Re: [gmx-users] NVE of water
Hi Andrea, Did you use double precision? Also, I'd try a lower dt (say 1fs) and shake tolerance (maybe 1E-8). Good luck, Ran Andrea wrote: Dear users, for test purposes in order to set up a bigger system, I try to run NVE simulations of SPC water, but the energy increases very rapidely. My guess is that the cutoffs I use are not good for water. I that the case ( I would be grateful for a good reference for suitable SPC water parameters) or do I miss something else? My parameter file for the NVE is: title= NVE cpp = /lib/cpp integrator = md dt = 0.002 ; ps ! = 2 fs nsteps = 5 ; total 100 ps nstxout = 5000 nstvout = 5000 nstxtcout= 0 nstlog = 5000 nstenergy= 5000 nstlist = 10 ns_type = grid rlist= 1.1 unconstrained-start = yes constraints = all-bonds constraint_algorithm = shake shake_tol= 0.0001 ;VdW vdwtype = Switch rvdw = 1.0 ; rvdw+ (0.1:0.3)= rlist rvdw_switch = 0.9 gen_vel = no ; yes gen_temp = 300 gen_seed = -1 ;Temperature coupling tc_grps = system tcoupl = no ;nose-hoover tau_t= 0.1 ref_t= 300 ;Pressure coupling pcoupl = no optimize_fft = yes Any suggesions are really welcome. Thank you. Regards, Andrea Muntean -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- -- 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] NVE of water
Hi, Shake is not relevant for water and also a time step of 2 fs should be fine. The cut-off's are the problem. You have a buffer size of 0.1 nm, which is already smaller than 2 times the distance from the center of geometry of a water molecule to a hydrogen. You need some additional distance for water diffusion. I would use a buffer of 0.25 to 0.3 nm. You don't list you coulombtype setting. Use pme (or if you want perfect energy conservation: pme-switch), you can also use reaction-field-zero if you really don't want to use PME. Then use nstlist=-1, run a short simulation and check in at the end of your log file that the neighbor list lifetime is somewhere between 5 and 20 steps. We should have a wiki entry for such details. Maybe there is one, but I was too lazy to check or make one. Berk Date: Mon, 1 Mar 2010 09:16:36 +0100 From: r.fried...@bioc.uzh.ch To: gmx-users@gromacs.org Subject: Re: [gmx-users] NVE of water Hi Andrea, Did you use double precision? Also, I'd try a lower dt (say 1fs) and shake tolerance (maybe 1E-8). Good luck, Ran Andrea wrote: Dear users, for test purposes in order to set up a bigger system, I try to run NVE simulations of SPC water, but the energy increases very rapidely. My guess is that the cutoffs I use are not good for water. I that the case ( I would be grateful for a good reference for suitable SPC water parameters) or do I miss something else? My parameter file for the NVE is: title= NVE cpp = /lib/cpp integrator = md dt = 0.002 ; ps ! = 2 fs nsteps = 5 ; total 100 ps nstxout = 5000 nstvout = 5000 nstxtcout= 0 nstlog = 5000 nstenergy= 5000 nstlist = 10 ns_type = grid rlist= 1.1 unconstrained-start = yes constraints = all-bonds constraint_algorithm = shake shake_tol= 0.0001 ;VdW vdwtype = Switch rvdw = 1.0 ; rvdw+ (0.1:0.3)= rlist rvdw_switch = 0.9 gen_vel = no ; yes gen_temp = 300 gen_seed = -1 ;Temperature coupling tc_grps = system tcoupl = no ;nose-hoover tau_t= 0.1 ref_t= 300 ;Pressure coupling pcoupl = no optimize_fft = yes Any suggesions are really welcome. Thank you. Regards, Andrea Muntean -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- -- 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 _ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop-- 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] NVE of water
Thank you for your hints. I'll give it a try right now. Regards, Andrea 2010/3/1 Berk Hess g...@hotmail.com Hi, Shake is not relevant for water and also a time step of 2 fs should be fine. The cut-off's are the problem. You have a buffer size of 0.1 nm, which is already smaller than 2 times the distance from the center of geometry of a water molecule to a hydrogen. You need some additional distance for water diffusion. I would use a buffer of 0.25 to 0.3 nm. You don't list you coulombtype setting. Use pme (or if you want perfect energy conservation: pme-switch), you can also use reaction-field-zero if you really don't want to use PME. Then use nstlist=-1, run a short simulation and check in at the end of your log file that the neighbor list lifetime is somewhere between 5 and 20 steps. We should have a wiki entry for such details. Maybe there is one, but I was too lazy to check or make one. Berk Date: Mon, 1 Mar 2010 09:16:36 +0100 From: r.fried...@bioc.uzh.ch To: gmx-users@gromacs.org Subject: Re: [gmx-users] NVE of water Hi Andrea, Did you use double precision? Also, I'd try a lower dt (say 1fs) and shake tolerance (maybe 1E-8). Good luck, Ran Andrea wrote: Dear users, for test purposes in order to set up a bigger system, I try to run NVE simulations of SPC water, but the energy increases very rapidely. My guess is that the cutoffs I use are not good for water. I that the case ( I would be grateful for a good reference for suitable SPC water parameters) or do I miss something else? My parameter file for the NVE is: title = NVE cpp = /lib/cpp integrator = md dt = 0.002 ; ps ! = 2 fs nsteps = 5 ; total 100 ps nstxout = 5000 nstvout = 5000 nstxtcout = 0 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1.1 unconstrained-start = yes constraints = all-bonds constraint_algorithm = shake shake_tol = 0.0001 ;VdW vdwtype = Switch rvdw = 1.0 ; rvdw+ (0.1:0.3)= rlist rvdw_switch = 0.9 gen_vel = no ; yes gen_temp = 300 gen_seed = -1 ;Temperature coupling tc_grps = system tcoupl = no ;nose-hoover tau_t = 0.1 ref_t = 300 ;Pressure coupling pcoupl = no optimize_fft = yes Any suggesions are really welcome. Thank you. Regards, Andrea Muntean -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- -- 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 -- New Windows 7: Find the right PC for you. Learn more.http://windows.microsoft.com/shop -- 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
