Re: [gmx-users] openmpi

Hi, I'm using openmpi on our 24-nodes 2 cores each cluster without any problem so far. I run my jobs under torque and I did not change any of default settings. With my system it scales rather well on 4 nodes, but I have no problems with running more. Grzegorz Wieczorek Department of

Re: [gmx-users] bond lost!

zzhwise1 wrote: good everyone i have 2 questions : 1) when i optimized my system of CH3(CH2)13COOH chains with l-bfgs for 5000steps,but it stopped at 467th step,and i found the conformation break,8chains'lost the C-OH bonds,why there was this and what cause this?was this the wrong itp

[gmx-users] The molecule size

Hi: Two meltmodels were built for polyethylene (PE) and polyvinylmethylether (PVME) melt with PBC condition. The density of both melt model agree with experimenal value well.But when one check the radius of gyration (Rg) of them, both of them were too small to accept as

Re: [gmx-users] Re: Using ACE and NAC with oplsaa

[EMAIL PROTECTED] wrote: Appologies, two entries are required (the first is for ACE and the second is for NAC): [ dihedraltypes ] ; ijkl func coefficients CT C N CT_23 30.28798 -4.81160 -25.47638 0.0 0.0 0.0 For ACE (Sept2006)

Re: [gmx-users] bond-bond and bond-angle cross terms

Camilo Calderon wrote: Hi all! I am new to the GROMACS-world, and I am mystified. How do I implement the 3 body potentials advertised in sec. 4.2.8 and sec. 4.2.9 of the GROMACS 3.3 manual? Right now I have the following: [ cross_cross_bond ] ;ai aj funct r1e r2e krr numbers here [

Re: [gmx-users] The molecule size

主月 ：） wrote: Hi: Two melt models were built for polyethylene (PE) and polyvinylmethylether (PVME) melt with PBC condition . The density of both melt model agree with experimenal value well.But when one check the radius of gyration (Rg) of them, both of them were too small to accept