Re: [gmx-users] free energy caculation error
Hi Justin, thank you very much! according to your advise, my error is solved successfully. -- View this message in context: http://gromacs.5086.x6.nabble.com/free-energy-caculation-error-tp5015758p5015783.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] free energy caculation error
Hi all, I want to caculate the free energy of a molecule, but when I run the MD, it appears the error: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 4.4 nm. Change the number of nodes or mdrun option -rdd or -dds.However, even though i added the -rdd and -dds, the error is same as the previous. my mdp file as follows. ; we'll use the sd integrator ;run parameters integrator = sd dt = 0.002 ; ps nsteps = 5000; total 1ns nstcomm = 100 ; turn off trajectory writing nstxout = 0 nstvout = 0 ; cut-offs at 1nm rlist= 1.0 nstlist = 10 coulombtype = pme vdw-type = cut-off rvdw = 1.0 constraints = all-bonds ; set temperature to 300K tcoupl = v-rescale tc-grps = system tau-t= 0.2 ref-t= 300 ; and pressure to 1 bar pcoupl = parrinello-rahman ref-p = 1 compressibility = 4.5e-5 tau-p = 5 ; and set the free energy parameters free-energy = yes couple-moltype = RNA_chain_A init-lambda = 0 ; these 'soft-core' parameters make sure we never get overlapping ; charges as lambda goes to 0 sc-power = 1 sc-sigma = 0.3 sc-alpha = 1.0 ; we still want the molecule to interact with itself at lambda=0 couple-intramol = no couple-lambda1 = vdwq couple-lambda0 = none foreign-lambda = 0 0.2 0.4 0.6 0.8 0.9 1 nstdhdl = 10 separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 5 dh_hist_spacing = 50 thanks for advances. -- View this message in context: http://gromacs.5086.x6.nabble.com/free-energy-caculation-error-tp5015758.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] free energy caculation error
On 4/9/14, 6:41 AM, jane wrote: Hi all, I want to caculate the free energy of a molecule, but when I run the MD, it appears the error: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 4.4 nm. Change the number of nodes or mdrun option -rdd or -dds.However, even though i added the -rdd and -dds, the error is same as the previous. my mdp file as follows. Use fewer processors. Not all systems can be decomposed into any arbitrary number of DD cells; there are limits related to cell size. Your system is too small to be effectively split over 8 nodes. -Justin ; we'll use the sd integrator ;run parameters integrator = sd dt = 0.002 ; ps nsteps = 5000; total 1ns nstcomm = 100 ; turn off trajectory writing nstxout = 0 nstvout = 0 ; cut-offs at 1nm rlist= 1.0 nstlist = 10 coulombtype = pme vdw-type = cut-off rvdw = 1.0 constraints = all-bonds ; set temperature to 300K tcoupl = v-rescale tc-grps = system tau-t= 0.2 ref-t= 300 ; and pressure to 1 bar pcoupl = parrinello-rahman ref-p = 1 compressibility = 4.5e-5 tau-p = 5 ; and set the free energy parameters free-energy = yes couple-moltype = RNA_chain_A init-lambda = 0 ; these 'soft-core' parameters make sure we never get overlapping ; charges as lambda goes to 0 sc-power = 1 sc-sigma = 0.3 sc-alpha = 1.0 ; we still want the molecule to interact with itself at lambda=0 couple-intramol = no couple-lambda1 = vdwq couple-lambda0 = none foreign-lambda = 0 0.2 0.4 0.6 0.8 0.9 1 nstdhdl = 10 separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 5 dh_hist_spacing = 50 thanks for advances. -- View this message in context: http://gromacs.5086.x6.nabble.com/free-energy-caculation-error-tp5015758.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- 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.