Re: [gmx-users] Constraining periodic cell
David, I get a different simulation result if I use isotropic or anisotropic cells. I am not sure yet which is (more) correct, but I would like to be able to run both types to see. I understand that a constrained anisotropic cell is not completely anisotropic, but a fully anistropic one clearly doesn't work. David Dear All, We are running some simulations using an anisotropic periodic cell. We are getting 'cell runaway' with the cell becoming very long and thin. This appears to being driven by the electrostatics of the system. The simulation then dies because the smallest cell dimension is less than 2*cutoff. Is there a way that we can apply some constraints to the periodic cell? Why not use isotropic pressure coupling? Regards David David Chalmers Lab: 9903 9110 Faculty of Pharmacy, Monash University 381 Royal Pde, Parkville, Vic 3053. Australia david.chalm...@pharm.monash.edu.au -- 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] Constraining periodic cell
On 2010-03-01 09.49, David Chalmers wrote: David, I get a different simulation result if I use isotropic or anisotropic cells. I am not sure yet which is (more) correct, but I would like to be able to run both types to see. I understand that a constrained anisotropic cell is not completely anisotropic, but a fully anistropic one clearly doesn't work. David You did not say which algorithm you use either, but making the time constant longer might help. However, depending on your system, you may need substantial surface tension to keep the system neutral if you do use anisotropic coupling. We do not completely understand these effects yet, see e.g http://bugzilla.gromacs.org/show_bug.cgi?id=165 for additional discussions. Dear All, We are running some simulations using an anisotropic periodic cell. We are getting 'cell runaway' with the cell becoming very long and thin. This appears to being driven by the electrostatics of the system. The simulation then dies because the smallest cell dimension is less than 2*cutoff. Is there a way that we can apply some constraints to the periodic cell? Why not use isotropic pressure coupling? Regards David David Chalmers Lab: 9903 9110 Faculty of Pharmacy, Monash University 381 Royal Pde, Parkville, Vic 3053. Australia david.chalm...@pharm.monash.edu.au -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://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
RE: [gmx-users] Constraining periodic cell
Hi, I would expect nearly any cell to deform to a very elongated shape, unless it contains a solid (crystal). In most cases an elongated shape has the lowest (electrostatic) energy. Therefore anisotropic coupling is only useful for crystal simulations. Berk Date: Mon, 1 Mar 2010 10:09:08 +0100 From: sp...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] Constraining periodic cell On 2010-03-01 09.49, David Chalmers wrote: David, I get a different simulation result if I use isotropic or anisotropic cells. I am not sure yet which is (more) correct, but I would like to be able to run both types to see. I understand that a constrained anisotropic cell is not completely anisotropic, but a fully anistropic one clearly doesn't work. David You did not say which algorithm you use either, but making the time constant longer might help. However, depending on your system, you may need substantial surface tension to keep the system neutral if you do use anisotropic coupling. We do not completely understand these effects yet, see e.g http://bugzilla.gromacs.org/show_bug.cgi?id=165 for additional discussions. Dear All, We are running some simulations using an anisotropic periodic cell. We are getting 'cell runaway' with the cell becoming very long and thin. This appears to being driven by the electrostatics of the system. The simulation then dies because the smallest cell dimension is less than 2*cutoff. Is there a way that we can apply some constraints to the periodic cell? Why not use isotropic pressure coupling? Regards David David Chalmers Lab: 9903 9110 Faculty of Pharmacy, Monash University 381 Royal Pde, Parkville, Vic 3053. Australia david.chalm...@pharm.monash.edu.au -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. sp...@xray.bmc.uu.sehttp://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 _ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop-- 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: Anisotropic pressure control
= 1.2 coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.2 epsilon-r= 1 epsilon_rf = 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.4 DispCorr = EnerPres table-extension = 1.5 energygrp_table = fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d optimize_fft = yes Tcoupl = Nose-hoover tc-grps = protres RUT solcl tau_t= 0.1 0.1 0.1 ref_t= 310 310 310 Pcoupl = Parrinello-Rahman Pcoupltype = anisotropic tau_p= 2.0 2.0 2.0 2.0 2.0 2.0 compressibility = 0.0 0.0 5e-5 0.0 0.0 0.0 ref_p= 0 0 1.01325 0 0 0 gen_vel = yes gen_temp = 310 gen_seed = 1993 constraints = hbonds constraint-algorithm = lincs continuation = yes lincs-order = 4 lincs-iter = 4 freezegrps = frozen freezedim= Y Y Y Thanks Matteus - Matteus Lindgren, graduate student Department of Chemistry, Umee University SE-901 87 Umee, Sweden Phone: +46 (0)90-7865368 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100301/7e534794/a ttachment.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 71, Issue 1 -- 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] Continuous trajectory from trjconv?
