[gmx-users] PME
Dear GMX Users I have a question about PME loading When executing mdrun. All my MD simulations (DNA-ligand interaction in triclinic box) are computed on in-house Linux 64-bit Intel Core-i7. According to gromacs tutorial in Justin web site (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html), "For a cubic box, the optimal setup will have a PME load of 0.25 and for a dodecahedral box, the optimal PME load is 0.33". Is this result should be obtained with my computer (with np=8)? or these PME load will be obtained only with np>8? Best Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx to amber
Dear GMX Users I want to access gmxtoamber script to convert gromacs output to amber. Could anyone give me this script? Best Regards Kiana -- gromacs.org_gmx-users mailing listgromacs.org_gmx-users@maillist.sys.kth.se https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pressure coupling
Dear GMX Users I have encountered with the following warning during NPT simulation of DNA-ligand interaction by Parrinello-Rahman pressure coupling (ref_p: 1bar). WARNING 1: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. After that, I used Berendsen pressure coupling without any warning. Pressure fluctuations were between -1000-1000 bar. There are 730 atoms and 13071 waters in my system. Although I didn't get any warning, I'm not sure that the Berendsen coupling and Pressure fluctuations for this system is correct? Please help me Best Regards kiana -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] simulated anealing
Dear GMX Users I want to run NVT equilibration and NPT equilibration (after NVT) for DNA-ligand interaction and want to increase temperature gradually i.e. from 0 to 300 K over a 100 ps, but i have some questions about this process: when I use simulated anealing in NVT as following annealing_time = 0 15 30 45 60 80 100 annealing_temp = 0 50 100 150 200 250 300 I don't know how to change gen_vel. > gen_vel = yes > gen-temp = 300 > gen-seed = 173529 is correct? or the gen_vel =No is correct? (After NVT equilibration, I want to equilibrate system during NPT condition at 300 K.) Please help me Best Regards Kiana -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] simulated anealing
Dear GMX Users I want to run NVT equilibration and NPT equilibration (after NVT) for DNA-ligand interaction and want to increase temperature gradually i.e. from 0 to 300 K over a 100 ps, but i have some questions about this process: when I use simulated anealing in NVT as following annealing_time = 0 15 30 45 60 80 100 annealing_temp = 0 50 100 150 200 250 300 I don't know how to change gen_vel. > gen_vel = yes > gen-seed = 173529 is correct? or the gen_vel =No is correct? (After NVT equilibration, I want to equilibrate system during NPT condition at 300 K.) Please help me Best Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] simulated anealing
ِDear Jastin Thanks your reply. In the first step (NVT equilibration) for heating system by simulated anealing from 0 to 300 K, what is the value of gen-temp? Thanks for your time and consideration. Best Regards Kiana On Sunday, December 1, 2013 4:31 PM, Justin Lemkul wrote: On 12/1/13 2:48 AM, kiana moghaddam wrote: > Dear > GMX Users > > I > want to run NVT equilibration and NPT equilibration (after > NVT) for DNA-ligand interaction and want to increase temperature > gradually i.e. > from > 0 to 300 K over a 100 ps, but i have some questions about this process: > when > I use simulated anealing in NVT as following > annealing_time > = 0 15 30 45 60 80 100 > annealing_temp = 0 > 50 100 150 200 250 300 > I > don't know how to change gen_vel. > > > > gen_vel = yes > > >> gen-seed = 173529 > is > correct? or the gen_vel =No is correct? > > (After NVT equilibration, I want to equilibrate system during NPT condition at > 300 K.) > Set "gen_vel = yes" at the beginning of the annealing run, then "gen_vel = no" for all subsequent steps, in which you preserve the previous ensemble using checkpoint files. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] heating
