Your first sentence sounds like you're after *static* quantities. If you do want kinetic quantities, then you're in trouble. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: Tabulated potentials and normal nonbonded interaction at the same time
- Original Message - From: Thomas Schlesier Date: Thursday, September 16, 2010 19:49 Subject: [gmx-users] Re: Tabulated potentials and normal nonbonded interaction at the same time To: gmx-users@gromacs.org > Hi, > first, thank you for you're answers. > I looked more into the stuff. > > I think i would use the following setup: > > Since the CG-solvent is uncharged, i can use the normal coulomb- > interaction (PME) for the system. > > For the vdw-part, i would use 'vdw_type=user' and: > energy_grps = CG Mol > energygrp_tables = CG CG (CG self-interaction) CG Mol (CG- > Molecule interaction) > (CG = CG-solvent; Mol=Molecule) > So i would need two tables (for each interaction one). > With this i should get all the vdw-interaction where the CG- > solvent is involved. > > But since i need normal vdw-interactions for the Molecule self- > interaction, i would need in the .mdp-file > 'vdw_type = user' AND 'vdw_type = cut-off' > > Or am i wrong (hope so)? Because the only way i can think of to > solve the problem, would be that i make for every vdw-self- > interaction of the Molecule an own table, which wouldn't be good > (since i read somewhere that tables are slower then to > calculated the interaction normally). > > So how could i solve the problem, or this there no problem > because i didn't understand the whole stuff correctly (seems so > because of Marks reply)? I haven't ever actually done it, but I'm expecting "vdw_type= cut-off" and "energygrp_tables = CG CG CG Mol" to work if you supply the two tables. What I can see in the manual neither confirms nor denies this, but it is cost-free to try :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] rerun warning
Hi, I am doing rerun to calculate LJ-SR & coul-SR interactions and other energy terms for energygrps defined in mdp file. I have constrained all bonds with lincs algorithm in mdp file. While running rerun i get following warnings WARNING: Some frames do not contain velocities. Ekin, temperature and pressure are incorrect, the virial will be incorrect when constraints are present. Please can I Know if the energy values generated are they incorrectif so how can i recalculate correct energies as i dont have velocities in my file to use g_traj Any suggestions will help me. cheers, chetan Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: Tabulated potentials and normal nonbonded interaction at the same time
Hi, first, thank you for you're answers. I looked more into the stuff. I think i would use the following setup: Since the CG-solvent is uncharged, i can use the normal coulomb-interaction (PME) for the system. For the vdw-part, i would use 'vdw_type=user' and: energy_grps = CG Mol energygrp_tables = CG CG (CG self-interaction) CG Mol (CG-Molecule interaction) (CG = CG-solvent; Mol=Molecule) So i would need two tables (for each interaction one). With this i should get all the vdw-interaction where the CG-solvent is involved. But since i need normal vdw-interactions for the Molecule self-interaction, i would need in the .mdp-file 'vdw_type = user' AND 'vdw_type = cut-off' Or am i wrong (hope so)? Because the only way i can think of to solve the problem, would be that i make for every vdw-self-interaction of the Molecule an own table, which wouldn't be good (since i read somewhere that tables are slower then to calculated the interaction normally). So how could i solve the problem, or this there no problem because i didn't understand the whole stuff correctly (seems so because of Marks reply)? Greetings Thomas >> Hello >> > >> > I think what you need to do is use multiple tables. So you >> > have one >> > table for your CG-solvent interaction with itself and then >> > another one >> > for your CG-solvent (uncharged) interactions. (This second table >> > would then just a tabulated version of the Lennard Jones >interaction >> > or whatever you are using.) This page might be of help: >> > >> > http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials > >While this would work, the key piece of information is that GROMACS >will permit you to use different tables only for selected >inter-energy-group interactions. So the OP needs suitable energy >groups, and only one table. The other groups use the normal >interactions. > >Mark > > > > > ciao > > Gareth > > > > On Wed, Sep 15, 2010 at 5:40 PM, Thomas Schlesier > > wrote: >> > > Dear Gromacs-User, >> > > i want to try to simulate an atomistic molecule with CG- > > solvent (uncharged). >> > > For the atomistic molecule i want to use the normal non-bonded > > interactions,> but for the CG-solvent interaction with itself > > and the molecule i need a >> > > tabulated potential. >> > > So my question is, is that possible to do in Gromacs? >> > > I looked a little bit into the manual and it seems that > > tabulated potentials >> > > use the 'vdw_type' and/or the 'coulomb_type' keyword, which i > > will need for >> > > the normal interactions. >> > > Greetings >> > > Thomas >> > > -- >> > > gmx-users mailing listgmx-users@gromacs.org >> > > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > > Please search the archive at >> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> > > Please don't post (un)subscribe requests to the list. Use the -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