Hi, I made an NpT MD simulation of 10 copies of the same small molecule in CHCl3 (dodecahedron unit cell) for 20 ns. I want to visualize the evolution of the system and the distance between the molecules. I tried to visualize the system, but I can't get a continuous trajectory (i.e., without jumps) without the solutes diffusing out of the simulation box. The same thing happens for the inter-molecule distance, it oscillates wildly between a reasonable value (say, 0.5 nm) and 1/2 the size of the periodic cell. When I use trjconv with the -pbc nojump -ur compact options, the molecules diffuse out of the box, in a continuous trajectory, until they are way further apart than the size of the cell. When visualizing it in VMD, however, it turns out that not all molecules are isolated, but instead some are interacting with the periodic image of another molecule. I used pbc wrap from the PBCTools module within VMD and that brings all the molecules into a single cell, but then the trajectory is not continuous, with compounds jumping around the edges of the unit cell. It is then not straightforward to see the interaction among different molecules, as in some cases they are in opposite edges of the cell. If I use the -pbc mol -ur compact option, all molecules stay within a single unit cell, but there are jumps across the border of the unit cell as in the above case. I tried also using the -center, -fit rot+trans and -fit progressive options (with groups containing either all molecules or a single residue) but this ultimately gave the same results. Would there be something else I could try to visualize the simulation so that the central unit cell would contain all residues in a continuous way? Thanks in advance for reading, and more for replying! Take care, Pablo -- Pablo Englebienne, PhD Institute of Complex Molecular Systems (ICMS) Eindhoven University of Technology, TU/e PO Box 513, HG -1.26 5600 MB Eindhoven, The Netherlands Tel +31 40 247 5349 -- 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] Continuous trajectory from trjconv?
Hi Pablo, You want to mutually exclusive things. That is by definition impossible. Sorry, Tsjerk On Mon, Mar 1, 2010 at 11:02 AM, Pablo Englebienne p.englebie...@tue.nl wrote: Hi, I made an NpT MD simulation of 10 copies of the same small molecule in CHCl3 (dodecahedron unit cell) for 20 ns. I want to visualize the evolution of the system and the distance between the molecules. I tried to visualize the system, but I can't get a continuous trajectory (i.e., without jumps) without the solutes diffusing out of the simulation box. The same thing happens for the inter-molecule distance, it oscillates wildly between a reasonable value (say, 0.5 nm) and 1/2 the size of the periodic cell. When I use trjconv with the -pbc nojump -ur compact options, the molecules diffuse out of the box, in a continuous trajectory, until they are way further apart than the size of the cell. When visualizing it in VMD, however, it turns out that not all molecules are isolated, but instead some are interacting with the periodic image of another molecule. I used pbc wrap from the PBCTools module within VMD and that brings all the molecules into a single cell, but then the trajectory is not continuous, with compounds jumping around the edges of the unit cell. It is then not straightforward to see the interaction among different molecules, as in some cases they are in opposite edges of the cell. If I use the -pbc mol -ur compact option, all molecules stay within a single unit cell, but there are jumps across the border of the unit cell as in the above case. I tried also using the -center, -fit rot+trans and -fit progressive options (with groups containing either all molecules or a single residue) but this ultimately gave the same results. Would there be something else I could try to visualize the simulation so that the central unit cell would contain all residues in a continuous way? Thanks in advance for reading, and more for replying! Take care, Pablo -- Pablo Englebienne, PhD Institute of Complex Molecular Systems (ICMS) Eindhoven University of Technology, TU/e PO Box 513, HG -1.26 5600 MB Eindhoven, The Netherlands Tel +31 40 247 5349 -- gmx-users mailing list 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.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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] RE: Anisotropic pressure control
Matteus Lindgren wrote: Thank you for the comment. I understand your confusion. Yes, the volume of the box volume should fluctuate with pressure control but not on the large scale that I get. The box fluctuates and does not seem to settle on a certain volume. I have tried with the Berendsen algorithm as well but that run crashed. When I remove the frozen TiO2 surface the box volume does not at all fluctuate as much. It therefore seems to be some problem with the frozen atoms and pressure control. Any ideas about this? Does the simulation still crash under NVT conditions? I know there has been a long-standing incompatibility of pressure coupling with frozen groups, although I believe that is the purpose of the new .mdp option refcoord_scaling - how are you setting this option? -Justin Thanks Matteus -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of gmx-users-requ...@gromacs.org Sent: den 1 mars 2010 01:18 To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 71, Issue 1 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. simulation settings (pol...@fh.huji.ac.il) 2. Re: simulation settings (Mark Abraham) 3. Question about distance restraints, energy minimization and time averaging. (Arthur Roberts) 4. Re: Question about distance restraints, energy minimization and time averaging. (Erik Marklund) 5. NVE of water (Andrea) 6. RE: Anisotropic pressure control (Dallas B. Warren) -- Message: 1 Date: Sun, 28 Feb 2010 15:00:11 +0200 From: pol...@fh.huji.ac.il Subject: [gmx-users] simulation settings To: gmx-users@gromacs.org Message-ID: 20100228150011.61721j3pdrw2e...@webmail.huji.ac.il Content-Type: text/plain; charset=UTF-8; DelSp=Yes; format=flowed Dear Gromacs users and developers, I want to perform simulation of peptide dissolved in water using NPT. For constant temperature I use Berendsen temperature coupling. Do I have to define tc-grps for 2 groups (protein and solvent) or I may use tc-grps =System. What is the difference? The person who introduced gromacs to me uses tc-grps = Protein Sol_Ions but he is not sure why it should be in this way if at all Can you, please elucidate this issue to me. Thank you a lot. Regina This message was sent using IMP, the Internet Messaging Program. -- Message: 2 Date: Mon, 01 Mar 2010 00:50:42 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] simulation settings To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4b8a74b2.3050...@anu.edu.au Content-Type: text/plain; charset=UTF-8; format=flowed On 1/03/2010 12:00 AM, pol...@fh.huji.ac.il wrote: Dear Gromacs users and developers, I want to perform simulation of peptide dissolved in water using NPT. For constant temperature I use Berendsen temperature coupling. Do I have to define tc-grps for 2 groups (protein and solvent) or I may use tc-grps =System. What is the difference? The person who introduced gromacs to me uses tc-grps = Protein Sol_Ions but he is not sure why it should be in this way if at all Can you, please elucidate this issue to me. There's some quick advice here http://www.gromacs.org/Documentation/Terminology/Thermostats, otherwise consult some textbook material. Mark -- Message: 3 Date: Sun, 28 Feb 2010 10:25:24 -0800 From: Arthur Roberts aroberts99...@yahoo.com Subject: [gmx-users] Question about distance restraints,energy minimization and time averaging. To: gmx users gmx-users@gromacs.org Message-ID: 9ed0aa2d-c946-40bc-b85b-844962c4d...@yahoo.com Content-Type: text/plain; charset=US-ASCII; format=flowed Hi, all, This is probably a very simple question. Does time averaging apply, when distance restraints are used during energy minimization (steepest descent or conjugate gradient)? Your input would be greatly appreciated. Art Roberts Dr. Arthur Roberts, Ph.D. University of California, San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences 9500 Gilman Drive #0703 La Jolla, CA 92093-0703 email: aroberts99...@yahoo.com cell: 206-850-7468 skype=aroberts92122 -- Message: 4 Date: Sun, 28 Feb 2010 20:53:38 +0100 From: Erik Marklund er...@xray.bmc.uu.se Subject: Re: [gmx-users] Question about
[gmx-users] Re: Continuous trajectory from trjconv?