Dear GMX Users I want to run NVT equilibration and NPT equilibration (after NVT) and want to increase temperature gradually i.e. from 0 to 300 K over 100 ps, but I have some questions about this process: when I use simulated annealing in NVT as following annealing_time = 0 15 30 45 60 80 100 annealing_temp = 0 50 100 150 200 250 300 I don't know how to change gen_temp. Should gen_temp be 0 or 300 K? At the first time, I did not use simulated annealing. I prepared 7 mdp files that in the first mdp file, I set nsteps=0, gen_temp=0, ref_t=0, then I use the output from first NVT equilibration for the second input. I repeat this to reach 300 K (in the second step nsteps=7500(*0.002=15), gen_temp=50, ref_t=50). I 'm not sure whether this process is correct? Could you please help me? Thanks for your time and consideration. Best Regards Kiana -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] constraint in Production
Dear Users I have a problem about production step in MD simulation. Can this step be run with constraints or unconstraints? Best Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] heating
Dear Jastin Thanks very much for your reply, when I heat system from 0 to 300 K with simulated annealing, ref_t =300 is correct? Best Regards On Tuesday, December 3, 2013 5:53 PM, Justin Lemkul wrote: On 12/3/13 2:17 AM, kiana moghaddam wrote: > Dear GMX Users > > I want to run NVT equilibration and NPT equilibration (after NVT) and want to > increase temperature gradually i.e. from 0 to 300 K over 100 ps, but I have > some questions about this process: > when I use simulated annealing in NVT as following > annealing_time = 0 15 30 45 60 80 100 > annealing_temp = 0 50 100 150 200 250 300 > I don't know how to change gen_temp. Should gen_temp be 0 or 300 K? > Generating velocities and then immediately freezing (in the strictest of sense) the system is likely not going to be stable or effective because the thermostat will go haywire trying to compensate for such a drastic change in temperature. It is an interesting question, because how does one generate velocities at 0 K? Theoretically, there are none. I would suggest setting gen_temp to 0; you can check the .tpr (via gmxdump) to see if any velocities are present, but even if they are they should be very small and largely irrelevant. The annealing protocol will warm the system relatively quickly, so even after a few dynamics steps, you will have small velocities within the system. > At the first time, I did not use simulated annealing. I prepared 7 mdp files > that in the first mdp file, I set nsteps=0, gen_temp=0, ref_t=0, then I use > the output from first NVT equilibration for the second input. I repeat this > to reach 300 K (in the second step nsteps=7500(*0.002=15), gen_temp=50, > ref_t=50). I 'm not sure whether this process is correct? Well, it works, but it's laborious and unnecessary because you're just manually doing what simulated annealing is doing. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] rcoulomb, rvdw and rlist value
Dear Users I want to use parmbsc0 force field for DNA-ligand interaction. I want some information about value of rcoulomb, rvdw and rlist in mdp file during equilibration & production steps. I set these values 1 nm . Is it correct? Best regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] rcoulomb, rvdw and rlist values
Dear Users I want to use parmbsc0 force field for DNA-ligand interaction. I want some information about value of rcoulomb, rvdw and rlist in mdp file during equilibration & production steps. I set these values 1 nm . Is it correct? Best regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] velocity generation
Dear GMX user I want to use NVT to heat my system (DNA-ligand) from 0 to 300K then NPT at 300 K in equilibration step. I 'm very confused about velocity generation. I use gen_vel= no in the first step (NVT) then generate velocity in the NPT step at 300 K. After that, in production step I use gen_vel= no. Is my process correct? Thank you Best Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] velocity generation
Dear Jastin Thanks your reply. as your email, I will generate velocity in NVT step with simulated annealing from 0 to 300K. What should be gen_temp value? Is 300 K correct? Best Regards On Thursday, December 5, 2013 9:15 PM, Justin Lemkul wrote: On 12/5/13 12:36 PM, kiana moghaddam wrote: > Dear GMX user > > I want to use NVT to heat my system (DNA-ligand) from 0 to 300K then NPT at > 300 K in equilibration step. > I 'm very confused about velocity generation. > I use gen_vel= no in the first step (NVT) then generate velocity in the NPT > step at 300 K. After that, in production step I use gen_vel= no. Is my > process correct? > If you generate new velocities at the outset of NPT, it introduces new instability and basically negates any benefit of having done any prior equilibration. Preserve the velocities from NVT (via the .cpt file) when continuing to NPT. Rule of thumb: do not generate velocities for any step in the protocol that is not the very first one. There are exceptions, but they are generally rare. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] fourierspacing value
