Re: 答复: [gmx-users] topology file of ligand

On 10/15/13 12:25 PM, sunyeping wrote: Thank you Dr. Lemkul, Could you recommand some primary literatures which are most usefule for me to understand the force field? The ones cited in the Gromacs manual are a good start. One should never attempt to use a force field without scrutinizing

答复: [gmx-users] topology file of ligand

Thank you Dr. Lemkul,   Could you recommand some primary literatures which are most usefule for me to understand the force field?  Yeping Sun Institute of Microbiology, Chinese Academy of Sciences --发件人：Justin Lemkul 发送时间：2013年10月1

Re: [gmx-users] topology file of ligand

On 10/15/13 11:24 AM, sunyeping wrote: Dear gromacs users, I am study the tutorial for protein-ligand complex system (gromacs tutorial 5: T4 lysozyme in complex with JZ4). The tutorial use PRODRG to produce the topology file. The author state that he immediately notice three things that ar

[gmx-users] topology file of ligand

Dear gromacs users,   I am study the tutorial for protein-ligand complex system (gromacs tutorial 5: T4 lysozyme in complex with JZ4). The tutorial use PRODRG to produce the topology file. The author state that he  immediately notice three things that are wrong with this topology, which include

Re: [gmx-users] jwe1050i + jwe0019i errors = SIGSEGV (Fujitsu)

On Thu, Oct 10, 2013 at 2:34 PM, James wrote: > Dear Mark, > > Thanks again for your response. > > Many of the regression tests seem to have passed: > > All 16 simple tests PASSED > All 19 complex tests PASSED > All 142 kernel tests PASSED > All 9 freeenergy tests PASSED > All 0 extra tests PASSE

Re: [gmx-users] Number of ligand contacts over the trajectories

Thanks a lot for reply. On Mon, Oct 14, 2013 at 12:34 PM, bipin singh wrote: > g_mindist with -on and -d option. > > > On Mon, Oct 14, 2013 at 11:37 AM, anu chandra wrote: > > > Dear Gromacs users, > > > > I am working with protein-ligand interaction. I would like to calculate > the > > number

Re: [gmx-users] recalculating .trr from .xtc

Interactions will be off, especially the bonded terms. > On Oct 15, 2013, at 7:21, Mark Abraham wrote: > > Also, the precision was selected when the xtc file was written, ie in the > mdp file. > > Mark >> On Oct 15, 2013 3:24 AM, "Justin Lemkul" wrote: >> >> >> >>> On 10/14/13 7:56 PM, Le