Re: [gmx-users] Threading in GROMACS

Zitat von "Jagan Mohan" <[EMAIL PROTECTED]>: Hello, Just wanted to know if GROMACS 3.3.3 supports multi threading that is can run four instances of mdrun in the same machine which has 4 cores... You can run GROMACS in parallel with MPI, which is much more efficient. Any decent distribution ha

Re: Fwd: [gmx-users] Performance problems with more than one node

Hi Tiago, if you swith off PME and suddenly your system scales, then the problems are likely to result from bad MPI_Alltoall performance. Maybe this is worth a check. If this is the case, there's a lot more information about this in the paper "Speeding up parallel GROMACS on high- latency network

[gmx-users] Threading in GROMACS

Hello, Just wanted to know if GROMACS 3.3.3 supports multi threading that is can run four instances of mdrun in the same machine which has 4 cores... Thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/li

[gmx-users] dna-protein simulation

Hello Tsjerk, while running pdb2gmx I was getting error like h1 is not found while assigning improper dihedral so I just modified the forcefield(ffG43a1.rtp)file by default it was considering ADE also inplace of considering DADE part only,so I removed ADE,CYT,GUA part also(is it right to do so?)

Re: [gmx-users] see some line in vmd

Morteza Khabiri wrote: Dear gmx user I have a box which contain protein and solution. Before running I minimized it very well and also system is running. After 2 ns when I saw the trajectory in vmd I saw that ther is some lines like bondes in the system. eg, between oxygen group of one water m

[gmx-users] see some line in vmd

Dear gmx user I have a box which contain protein and solution. Before running I minimized it very well and also system is running. After 2 ns when I saw the trajectory in vmd I saw that ther is some lines like bondes in the system. eg, between oxygen group of one water molecule in one part of box

[gmx-users] Re: help on parameterization

Julio Benegas wrote: Dear David, We are sorry to bother you on perhaps a simple question, but elusive to us. We want to run a MD simulation of three units of chitosan. We are using Gromacs ffG53A6 force field and we can not find in the corresponding library the parameters corresponding to the NH2

[gmx-users] HEME topology

Take a look at the charm file: top_all22_prot.inp Specifically, RESI HEME ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Ple

Re: [gmx-users] urey-bradley format

Piotr Adam Pieniazek wrote: Hi, I'm trying to put in a Urey-Bradly type term into my force field, but the format is not specified in the manual. atom_1 atom_2 atom_3 5 angle angle_force bond bond_force I'm particularly confused about the last two terms. I've tried both combinations and th

[gmx-users] angles125 test fails on Altix4700 with gcc or intel

Hi, I recently installed gromacs in single precision on an Altix4700 using either intel 10.1.0008 or gcc 4.2.3 and in both cases the installation passes all of the gmxtests except for angles125. The differences in the energy appear to be rather significant (see below). Can anyone offer an explan

[gmx-users] HEME topology

Hi, I am trying to simulate HEME in a water box. I generated HEME topology based on the parameters in the ffG43a2.rtp file. When I run a short burst of unrestrained dynamics, it does not remain planar. I understand that there might be some buckling but not to the extent that I am observing.

Re: [gmx-users] Performance problems with more than one node

vivek sharma wrote: Sorry for the incomplete mail...i sent it by mistake what i want to add is I am not able to run it with any of the option.any help and suggestion will be highly appreciated. FYI size of my system is around 45000 atoms. The performance will depend upon a lot of fact

Re: [gmx-users] Performance problems with more than one node

Sorry for the incomplete mail...i sent it by mistake what i want to add is I am not able to run it with any of the option.any help and suggestion will be highly appreciated. FYI size of my system is around 45000 atoms. Thanks in advance, Vivek 2008/9/25 vivek sharma <[EMAIL PROTECTED]> > Hi

Re: [gmx-users] Performance problems with more than one node

Hi friends, I am also facing the similar problem when tried to scale gromacs for more number of processors , I have tried one job using gromacs on EKA, in an attempt to scale it for more number of processor I am able to get the reduction in simulation time upto 20 processors, it is taking more time

Fwd: [gmx-users] Performance problems with more than one node

We currently have no funds available to migrate to infiniband but we will in the future. I thought on doing interface bonding but I really think that isn't really the problem here, there must be something I'm missing, since most applications scale well to 32 cores on GbE. I can't scale any applica

[gmx-users] Performance problems with more than one node

Hmmm... I don't have any .pdb file, what can I look for then? Best regards, Tiago Marques On Tue, Sep 23, 2008 at 5:48 PM, Jochen Hub <[EMAIL PROTECTED]> wrote: > Tiago Marques wrote: > > I don't know how large the system is. I'm the cluster's system > administrator >