Re: [gmx-users] suggest small revision to genbox

genbox works fine for me. i use 3.3.1 version. it works fine with and without script. but i don't understand how will u get rid of backup files in the permanent directory from whatever u have mentioned, because gromacs creates the output topology in the same location where it reads the

Re: [gmx-users] suggest small revision to genbox

David Mobley wrote: All, I'm trying to write some wrappers to set up a project using standard gromacs tools. Anyway, it looks to me like genbox is not handling its path names correctly. In particular, here's what I did: - Make temporary directory in which to run genbox - Move to temporary

[gmx-users] Error while running MD in DMSO!

Dear All, I am running my simulations in explicit MeOH and DMSO. In case of MeOH, it is running fine but while running in DMSO. After running genbox i am having problem in running grompp for energy minimization. Error which i got is given below. Cleaning up temporary file gromppkkHvWC Fatal

[gmx-users] Error while running grompp for em (MD) in Urea

Dear All, Can anyone help me in running simulation in explicit urea. When i was using urea+h2o.gro and urea.itp and tried to do simulation in explicit urea. After doing genbox, i am not able to do the grompp for energy minimization and getting the error which is given below. I have added masses

RE: [gmx-users] problem with freeze-group : Large VCM(Berk Hess)

Hi Berk, Thanks a lot for your reply. According to your suggestion, I did not remove the cmm for the WHOLE molecule i.e I used 'cmm-mode=None'for the entire system. (Did you mean that I should have removed the restriction only for freeze-group or for whole system?) But now I have

Re: [gmx-users] Error while running MD in DMSO!

Anil Kumar wrote: Dear All, I am running my simulations in explicit MeOH and DMSO. In case of MeOH, it is running fine but while running in DMSO. After running genbox i am having problem in running grompp for energy minimization. Error which i got is given below. Cleaning up temporary file

Re: [gmx-users] Error while running grompp for em (MD) in Urea

Anil Kumar wrote: Dear All, Can anyone help me in running simulation in explicit urea. When i was using urea+h2o.gro and urea.itp and tried to do simulation in explicit urea. After doing genbox, i am not able to do the grompp for energy minimization and getting the error which is given below.

Re: [gmx-users] Re: Parameterizing a force field (Mark Abraham)

Lee-Ping wrote: Thank you both for the response! I looked at the -j option in mdrun, but it looks like that has about as much documentation as ffscan (i.e. none at all). I also fruitlessly checked the mailing list archives for the past year and a half; there are some questions about ffscan,

Re: [gmx-users] CNT Potassium doping with GROMACS

George Abadir wrote: Hi, I want to make a simulation of CNT in an environment of potassium atoms to see how they will be adsorbed on the CNT surface (this is a way of doping carbon nanotubes). I built a .pdb file with a CNT and some potassium atoms with random coordinates around the

Re: [gmx-users] carbon atom not found by pdb2gmx and modification of specbond.dat

Nicolas Sapay wrote: Hello, I'm trying to create a topology file of a system made of a protein homodimer (2x198 residues), water (TIP3P x 900) and some ions (CLA, SOD, ZN2). The system has been initially built with CHARMM and all hydrogens are already included. I use an implementation of