Re: [gmx-users] Re: g_velacc

Florian Dommert wrote: Hello, regard the topic about calculating diffusion coefficients, I also have a question regarding the code of g_velacc. To calcalute the diffusion coefficient of a molecule with the help of its VACF, I think the center of mass velocity the protein is required.

[gmx-users] Re: g_velacc

No special reason, just mundane ones: computing the diffusion constant through mean square displacement is easier in terms of convergence. But it is not applicable in the anisotropic systems, for example in ones with spatial confinements present... :) -- Vitaly V. Chaban School of Chemistry

[gmx-users] Multiple ppa files from a single parallel mdrun_mpi job

Hello, I am running gromacs in parallel on a new system. I am also using the pull code. Everything appears to be going fine, except that I get backup copies of the .ppa files during a single call to mdrun_mpi. My best guess is that this is some type of mpi problem, but any pointers would

[gmx-users] LINCS error

 Hi, I am trying to simulate a peptide whose structure is yet to be validated experimentally. It has 3 protonated lysine residues. I have used oplsaa force filed with spc water model and had added 3 CL ions into the box. Everything works fine till energy minimisation but after that

Re: [gmx-users] Re: g_velacc

How to monitor the motion of center of mass of a protein as it is the case all the time to monitor this during the calculations of diffusion and correlation functions. How far the values will be different if we monitor the motion of backbone atoms rather than the center of mass motion. I still

Re[2]: [gmx-users] Re: g_velacc

rr. How far the values will be different if we monitor the motion of backbone atoms rather than the center of mass motion. If the particle is rigid, no difference. If no, it depends on the concrete particle. In most cases, the difference will not be huge. rr I still dont have any idea how

Re: [gmx-users] LINCS error

sarbani chattopadhyay wrote: Hi, I am trying to simulate a peptide whose structure is yet to be validated experimentally. It has 3 protonated lysine residues. I have used oplsaa force filed with spc water model and had added 3 CL ions into the box. Everything works fine till energy

[gmx-users] How to calculate van der Waals potential between a given residue and the rest of residues in the protein?

Dear all, Is it possible to use GROMACS function(s) to calculate the averaged van der Waals potential /Coulomb potential between a given residue and the rest residues in the protein during a certain time of simulation? Thanks, LZhang ___

Re: [gmx-users] QMMM

I believe it supports GAMESS UK, not US. Gerrit ([EMAIL PROTECTED]) can assist you further. pb On Mon, Aug 25, 2008 at 4:30 AM, ha salem [EMAIL PROTECTED] wrote: hello I want install gromacs with gamess US for QMMM can you guide me for installation procedure thank you

Re: [gmx-users] How to calculate van der Waals potential between a given residue and the rest of residues in the protein?

Limei Zhang wrote: Dear all, Is it possible to use GROMACS function(s) to calculate the averaged van der Waals potential /Coulomb potential between a given residue and the rest residues in the protein during a certain time of simulation? Different contributions to the potential can

Re: [gmx-users] How to calculate van der Waals potential between a given residue and the rest of residues in the protein?

A more complete answer is that to define energy groups for this reside and rest residues respectively, generate the tpr with grompp and then use mdrun -rerun to run through the existing trajectory to obtain what you wanted.  Regards, Yang Ye - Original Message From: Justin A. Lemkul