Thanks Tsjerk, I figured as much, but wanted to make sure I wasn't overlooking something... Take care, Pablo Hi Pablo, You want to mutually exclusive things. That is by definition impossible. Sorry, Tsjerk On Mon, Mar 1, 2010 at 11:02 AM, Pablo Englebienne p.englebie...@tue.nl wrote: Hi, I made an NpT MD simulation of 10 copies of the same small molecule in CHCl3 (dodecahedron unit cell) for 20 ns. I want to visualize the evolution of the system and the distance between the molecules. I tried to visualize the system, but I can't get a continuous trajectory (i.e., without jumps) without the solutes diffusing out of the simulation box. The same thing happens for the inter-molecule distance, it oscillates wildly between a reasonable value (say, 0.5 nm) and 1/2 the size of the periodic cell. When I use trjconv with the -pbc nojump -ur compact options, the molecules diffuse out of the box, in a continuous trajectory, until they are way further apart than the size of the cell. When visualizing it in VMD, however, it turns out that not all molecules are isolated, but instead some are interacting with the periodic image of another molecule. I used pbc wrap from the PBCTools module within VMD and that brings all the molecules into a single cell, but then the trajectory is not continuous, with compounds jumping around the edges of the unit cell. It is then not straightforward to see the interaction among different molecules, as in some cases they are in opposite edges of the cell. If I use the -pbc mol -ur compact option, all molecules stay within a single unit cell, but there are jumps across the border of the unit cell as in the above case. I tried also using the -center, -fit rot+trans and -fit progressive options (with groups containing either all molecules or a single residue) but this ultimately gave the same results. Would there be something else I could try to visualize the simulation so that the central unit cell would contain all residues in a continuous way? Pablo Englebienne, PhD Institute of Complex Molecular Systems (ICMS) Eindhoven University of Technology, TU/e PO Box 513, HG -1.26 5600 MB Eindhoven, The Netherlands Tel +31 40 247 5349 -- 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] NVE of water
Berk Hess wrote: Hi, Shake is not relevant for water and also a time step of 2 fs should be fine. The cut-off's are the problem. You have a buffer size of 0.1 nm, which is already smaller than 2 times the distance from the center of geometry of a water molecule to a hydrogen. You need some additional distance for water diffusion. I would use a buffer of 0.25 to 0.3 nm. You don't list you coulombtype setting. Use pme (or if you want perfect energy conservation: pme-switch), you can also use reaction-field-zero if you really don't want to use PME. Then use nstlist=-1, run a short simulation and check in at the end of your log file that the neighbor list lifetime is somewhere between 5 and 20 steps. We should have a wiki entry for such details. Maybe there is one, but I was too lazy to check or make one. There was a basic NVE page; I have updated it based on your notes above: http://www.gromacs.org/Documentation/Terminology/NVE -Justin Berk Date: Mon, 1 Mar 2010 09:16:36 +0100 From: r.fried...@bioc.uzh.ch To: gmx-users@gromacs.org Subject: Re: [gmx-users] NVE of water Hi Andrea, Did you use double precision? Also, I'd try a lower dt (say 1fs) and shake tolerance (maybe 1E-8). Good luck, Ran Andrea wrote: Dear users, for test purposes in order to set up a bigger system, I try to run NVE simulations of SPC water, but the energy increases very rapidely. My guess is that the cutoffs I use are not good for water. I that the case ( I would be grateful for a good reference for suitable SPC water parameters) or do I miss something else? My parameter file for the NVE is: title = NVE cpp = /lib/cpp integrator = md dt = 0.002 ; ps ! = 2 fs nsteps = 5 ; total 100 ps nstxout = 5000 nstvout = 5000 nstxtcout = 0 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1.1 unconstrained-start = yes constraints = all-bonds constraint_algorithm = shake shake_tol = 0.0001 ;VdW vdwtype = Switch rvdw = 1.0 ; rvdw+ (0.1:0.3)= rlist rvdw_switch = 0.9 gen_vel = no ; yes gen_temp = 300 gen_seed = -1 ;Temperature coupling tc_grps = system tcoupl = no ;nose-hoover tau_t = 0.1 ref_t = 300 ;Pressure coupling pcoupl = no optimize_fft = yes Any suggesions are really welcome. Thank you. Regards, Andrea Muntean -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- -- 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 New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop -- 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] NVE of water
Hi, I would still argue that double precision is important. My comment on SHAKE was based on CHARMM - in Gromacs it indeed doesn't matter for water. Ran Justin A. Lemkul wrote: Berk Hess wrote: Hi, Shake is not relevant for water and also a time step of 2 fs should be fine. The cut-off's are the problem. You have a buffer size of 0.1 nm, which is already smaller than 2 times the distance from the center of geometry of a water molecule to a hydrogen. You need some additional distance for water diffusion. I would use a buffer of 0.25 to 0.3 nm. You don't list you coulombtype setting. Use pme (or if you want perfect energy conservation: pme-switch), you can also use reaction-field-zero if you really don't want to use PME. Then use nstlist=-1, run a short simulation and check in at the end of your log file that the neighbor list lifetime is somewhere between 5 and 20 steps. We should have a wiki entry for such details. Maybe there is one, but I was too lazy to check or make one. There was a basic NVE page; I have updated it based on your notes above: http://www.gromacs.org/Documentation/Terminology/NVE -Justin Berk Date: Mon, 1 Mar 2010 09:16:36 +0100 From: r.fried...@bioc.uzh.ch To: gmx-users@gromacs.org Subject: Re: [gmx-users] NVE of water Hi Andrea, Did you use double precision? Also, I'd try a lower dt (say 1fs) and shake tolerance (maybe 1E-8). Good luck, Ran Andrea wrote: Dear users, for test purposes in order to set up a bigger system, I try to run NVE simulations of SPC water, but the energy increases very rapidely. My guess is that the cutoffs I use are not good for water. I that the case ( I would be grateful for a good reference for suitable SPC water parameters) or do I miss something else? My parameter file for the NVE is: title = NVE cpp = /lib/cpp integrator = md dt = 0.002 ; ps ! = 2 fs nsteps = 5 ; total 100 ps nstxout = 5000 nstvout = 5000 nstxtcout = 0 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1.1 unconstrained-start = yes constraints = all-bonds constraint_algorithm = shake shake_tol = 0.0001 ;VdW vdwtype = Switch rvdw = 1.0 ; rvdw+ (0.1:0.3)= rlist rvdw_switch = 0.9 gen_vel = no ; yes gen_temp = 300 gen_seed = -1 ;Temperature coupling tc_grps = system tcoupl = no ;nose-hoover tau_t = 0.1 ref_t = 300 ;Pressure coupling pcoupl = no optimize_fft = yes Any suggesions are really welcome. Thank you. Regards, Andrea Muntean -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- -- 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 New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop -- 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] NVE of water
