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] 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
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
[gmx-users] NVE of water
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 -- 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
