[gmx-users] Re: how to remove periodicity when using g_rmsd

... and, in the case that you have several not-covalently-bound chains, use a 'topol.tpr' corresponding to a simulation beginning with all the chains within the same box. (I think Tsjerk suggested that to me several months ago) Mauricio Sica > > Hi Tangj Jioawei, Erik. > > This is due to per

[gmx-users] ACE parameter error in ffG53a5-6?

Dear all sorry for being here the 3rd time with this same (maybe trivial) question. I have found what appears to be an error in the files ffG53a(5 and 6).rtp related to the ACE group topology. Maybe it is a trivial error, or a change due to something I am missing. I was constructing the top

[gmx-users] ACE group parameter error un ffG53a5-6?

Dear all Sorry for repeating this message. I have found what appears to be an error in the files ffG53a(5 and 6).rtp related to the ACE group topology. Maybe it is a trivial error, or a change due to something I am missing. I’m sure you experts will ponder it much better than me. I was constru

[gmx-users] ACE parameter error in ffG53a5/6?

Dear gmx-users I think that I have found an error in the files ffG53a(5 and 6).rtp related to ACE topology. Maybe it is a trivial error, but I’m sure someone of you will ponder it much better than me. I am constructing the topology for an N-acetylated 2-amino sugar (N- acetylgalactosamine) usin

[gmx-users] trjconv -pbc

> Hello all, > > I have tried using trjconv -pbc(all options) to get a continuous > trjactoary visulations on VMD. I am modeling an 11 residue receptor > antiparellel to itself and one of the receptor strand jumps outside the > box sometimes. > > I have used search to solve the problem but evert

[gmx-users] Re:Re:Re: simulate a substrate-bound enzyme

> Dear Dr. Mauricio P. Sica, > > Thank you for your reply! > Can you give me an detailed example? Sorry, but it could not be possible. I don't feel confident as to make something like a tutorial. In addition, a lot of space and time not available should be spent. And, finally, everything depen

[gmx-users] Re: simulate a substrate-bound enzyme

> hello,everyone > > I am new to gromacs. I am studing gromacs following the Tutorial for > Drug - > Enzyme Complex,which was written by John E.Kerrigan,Ph.D. In the > Tutorial, they > simulated a ligand-protein system, and they stripped the > drug,parameterized it > using the PRODRG2 server. >

[gmx-users] Re: Can you help me ? (Yang Ye)

> Fatal error: > No such moleculetype Cl Maybe, you did not have 'ions.itp' in your working directory. If you have it, check that the names of the ions in 'ions.itp' and 'topol.top' coincide. Dr. Mauricio P. Sica                  

[gmx-users] Re: electrostatic and vdw energies from snapshots

Maybe it is an obvious observation, but reruns are not as time consuming as original runs. If I'm not wrong, as snapshots are generally saved every 2500-1 time-steps, reruns are 2500-1 faster than original runs. So, maybe a simple rerun with new 'energygrps' is your option. Additionall