On 2/03/2010 12:39 AM, Ran Friedman wrote: Hi, I would still argue that double precision is important. Oh? The discussion of Table 4 of http://pubs.acs.org/doi/abs/10.1021/ct700301q (2008 GROMACS 4 JCTC paper) suggested to me that single-precision NVE could be done well in GROMACS. Am I missing something? Mark My comment on SHAKE was based on CHARMM - in Gromacs it indeed doesn't matter for water. Ran Justin A. Lemkul wrote: Berk Hess wrote: Hi, Shake is not relevant for water and also a time step of 2 fs should be fine. The cut-off's are the problem. You have a buffer size of 0.1 nm, which is already smaller than 2 times the distance from the center of geometry of a water molecule to a hydrogen. You need some additional distance for water diffusion. I would use a buffer of 0.25 to 0.3 nm. You don't list you coulombtype setting. Use pme (or if you want perfect energy conservation: pme-switch), you can also use reaction-field-zero if you really don't want to use PME. Then use nstlist=-1, run a short simulation and check in at the end of your log file that the neighbor list lifetime is somewhere between 5 and 20 steps. We should have a wiki entry for such details. Maybe there is one, but I was too lazy to check or make one. There was a basic NVE page; I have updated it based on your notes above: http://www.gromacs.org/Documentation/Terminology/NVE -Justin Berk Date: Mon, 1 Mar 2010 09:16:36 +0100 From: r.fried...@bioc.uzh.ch To: gmx-users@gromacs.org Subject: Re: [gmx-users] NVE of water Hi Andrea, Did you use double precision? Also, I'd try a lower dt (say 1fs) and shake tolerance (maybe 1E-8). Good luck, Ran Andrea wrote: Dear users, for test purposes in order to set up a bigger system, I try to run NVE simulations of SPC water, but the energy increases very rapidely. My guess is that the cutoffs I use are not good for water. I that the case ( I would be grateful for a good reference for suitable SPC water parameters) or do I miss something else? My parameter file for the NVE is: title = NVE cpp = /lib/cpp integrator = md dt = 0.002 ; ps ! = 2 fs nsteps = 5 ; total 100 ps nstxout = 5000 nstvout = 5000 nstxtcout = 0 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1.1 unconstrained-start = yes constraints = all-bonds constraint_algorithm = shake shake_tol = 0.0001 ;VdW vdwtype = Switch rvdw = 1.0 ; rvdw+ (0.1:0.3)= rlist rvdw_switch = 0.9 gen_vel = no ; yes gen_temp = 300 gen_seed = -1 ;Temperature coupling tc_grps = system tcoupl = no ;nose-hoover tau_t = 0.1 ref_t = 300 ;Pressure coupling pcoupl = no optimize_fft = yes Any suggesions are really welcome. Thank you. Regards, Andrea Muntean -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- -- 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 New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop -- 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] NVE of water
Date: Mon, 1 Mar 2010 15:44:28 +0100 From: r.fried...@bioc.uzh.ch To: gmx-users@gromacs.org Subject: Re: [gmx-users] NVE of water Mark Abraham wrote: On 2/03/2010 12:39 AM, Ran Friedman wrote: Hi, I would still argue that double precision is important. Oh? The discussion of Table 4 of http://pubs.acs.org/doi/abs/10.1021/ct700301q (2008 GROMACS 4 JCTC paper) suggested to me that single-precision NVE could be done well in GROMACS. Am I missing something? Mark The presented benchmarks were performed in the NVT ensemble (section IX). Or am I missing something? No, but everything that affects energy conservation in NVE also affects it in NVT, in addition the thermostat affect the integration accuracy in NVT (and in NVT you do not measure energy conservation from the total energy, but from the conserved energy quantity). Double precision can be important for energy conservation, but often other factors deteriorate the energy conservation orders of magnitude from what can be reached in single precision already. Double precision is only required for testing or when you really need to generate an NVE ensemble. Berk Ran -- 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 _ New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop-- 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] Temperature Coupling and Coupling-Groups
Greetings dear Gromacs users, I would like to create a membrane-protein simulations (popc + protein, water, Na Cl ions, using Berendsen thermostat) and I am not sure which coupling-groups I should use. For example, why not couple the whole system together? I do realize that this is a large request on this type of mailing list. I will also be happy to receive references to relevant literature. Thanks in advance, -Shay -- 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] Temperature Coupling and Coupling-Groups
shaya...@post.tau.ac.il wrote: Greetings dear Gromacs users, I would like to create a membrane-protein simulations (popc + protein, water, Na Cl ions, using Berendsen thermostat) and I am not sure which coupling-groups I should use. For example, why not couple the whole system together? I do realize that this is a large request on this type of mailing list. I will also be happy to receive references to relevant literature. Most reports in the literature describe protein, lipids, and solvent+ions in separate groups. The reasons for not coupling the whole system together are well-documented, and as a matter of fact, I just updated the Gromacs wiki this weekend to point to several papers describing this phenomenon: http://www.gromacs.org/Documentation/Terminology/Thermostats There are also numerous threads in the list archive on this topic, likely with other references that I did not link. -Justin Thanks in advance, -Shay -- 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] NVE of water
