[gmx-users] Re: Simulating a large system
Sure, it's basically improving minimization time. if i can focus all my resources in simulating or minimizing a portion of the system while ignoring other parts that are too far away from the selected portion, it can also be possible to run some simulations without the need of a big cluster and sort of obtaining about the same results. This goes to my interest of harnessing small computing systems for doing all these tasks. There are systems like rna molecules where i could get the fine grained structure first and then running the entire molecule to obtain the coarser structure. As someone says it might not improve time but at least having the ability to run portions only on my small desktop overnight or just leave it there running a lot of this could be accomplished. I do have access to a cluster but having to wait in the queue is time that can be used to getting somewhere, maybe slower but you're moving. On Apr 8, 2013, at 5:20 AM, Dr. Vitaly Chaban wrote: Vitaly Chaban -- gmx-users mailing listgmx-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
[gmx-users] Simulating a large system
Hi, is it possible to instruct gromacs to only perform the dynamics on half of the system or protein while ignoring the rest? thanks-- gmx-users mailing listgmx-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
[gmx-users] Restarting minimization
Hi, i'm new to grimaces and want to run a minimization process in parts, but
i'm having problems extracting the last frame, when i try the following command:
trjconv -s em-vac${ID}.tpr -f em-vac${ID}.trr -o mintmp.pdb -e 0
it returns no data, if i try 11 in the frame number it prints out a model, but
when trying to run mintmp.pdb, i get the following error:
Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the given
box and a minimum cell size of 23.38 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition
what am i doing wrong? or is there a tutorial where someone does this.
Thanks
em-vac-pbe.mdp
; Define can be used to control processes
define = -DFLEXIBLE ; Use flexible water model
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 500.0 ; Stop minimization when the maximum force 1.0 kJ/mol
nsteps = 100 ; Maximum number of (minimization) steps to perform
nstenergy = 1 ; Write energies to disk every nstenergy steps
energygrps = System ; Which energy group(s) to write to disk
nstlist = 1 ; Frequency to update the neighbor list
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = PME ; Treatment of long range electrostatic interactions
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
constraints = none ; Bond types to replace by constraints
pbc = xyz ; Periodic Boundary Conditions--
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[gmx-users] H2U residue
Hi, i'm trying to run an MD simulation of a protein with a tRNA and i'm getting an error that it does not recognize the modified residue H2U (DHU), i tried changing the forcefield to one that was user contributed but didn't work either. can anyone point me to some resource or tell he how you solved it? i've already googled it without success thanks -- gmx-users mailing listgmx-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
