Re: [gmx-users] Re: gmx-users Digest, Vol 30, Issue 18

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi, Stefan, To the first question: (run in Ubuntu) > locate cpp | grep "/cpp$" /lib/cpp /usr/bin/cpp /usr/share/doc/cpp For the second, you must make sure that the atom names, for example, from your Prodrg topology are compatible with those in the f

Re: [gmx-users] Re: gmx-users Digest, Vol 30, Issue 18

Stefan Schöbel wrote: Hi folks, I am running Gromacs under Linux Ubuntu. My question: where is my cpp located? It is not under /usr/bin/cpp. "which cpp" And the other question: I try to simulate a protease together with its lipopeptide inhibitor, so I used Prodrg to get the files of the in

[gmx-users] Re: gmx-users Digest, Vol 30, Issue 18

Hi folks, I am running Gromacs under Linux Ubuntu. My question: where is my cpp located? It is not under /usr/bin/cpp. And the other question: I try to simulate a protease together with its lipopeptide inhibitor, so I used Prodrg to get the files of the inhibitor but I get warnings that some a

Re: [gmx-users] no coordinates in .top file

Owen, Michael wrote: Fellow gmx users, I made a tolopgy file for TFE in water by "hand" for the OPLSAA/L force field to be used in a simulation containing a mixed solvent. I made a similar TFE.itp file and included it in the mixed solvent topology file. when I ran grompp before equilibrat

[gmx-users] no coordinates in .top file

Title: no coordinates in .top file Fellow gmx users, I made a tolopgy file for TFE in water  by "hand" for the OPLSAA/L force field to be used in a simulation containing a mixed solvent.  I made a similar TFE.itp file and included it in the mixed solvent topology file.  when I ran grompp be

Re: [gmx-users] PCA average structure

[EMAIL PROTECTED] wrote: Hi gromacs users, Recently I asked about running PCA on MD output from Amber which was helpful.Based on the advise I used g_covar to run PCA on all atoms. When I look at my average structure or filtered trajectory, I notice that some of the bonds are much shorter t

[gmx-users] PCA average structure

Hi gromacs users, Recently I asked about running PCA on MD output from Amber which was helpful.Based on the advise I used g_covar to run PCA on all atoms. When I look at my average structure or filtered trajectory, I notice that some of the bonds are much shorter than expected, and in the ca

Re: [gmx-users] ffscan trouble

Zlenko Dmitry wrote: David van der Spoel wrote what do you want to do? it is meant to do parameter scan for forcefield optimization. I need to create a force field for my system. From the description of ffscan I've concluded that this utility may help me. Am I write or not? If so, whould yo

Re[2]: [gmx-users] ffscan trouble

> David van der Spoel wrote > >what do you want to do? > >it is meant to do parameter scan for forcefield optimization. > I need to create a force field for my system. From the description of ffscan I've concluded that this utility may help me. Am I write or not? If so, whould you explain me how

[gmx-users] nsgrid.c problem

In God We TrustHello Dear gmx users I made a topology and a gro file for a modified protein,when I run mdrun for energy minimization it says " "Program mdrun, VERSION 3.3.1Source code file: nsgrid.c, line: 226 Range checking error:Explanation: During neighborsearching, we assign each particle t

Re: [gmx-users] ffscan trouble

Zlenko Dmitry wrote: Hi, everybody!!! I have a trouble whith ffscan utility. How does it works? What kind of *.dat files it can digest? What kind of "appropriate file" should I pass to it whith -ga option, if I want to use a genetic algorithm? Native description of this utility on this site i

[gmx-users] ffscan trouble

Hi, everybody!!! I have a trouble whith ffscan utility. How does it works? What kind of *.dat files it can digest? What kind of "appropriate file" should I pass to it whith -ga option, if I want to use a genetic algorithm? Native description of this utility on this site is very poor, so if an