Berk Hess wrote: Date: Mon, 1 Mar 2010 15:44:28 +0100 From: r.fried...@bioc.uzh.ch To: gmx-users@gromacs.org Subject: Re: [gmx-users] NVE of water Mark Abraham wrote: On 2/03/2010 12:39 AM, Ran Friedman wrote: Hi, I would still argue that double precision is important. Oh? The discussion of Table 4 of http://pubs.acs.org/doi/abs/10.1021/ct700301q (2008 GROMACS 4 JCTC paper) suggested to me that single-precision NVE could be done well in GROMACS. Am I missing something? Mark The presented benchmarks were performed in the NVT ensemble (section IX). Or am I missing something? No, but everything that affects energy conservation in NVE also affects it in NVT, in addition the thermostat affect the integration accuracy in NVT (and in NVT you do not measure energy conservation from the total energy, but from the conserved energy quantity). Double precision can be important for energy conservation, but often other factors deteriorate the energy conservation orders of magnitude from what can be reached in single precision already. Double precision is only required for testing or when you really need to generate an NVE ensemble. Berk Thanks for clarifying Berk - I was referring to the latter (i.e., when you really need to generate an NVE ensemble). I guess this is the main reason to run with NVE. Since most people are not running NVE with large systems or for production simulations, the added accuracy often justifies the use of double precision. Best, Ran -- 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] Temperature Coupling and Coupling-Groups
Hi Justin, Thank you very much for your prompt reply. I will make sure to review the aforementioned references. Regards, -Shay Quoting Justin A. Lemkul jalem...@vt.edu: shaya...@post.tau.ac.il wrote: Greetings dear Gromacs users, I would like to create a membrane-protein simulations (popc + protein, water, Na Cl ions, using Berendsen thermostat) and I am not sure which coupling-groups I should use. For example, why not couple the whole system together? I do realize that this is a large request on this type of mailing list. I will also be happy to receive references to relevant literature. Most reports in the literature describe protein, lipids, and solvent+ions in separate groups. The reasons for not coupling the whole system together are well-documented, and as a matter of fact, I just updated the Gromacs wiki this weekend to point to several papers describing this phenomenon: http://www.gromacs.org/Documentation/Terminology/Thermostats There are also numerous threads in the list archive on this topic, likely with other references that I did not link. -Justin Thanks in advance, -Shay -- 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 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] Temperature Coupling and Coupling-Groups
On 3/1/10 5:13 PM, Justin A. Lemkul wrote: shaya...@post.tau.ac.il wrote: Greetings dear Gromacs users, I would like to create a membrane-protein simulations (popc + protein, water, Na Cl ions, using Berendsen thermostat) and I am not sure which coupling-groups I should use. For example, why not couple the whole system together? I do realize that this is a large request on this type of mailing list. I will also be happy to receive references to relevant literature. Most reports in the literature describe protein, lipids, and solvent+ions in separate groups. The reasons for not coupling the whole system together are well-documented, and as a matter of fact, I just updated the Gromacs wiki this weekend to point to several papers describing this phenomenon: http://www.gromacs.org/Documentation/Terminology/Thermostats That's interesting, thanks for putting this together Justin. I haven't read the paper from the Tavan group completely, but I don't think they truly solve the problem, do they? It reads more like some workaround. The origin of the problem is the lack of coupling between the different degrees of freedom, and as such one would expect united atom force fields to show this effect to a larger degree than all-atom force fields. It could also be that the use of constraints makes that the effective number of degrees of freedom per atom is different for proteins and water. It seems that this still hasn't been investigated properly... There are also numerous threads in the list archive on this topic, likely with other references that I did not link. -Justin Thanks in advance, -Shay -- 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
Re: [gmx-users] Temperature Coupling and Coupling-Groups
David van der Spoel wrote: On 3/1/10 5:13 PM, Justin A. Lemkul wrote: shaya...@post.tau.ac.il wrote: Greetings dear Gromacs users, I would like to create a membrane-protein simulations (popc + protein, water, Na Cl ions, using Berendsen thermostat) and I am not sure which coupling-groups I should use. For example, why not couple the whole system together? I do realize that this is a large request on this type of mailing list. I will also be happy to receive references to relevant literature. Most reports in the literature describe protein, lipids, and solvent+ions in separate groups. The reasons for not coupling the whole system together are well-documented, and as a matter of fact, I just updated the Gromacs wiki this weekend to point to several papers describing this phenomenon: http://www.gromacs.org/Documentation/Terminology/Thermostats That's interesting, thanks for putting this together Justin. I haven't read the paper from the Tavan group completely, but I don't think they truly solve the problem, do they? It reads more like some workaround. Right, I just included that paper because I came across it when exploring these thermostat issues myself, and I think they have a really nice discussion of some of the problems one faces when using thermostats, in general. The paper also points to a lot of other references that delve more deeply into the underlying issues. Hopefully these sorts of links will be useful. -Justin The origin of the problem is the lack of coupling between the different degrees of freedom, and as such one would expect united atom force fields to show this effect to a larger degree than all-atom force fields. It could also be that the use of constraints makes that the effective number of degrees of freedom per atom is different for proteins and water. It seems that this still hasn't been investigated properly... There are also numerous threads in the list archive on this topic, likely with other references that I did not link. -Justin Thanks in advance, -Shay -- 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] correlation function 'time value' ?
