Re:Re: [gmx-users] How to calculate the potential energy of a molecule in a fixed conformation.

2013-07-27 Thread xiao
Dear Justin, Thank you so much for your help! Best wishes Fugui At 2013-07-28 03:52:47,"Justin Lemkul" wrote: > > >On 7/27/13 11:48 AM, xiao wrote: >> Dear Gromacs users, >> >> I am developing the force field parameters of an organic molecule. I need to >> calculate the MM energy of

Re: [gmx-users] How to calculate the potential energy of a molecule in a fixed conformation.

2013-07-27 Thread Justin Lemkul
On 7/27/13 11:48 AM, xiao wrote: Dear Gromacs users, I am developing the force field parameters of an organic molecule. I need to calculate the MM energy of the molecule in a fixed conformation. For example, in order to get the force constant of a bond, i need to calculate the energy of the

Re: Aw: [gmx-users] Free Energy Simulations in Parallel

2013-07-27 Thread Justin Lemkul
On 7/27/13 7:02 AM, lloyd riggs wrote: Play with the domain decomposition, lincs itr/order, -ntomp and -ntmpi, etc... I was able to get a 4 day simulation which often gave that error to speed up to 12 hours on 24 CPU/3 nodes/144 cores but it took 2 days of submitting, checking speed, and killin

[gmx-users] How to calculate the potential energy of a molecule in a fixed conformation.

2013-07-27 Thread xiao
Dear Gromacs users, I am developing the force field parameters of an organic molecule. I need to calculate the MM energy of the molecule in a fixed conformation. For example, in order to get the force constant of a bond, i need to calculate the energy of the bond in different distance by using

Aw: [gmx-users] Free Energy Simulations in Parallel

2013-07-27 Thread lloyd riggs
  Play with the domain decomposition, lincs itr/order, -ntomp and -ntmpi, etc...  I was able to get a 4 day simulation which often gave that error to speed up to 12 hours on 24 CPU/3 nodes/144 cores but it took 2 days of submitting, checking speed, and killing jobs to try another grid routine.  My