[gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours

Hi Folks, My simulation is running too slow. It took 10 wall clock hours (40 cpu hours) for a short 50 ps simulation of a ~ 23000 atom DPPC bilayer. The hardware is a 4-cpu core. The installation is gromacs 3.3.1. I have run much larger systems (~ 16 atoms) using the same gromacs installation

Re: [gmx-users] pr.mdp file

Quoting s lal badshah <[EMAIL PROTECTED]>: > Dear Justin and Mark, > My pr.mdp file is: > > title = pr.mdp > cpp = /usr/bin/cpp > define = -DPOSRES > constraints = all-bonds > integrator = md > dt = 0.002 > nsteps =10 > nstcomm

Re: [gmx-users] FF for membrane protein simulation in water

Quoting sudheer babu <[EMAIL PROTECTED]>: > Hi all, > I want to simulate my protein in water first, later insert into POPC > bilayer. Could you suggest which force field use protein in water and > protein in POPC, it should be same or different FF in both cases. > Pls help me.. > Thanks in advance

Re: [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours

Am 24.03.2008 um 10:17 schrieb maria goranovic: Hi Folks, My simulation is running too slow. It took 10 wall clock hours (40 cpu hours) for a short 50 ps simulation of a ~ 23000 atom DPPC bilayer. The hardware is a 4-cpu core. The installation is gromacs 3.3.1. I have run much larger syst

Re: [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours

The end of the log files after the simulation finishes might help you understand if there's anything odd that's taking more computation than normal. Also, just one extra running process can slow down the entire simulation as all processors will wait for the slowest. Check if it takes as long if

Re: [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours

Dear All, My apologies. I had too big a simulation cell, and too few atoms, hence the problem. No particular reason to choose order 5. I will try with pme_order 4 and see if it improves performance anyway. thanks ! -maria On Mon, Mar 24, 2008 at 2:19 PM, Carsten Kutzner <[EMAIL PROTECTED]> wro

[gmx-users] OPLS-FF

Hi all, My protein contain some missing residues , so I rebuilt missing residues, although gap is there between helices, my idea is when do minimisation these gap should disappear. Later trying to use pdb2gmx with OPLS/aa-L FF for generating gro file for two systems containing protonated and anothe

[gmx-users] amber force field problem: ignh doesnot work

Hi, I install amber force filed according to source: http://chemistry.csulb.edu/ffamber/index.html But , I run pdb2gmx, I got a problem. Program pdb2gmx, VERSION 3.3.1 pdb2gmx -ignh -ff amber99 -f r-l_1.pdb Opening library file /export/apps/gromacs-3.3.1-Amber /share/gromacs/top//ffamber99

Re: [gmx-users] amber force field problem: ignh doesnot work

Read the documentation on the site where you got the ffamber ports: http://chemistry.csulb.edu/ffamber/index.html#usage The Amber force fields are particular about residue nomenclature. -Justin Quoting Liu Shiyong <[EMAIL PROTECTED]>: > Hi, > > I install amber force filed according to source

[gmx-users] OPLS-FF

If I understand correctly, the rebuilt residues do not connect to each side of the gap correctly? You state about gaps: "actually it shouldn't appear after minimisation.", but it is not necessarily true that EM is capable of bringing the residues properly close together. I think you mean th

Re: [gmx-users] error of equilibration

s lal badshah wrote: Now will I start again from the begining by taking PDB file from RCSB ? or something else. I am checking the lincs warning page of gromacs but if you suggest me some correction it will be helpful. We can't, because you're the only person who knows anything about your sys

Re: [gmx-users] LINCS problem

s lal badshah wrote: Dear Experts, I checked the error lincs page and from that what I ignored in my work are the two errors these are: Warning: there are 0 atoms with zero occupancy and 1 atom with occupancy unequal to one (out of 1480 atoms).Check your pdb file Warning: masses will be d

[gmx-users] Error in equilibration

Dear Justin & Mark, Hi! I made changes in my pr.mdp file but still the errors came.Please guide me. title = pr.mdp cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 nsteps = 10 nstcomm =