Dear Mark and David, Thanks you, i will check the paper very carefully and try again. regards, Rama On Sat, Feb 27, 2010 at 1:13 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 27/02/2010 7:31 PM, Ramachandran G wrote: Dear Dr. van der Spoel: Thanks for the clarification in your reply. One more thing I was just curious is that, for C(t) = f(x).f(x+t) , what is the default value for t, which is often called correlation time, in gromacs for correlation function calculation, especially in g_hbond, and/or is it possible to customize the t in gromacs? t is not the correlation time. t is an arbitrary amount of time, at which the magnitude of C(t) indicates the extent to which f is correlated with itself when a set of samples are examined at time interval t. The (integrated) correlation time is the integral of (normalized) C(t) over 0 t infinity. See section 8.5 of the manual. I also found the explanations in Wolff, U. Comput. Phys. Commun. 2004, 156, 143-153. Madras, N.; Sokal, A. D. J. Stat. Phys. 1988, 50, 109-186. useful. Mark On Fri, Feb 26, 2010 at 10:03 PM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2010-02-27 03.27, Ramachandran G wrote: Hi gromacs users: As you know autocorrelation function C(t) C(t) = f(0).f(t) 't' value can start from 0 but, i would like to know what value does gromacs use, more specifically for g_hbond. Can anyone help me? Thank you. Rama The tell you that all time origins x are used, so C(t) = f(x).f(x+t) _x -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- 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 -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- 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: Choice of value of rlist, rvdw and rcoulomb
Dear Mark and Amit, I appreciate your replies. I have read this portion of the gromacs manual which talks about cut-offs, but I don't clearly understand the physical significance of the choice of values. I am using for my experiments vdwtype = cutoff, which is twin-range cut-off with rlist = neighbour list cut off and rvdw = vdw cut-off where rvdw = rlist. I have run three different experiments (NPT simulation of 200 particles of oxygen at 80K ie liquid oxygen) but with different rlist and rvdw values to evaluate the influence of these values on my Lennard-Jones plots. The literature Lennard-Jones parameters for oxygen which I have been using are epsilon = 0.939482 KJ/mol and sigma = 0.3433 nm. The book Computer Simulation of Liquids by Allen and Tildesley recommends the use of rvdw = 2.5xsigma. In my case, if I use this recommendation, my rvdw value would be 0.86. The values I have used and the results are as follows: RLIST = 0.3, RVDW = 0.7 RESULT: RDF Plot converges to 1 (WORKS). RLIST = 0.3, RVDW = 1.0 RESULT: RDF Plot converges to 0 after third peak (DOES NOT WORK). RLIST = 0.7, RVDW = 0.7 RESULT: RDF Plot converges to 0 after third peak (DOES NOT WORK). I know that the problem is not about equilibration, because the first experiment which worked did not even equilibrate fully but gave the right plot. My question is: what is the physical significance of choosing these values? I know that rlist is used as cut-off for neighbour list generation and to specify which atom pairs are interacting, so that these interactions can be calculated at every step of the simulation. rvdw specifies the radius of atoms which will interact in a vdw manner. Why would a rvdw = 0.7 work and rvdw = 1.0 not work looking at a system in a physical sense? 0.7 and 1.0 are both close to the recommended 0.86 value for rvdw, so why does one work and not other? What could be happening in the system? If I don't understand physically what these values really mean, I may never fully grasp what is going on in the system. Please help me out. The .mdp file I have used below is the same in all three cases, the only modifications being the rlist and rvdw values. integrator = md ; a leap-frog algorithm for integrating Newton's equations of motion dt = 0.002 ; time-step in ps nsteps = 50 ; total number of steps; total time (1 ns) nstcomm = 1 ; frequency for com removal nstxout = 1000 ; freq. x_out nstvout = 1000 ; freq. v_out nstfout = 0 ; freq. f_out nstlog = 100 ; energies to log file nstenergy= 100 ; energies to energy file nstlist = 10 ; frequency to update neighbour list ns_type = grid ; neighbour searching type rlist= 0.3; cut-off distance for the short range neighbour list pbc = xyz; Periodic boundary conditions:xyz, use periodic boundary conditions in all directions periodic_molecules = no ; molecules are finite, fast molecular pbc can be used vdw-type = Cut-off; van der Waals interactions rvdw = 0.7; distance for the LJ or Buckingham cut-off fourierspacing = 0.135 ; max. grid spacing for the FFT grid for PME fourier_nx = 0 ; highest magnitude in reciprocal space when using Ewald fourier_ny = 0 ; highest magnitude in reciprocal space when using Ewald fourier_nz = 0 ; highest magnitude in reciprocal space when using Ewald pme_order= 4 ; cubic interpolation order for PME ewald_rtol = 1e-5 ; relative strength of the Ewald-shifted direct potential optimize_fft = yes; calculate optimal FFT plan for the grid at start up. DispCorr = no ; Tcoupl = v-rescale ; temp. coupling with vel. rescaling with a stochastic term. tau_t= 0.1; time constant for coupling tc-grps = OXY; groups to couple separately to temp. bath ref_t= 80 ; ref. temp. for coupling Pcoupl = berendsen ; exponential relaxation pressure coupling (box is scaled every timestep) Pcoupltype = isotropic ; box expands or contracts evenly in all directions (xyz) to maintain proper pressure tau_p= 0.5; time constant for coupling (ps) compressibility = 4.5e-5 ; compressibility of solvent used in simulation ref_p= 1.0; ref. pressure for coupling (bar) gen_vel = yes; generate velocities according to a Maxwell distr. at gen_temp gen_temp = 80 ; temperature for
[gmx-users] How to add a new non-bonded interaction into Gromacs