I am now using Gromacs4.6.3 to deal with DNA-ligand interaction. I use the parameters rvdw = 1, rlist =1, rcoulomb =1, fourierspacing = 0.16 and pme_order=4, but I know that the values of fourierspacing and pme_order are correct. what are the correct values for these two parameters? Could anyone please help me? Best regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pressure average
Dear GMX Users I want to study DNA-ligand interaction. I run simulation in NVT (from 0 to 300K) then NPT(300K) step for equilibration. After 200 ps equilibration in 2 steps, average of temperature and pressure reach to 299.9 K and -0.5 bar. I have a question about pressure average. Should the average pressure reach to 1bar (ref pressure) in equilibration step or in production step? Should I run equilibration step in the longer time until the average pressure reach to 1bar? Best Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] average of pressure
Dear GMX Users I want to study DNA-ligand interaction. I run simulation in NVT (from 0 to 300K) then NPT(300K) step for equilibration. After 200 ps equilibration in 2 steps, average of temperature and pressure reach to 299.9 K and -0.5 bar. I have a question about pressure average. Should the average pressure reach to 1bar (ref pressure) in equilibration step or in production step? Should I run equilibration step in the longer time until the average pressure reach to 1bar? Best Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Acpype charge
Dear GMX Users I 'm running MD Simulation between DNA-ligand interaction using parmbsc0 force field. I use ACPYPE tool for calculation of the lignad topologies and other parameters. Is the charge in the itp file achieved from ACPYPE reliable? or Should it be reassign? Best Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] NVT equilibration
Dear GMX Users I want to equilibrate my system in NVT from 0 to 300 K then in NPT (300K). Is my mdp file in NVT equilibration is correct? define = -DPOSRES ; Run control integrator = md dt = 0.002 ; ps ! nsteps = 5 ; total 100.0 ps. ; Output control nstxout = 500 ; collect data every 1.0 ps nstvout = 500 ; collect data every 1.0 ps nstfout = 0 nstlog = 500 ; collect data every 1.0 ps nstenergy = 500 ; collect data every 1.0 ps nstxtcout = 500 xtc-precision = 500 nstcalcenergy = 10 energygrps = DNA_LIG Water_counterions ; Neighbor searching and short-range nonbonded interactions nstlist = 5 ns_type = grid pbc = xyz rlist = 1.0 ; Electrostatics coulombtype = PME rcoulomb = 1.0 ; van der Waals vdw-type = cut-off rvdw = 1.0 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order = 4 ; Temperature coupling tcoupl = V-rescale tc_grps = DNA_LIG Water_counterions tau_t = 0.1 0.1 ref_t = 300 300 ; SIMULATED ANNEALING annealing = single single annealing_npoints = 7 7 annealing_time = 0 15 30 45 60 80 100 0 15 30 45 60 80 100 annealing_temp = 0 50 100 150 200 250 300 0 50 100 150 200 250 300 ; Pressure coupling is on for NPT pcoupl = no ; Dispersion correction DispCorr = EnerPres ; generate velocities gen_vel = yes gen_temp = 300 gen_seed = -1 ; options for bonds continuation = no constraints = all-bonds constraint-algorithm = lincs ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 lincs_iter = 1 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fw: NVT equilibration
Dear Justin I absolutely know that this equilibration and heating are suitable for my system, but I want to sure whether the other parameters for example ref_t =300 is correct or not. Maybe it is true that 100ps run is very very faster than your email, but reliable answer is more important than lag time. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PME
Dear GMX users I run gromacs 4.6.3 in parallel for my system. My simulation box is triclinic. My MD simulation is computed on in-house Linux 64-bit Intel Core-i7. As far as I know, for triclinic box, the optimal setup will have a PME load of 0.25, so I change pme order and grid spacing in my mdp file to get this value. According to manual, I should change pme order to 6/8/10 when running in parallel. when I change it to 6, PME load become 0.33 (> 0.25). I do not know if it is correct. Please help me about this issue. Best Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
