So I would have to successively set tinit to the time of the last restart? Can I ask why that doesn't seem to be a problem when I am simply switching from saving every 10steps to every 100 steps? I am not at time zero then either, but at 2ps and grompp and mdrun did not complain then.
Justin Lemkul wrote > On Tue, Jul 2, 2013 at 1:23 PM, Neha < > nshafique@ > > wrote: > >> Hi, >> >> So the commands are: >> >> grompp -f 10step.mdp -p dppc_bilayer.top -o 10step.tpr -c >> dppc_bilayer.gro >> >> mdrun -nt 4 -s 10step.tpr -c nonlinear.gro -e nonlinear.edr -x >> nonlinear.xtc >> -o nonlinear.trr -g nonlinear.log -cpo nonlinear.cpt -rdd 2.5 >> >> grompp -f 100step.mdp -c 10step.tpr -p dppc_bilayer.top -o 100step.tpr -t >> nonlinear.cpt >> >> mdrun -nt 4 -s 100step.tpr -c nonlinear.gro -e nonlinear.edr -x >> nonlinear.xtc -o nonlinear.trr -g nonlinear.log -cpi nonlinear.cpt -cpo >> nonlinear.cpt -rdd 2.5 >> >> Up till this point the output is what I would expect. However now I try >> to >> use the 10step mdp again in order to save it every ten time steps - >> >> grompp -f 10step.mdp -c 100step.tpr -p dppc_bilayer.top -o 10step.tpr -t >> nonlinear.cpt >> >> mdrun -nt 4 -v -s 10step.tpr -c nonlinear.gro -e nonlinear.edr -x >> nonlinear.xtc -o nonlinear.trr -g nonlinear.log -cpi nonlinear.cpt -cpo >> nonlinear.cpt -rdd 2.5 >> >> And at this mdrun I get WARNING: This run will generate roughly >> 186617909559164928 Mb of data >> >> starting mdrun 'DPPC BILAYER' >> 100 steps, infinite ps (continuing from step 1000, 20.0 ps). >> >> >> This is the saving every 10 steps mdp file, the hundred step is identical >> except steps is a 1000 and nstxout is 100. >> >> ; VARIOUS PREPROCESSING OPTIONS = >> title = Martini >> cpp = /usr/bin/cpp >> >> ; RUN CONTROL PARAMETERS = >> integrator = md >> ; start time and timestep in ps = >> tinit = 0.0 >> > > This is your problem. You're no longer at t = 0. The checkpoint file > specifies some time in the future, so grompp thinks you're going backwards > in time and thinks you're going to generate infinite data by doing so. > Then mdrun gets confused, because it thinks you're trying to go backwards > as well, from step 1000 to step 100. Proper use of tinit and init_step in > the .mdp file should alleviate this problem. > > -Justin > > -- > > ========================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Associate > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > jalemkul@.umaryland > | (410) 706-7441 > > > ========================================== > -- > gmx-users mailing list > gmx-users@ > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to > gmx-users-request@ > . > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.x6.nabble.com/Is-non-linear-data-output-storage-possible-tp5008858p5009510.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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/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