Dear ALL: I would like to add a new 2-body non-bonded interaction into Gromacs. Has anybody done this yet? Help is dearly appreciated. Regards, Adama Adama Tandia, Corning INC, SP-TD-01-01 Corning NY 14831 USA, Tel: 607 248 1036 -GoogleVoice: 708 433 9430 -- 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] Re: Choice of value of rlist, rvdw and rcoulomb
Lum Nforbi wrote: Dear Mark and Amit, I appreciate your replies. I have read this portion of the gromacs manual which talks about cut-offs, but I don't clearly understand the physical significance of the choice of values. I am using for my experiments vdwtype = cutoff, which is twin-range cut-off with rlist = neighbour list cut off and rvdw = vdw cut-off where rvdw = rlist. I have run three different experiments (NPT simulation of 200 particles of oxygen at 80K ie liquid oxygen) but with different rlist and rvdw values to evaluate the influence of these values on my Lennard-Jones plots. The literature Lennard-Jones parameters for oxygen which I have been using are epsilon = 0.939482 KJ/mol and sigma = 0.3433 nm. The book Computer Simulation of Liquids by Allen and Tildesley recommends the use of rvdw = 2.5xsigma. In my case, if I use this recommendation, my rvdw value would be 0.86. The values I have used and the results are as follows: RLIST = 0.3, RVDW = 0.7 RESULT: RDF Plot converges to 1 (WORKS). RLIST = 0.3, RVDW = 1.0 RESULT: RDF Plot converges to 0 after third peak (DOES NOT WORK). RLIST = 0.7, RVDW = 0.7 RESULT: RDF Plot converges to 0 after third peak (DOES NOT WORK). I know that the problem is not about equilibration, because the first experiment which worked did not even equilibrate fully but gave the right plot. Just because you got the desired result does not mean what you did was right. Haphazard combinations of parameters lead to unpredictable and unreliable results. I think your rlist is absurdly short - what motivated this choice? Why have you yet to use the value calculated based on the Allen and Tildesley rule of thumb (0.9 nm)? My question is: what is the physical significance of choosing these values? I know that rlist is used as cut-off for neighbour list generation and to specify which atom pairs are interacting, so that these interactions can be calculated at every step of the simulation. rvdw specifies the radius of atoms which will interact in a vdw manner. To quote from the manual (section 4.6.3): In the neighbor list all interaction pairs that fall within rlist are stored. Furthermore, the interactions between pairs that do not fall within rlist but do fall within max(rcoulomb,rvdw) are computed during NS, and the forces and energy are stored separately, and added to short-range forces at every time step between successive NS. The neighbor list is updated every step for particles within rlist. The neighbor list between rlist and rvdw is updated every nstlist steps; between these neighbor-searching steps, the neighbor list is considered to be constant. Beyond rvdw, the van der Waals interaction is assumed to be zero (hence cut off). I see that you're setting DispCorr = no, so you may be getting cutoff artifacts. All long-range interactions should be attractive, so the problem with plain cutoffs is system expansion which is not compensated for when dispersion correction is off. Why would a rvdw = 0.7 work and rvdw = 1.0 not work looking at a system in a physical sense? 0.7 and 1.0 are both close to the recommended 0.86 Close enough does not mean good enough. For a system of only LJ particles, your choice of rvdw will likely have a huge impact on your results. You may just be getting some random success based on some fortuitous combination. value for rvdw, so why does one work and not other? What could be happening in the system? If I don't understand physically what these values really mean, I may never fully grasp what is going on in the system. Please help me out. I would suggest to you that you read some basic literature on force field derivation. While not necessarily directly related to what you're doing, you could benefit from understanding how reliable parameter sets are determined. If you don't comprehend what you're doing yet, you shouldn't be diving in head first. -Justin The .mdp file I have used below is the same in all three cases, the only modifications being the rlist and rvdw values. -- 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_cluster
Hi All, Greetings !I have a question about g_cluster. I have a configuration of Lennard Jones particles. For each particle I calculate an individual bond orientational order parameter Q4. Based on this order parameter I want to calculate the clusters in the system. Meaning - particles connected to each other sharing similar values of Q4. How would I have to go about this problem ?Thanks in advane. - Rohit -- 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
SV: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel
Sarah, I remember some changes to the double bond awhile back, perhaps you're using those? POPC (Berger/Tielman) is normally 'smoother' as Justin says. Maybe someone has a reference for the updates. Tim Sirk -- 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 add a new non-bonded interaction into Gromacs
On 2/03/2010 4:22 AM, Tandia, Adama wrote: Dear ALL: I would like to add a new 2-body non-bonded interaction into Gromacs. Has anybody done this yet? Help is dearly appreciated. This is what user-tables are for. Check out the manual for detailed information. 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/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] g_cluster
On 2010-03-02 00.13, ROHIT MALSHE wrote: Hi All, Greetings ! I have a question about g_cluster. I have a configuration of Lennard Jones particles. For each particle I calculate an individual bond orientational order parameter Q4. Based on this order parameter I want to calculate the clusters in the system. Meaning - particles connected to each other sharing similar values of Q4. How would I have to go about this problem ? Thanks in advane. - Rohit You need to implement a criterion like this in the program, instead of the RMSD matrix. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://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
