[gmx-users] NVT equilibration of ethanol in OPLSAA ff

2011-10-05 Thread Ravi Kumar Venkatraman
Dear All, I downloaded ethanol.pdb file from prodrg server (all-atom). I used ethanol.itp file that was in oplsaa.ff directory of gromacs to create topology file for ethanol. I used genconf_d command to generate solvent box of 512 molecules (as of Bevan's gromacs tutorial) and then I

Re: [gmx-users] NVT equilibration of ethanol in OPLSAA ff

2011-10-05 Thread Mark Abraham
On 5/10/2011 6:36 PM, Ravi Kumar Venkatraman wrote: Dear All, I downloaded ethanol.pdb file from prodrg server (all-atom). I used ethanol.itp file that was in oplsaa.ff directory of gromacs to create topology file for ethanol. I used genconf_d command to generate solvent box of

[gmx-users] NVT equilibration of Ethanol in OPLSAA.

2011-10-04 Thread Ravi Kumar Venkatraman
*Dear all, I have been trying to generate pre-equilibrated ethanol solvent box of 512 molecules in **OPLSAA ff. I used ethanol.itp in oplsaa.ff directory for generating the topology file for ethanol. After NVT equilibration some of the molecules get aggregated and there is some void

Re: [gmx-users] NVT equilibration of Ethanol in OPLSAA.

2011-10-04 Thread Mark Abraham
On 4/10/2011 6:16 PM, Ravi Kumar Venkatraman wrote: *Dear all, I have been trying to generate pre-equilibrated ethanol solvent box of 512 molecules in **OPLSAA ff. I used ethanol.itp in oplsaa.ff directory for generating the topology file for ethanol. After NVT equilibration some

RE: [gmx-users] NVT equilibration of Ethanol in OPLSAA.

2011-10-04 Thread Dallas Warren
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Ravi Kumar Venkatraman Sent: Tuesday, 4 October 2011 6:17 PM To: gmx-users@gromacs.org Subject: [gmx-users] NVT equilibration of Ethanol in OPLSAA. Dear all, I have been trying to generate pre-equilibrated ethanol solvent box of 512