Re: [gmx-users] how to increase the number of

ROTECTED]> wrote: Pradeep Kota wrote: > Hi Afonso, > > An easier way would be to use the -time flag with grompp. it would > basically set the first time frame for the new tpr to what you give it. > jus play around with it and i'm sure you can get what you wanted. dont > forget

[gmx-users] energy minimization - double precision

Dear users, I'm trying to minimize the energy of a protein in vacuum. I have restrained the backbone with posre.itp generated using genpr. when i try to minimize the energy of this protein using single precision grompp followed by an mdrun, it does not converge even after 600 steps and returns say

Re: [gmx-users] how to increase the number of

Hi Afonso, An easier way would be to use the -time flag with grompp. it would basically set the first time frame for the new tpr to what you give it. jus play around with it and i'm sure you can get what you wanted. dont forget to include the -np flag of course. :) hope this helps. Kota. On 5/1

Re: [gmx-users] energy of each residue??

Thanks a lot Tsjerk ! I joined SOL and Cl into one index group and removed Protein and SOLCL (the new one with SOL and CL) from energy monitoring list. It works now. i got the energy of a particular residue. thanks for the help. kota. On 5/1/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: Hi K

Re: [gmx-users] energy of each residue??

didn't give much more information, it's hard to tell why grompp bailed out. The error message is usually a good thing to add to a mail, and in this case, the .mdp file might be too. Cheers, Tsjerk On 5/1/07, Pradeep Kota <[EMAIL PROTECTED]> wrote: > Dear users, > >

[gmx-users] energy of each residue??

Dear users, I'm trying to compute the contribution of each residue to the total energy of a protein. I neutralized my system with 8 chloride ions and then made an index file with each residue in a different index group, using 'splitres' via make_ndx. it gave me an index file with atoms of each re