Re: [gmx-users] mdrun with multi option
Thank you Mark. Let me explain my scenario here - Umbrella sampling simulations with 15 windows are run using -multi option to obtain PMFs. I have not noticed any issues with the output files (trr, pullf etc.) yet. I have carried out WHAM analysis using gmx wham option and obtained smooth PMFs. Please explain me in which way 'gmx mdrun -multi' option may lead to less reliable with output file and how I can be sure of it. Thanks again. regards, Debdip On 07.06.2017 12:39, Mark Abraham wrote: Hi, gmx mdrun -multidir is a good way to run a group of similar but otherwise uncoupled simulations - they remain uncoupled unless you choose something that couples them, such as replica exchange. gmx mdrun -multi is a bit less reliable with output files. Mark On Wed, Jun 7, 2017 at 12:34 PM Debdip Bhandary < debdip.bhand...@mv.uni-kl.de> wrote: Dear Users, I have doubts regarding simulating multiple systems using mdrun '-multi' option. I have seen that people have used this option for replica exchange (with '-replex' option, of course) where information are exchanged between the systems. In case of different systems (such as different windows in Umbrella sampling simulations, liquid water systems at different temperatures, etc.), as per my understanding (from user manual), there is no exchange of information between the systems and simulations are run without any influence of each other. Am I correct here? or is there any issue when different systems are simulated using -multi/multidir options? Any information regarding this would be appreciated. Thank you in advance. Best regards, Debdip Bhandary -- 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] mdrun with multi option
Dear Users, I have doubts regarding simulating multiple systems using mdrun '-multi' option. I have seen that people have used this option for replica exchange (with '-replex' option, of course) where information are exchanged between the systems. In case of different systems (such as different windows in Umbrella sampling simulations, liquid water systems at different temperatures, etc.), as per my understanding (from user manual), there is no exchange of information between the systems and simulations are run without any influence of each other. Am I correct here? or is there any issue when different systems are simulated using -multi/multidir options? Any information regarding this would be appreciated. Thank you in advance. Best regards, Debdip Bhandary -- 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] sequential simulations with mdrun -multi option
Dear Users, I am trying to perform n number of simulations in parallel using -multi option with mdrun (version 5.0.4). I want to simulate the system at different conditions in parallel using '-multi' option. The process involves nvt followed by NpT step. The jobscript is as following: #--- for ((i=0;i<20;i++)) do aprun -n 1 grompp_mpi -f nvt$i.mdp -c emin.gro -p topol.top -n index.ndx -o topol$i.tpr done aprun -n 240 mdrun_mpi -multi 20 -s topol -pf pullf #--- for ((i=0;i<20;i++)) do aprun -n 1 grompp_mpi -f npt$i.mdp -c confout$i.gro -t state$i.cpt -p topol.top -n index.ndx -o topol$i.tpr done aprun -n 240 mdrun_mpi -multi 20 -s topol -pf pulf #--- With this script, the nvt step is performed. The simulation stops when it is executing the npt step. the error is following: Time or ensemble averaged or multiple pair distance restraints do not work (yet) with domain decomposition, use a single MPI rank per simulation. Is there any suggestion for this? I could not able to figure out how to use a single mpi rank per simulations. Thanks in advance. with regards, Debdip Bhandary -- 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.
