Re: Re: [gmx-users] Melittin in methanol...

2009-01-31 Thread sharada
Hello Justin, Thanks for the reply . I apologise for the repeat mail. The parameters are for ffG43a3 forcefield. Yes I am using the default electrotatics cutoff values as an initial run. I would change to PME method as you say. However I was wondering If r_epsilon value equals to 66 contributes

[gmx-users] pressure component

2009-01-31 Thread avinash kumar
Dear All, I wish to calculate the components of pressure (pressure tensor) of a group, ie x,y and z components . Is there any any function in GROMACS which will do it for a group as a function of height. Or do I have to write my own code for postprocessing. Thank you. -- Avinash Kumar. _

[gmx-users] COM motion removal

2009-01-31 Thread priyanka srivastava
Dear Gromacs users!! I have a lipid - peptide system which I simulated for 50ns. Now in the beginning of the simulation the peptide was at the center of the bilayer but with time the peptide moved and came very close to the edge. Now near the edge it is having the interactions with the images o

Re: [gmx-users] Melittin in methanol...

2009-01-31 Thread Justin A. Lemkul
sharada wrote: Hello Justin, Thanks for the reply . I apologise for the repeat mail. The parameters are for ffG43a3 forcefield. Yes I am using the default electrotatics cutoff values as an initial run. I would change to PME method as you say. However I was wondering If r_epsilon value equal

Re: [gmx-users] COM motion removal

2009-01-31 Thread Justin A. Lemkul
priyanka srivastava wrote: Dear Gromacs users!! I have a lipid - peptide system which I simulated for 50ns. Now in the beginning of the simulation the peptide was at the center of the bilayer but with time the peptide moved and came very close to the edge. Now near the edge it is having the

Re: [gmx-users] "No default proper Dih.type

2009-01-31 Thread Justin A. Lemkul
varsha gautham wrote: Dear all, Am trying to do simulation of DPPC membrane.Am using ffgmx force field,because other force fields doesnt have DPP residue,so got an error saying "Residue DPP not in topology database. Don't use ffgmx for anything. It is long-since deprecated. The paramet