Re: [gmx-users] How long run should be enough for Free Energy Calculation of a protein?

2014-10-18 Thread Batdorj Batsaikhan
Dear gmx user, please give me advice about above calculations. Thanks. Batsaikhan On Thursday, October 16, 2014 2:51 PM, Batdorj Batsaikhan wrote: I want to calculate free energy of 2 different types of 71 amino acids long protein. I run General Equilibration (NPT). Then I run free e

Re: [gmx-users] How long run should be enough for Free Energy Calculation of a protein?

2014-10-18 Thread Batdorj Batsaikhan
I want to calculate free energy of 2 different types of 71 amino acids long protein. I run General Equilibration (NPT). Then I run free energy calculation of 200 ps. When calculation start, I got following warming message: ** WARNING: Listed nonbonded intera

Re: [gmx-users] How long run should be enough for Free Energy Calculation of a protein?

2014-10-16 Thread Justin Lemkul
On 10/16/14 2:51 AM, Batdorj Batsaikhan wrote: I want to calculate free energy of 2 different types of 71 amino acids long protein. I run General Equilibration (NPT). Then I run free energy calculation of 200 ps. When calculation start, I got following warming message: ***

Re: [gmx-users] How long run should be enough for Free Energy Calculation of a protein?

2014-10-15 Thread Batdorj Batsaikhan
I want to calculate free energy of 2 different types of 71 amino acids long protein. I run General Equilibration (NPT). Then I run free energy calculation of 200 ps. When calculation start, I got following warming message: ** WARNING: Listed nonbonded interact

Re: [gmx-users] How long run should be enough for Free Energy Calculation of a protein?

2014-10-15 Thread Justin Lemkul
On 10/14/14 11:37 PM, Batdorj Batsaikhan wrote: Dear gmx-users, Hello, I am working on free energy calculation of a protein. How long run should be enough for Free Energy Calculation of a protein? How is it that you're attempting to calculate this quantity? -Justin -- ===

[gmx-users] How long run should be enough for Free Energy Calculation of a protein?

2014-10-14 Thread Batdorj Batsaikhan
Dear gmx-users, Hello, I am working on free energy calculation of a protein. How long run should be enough for Free Energy Calculation of a protein? Batsaikhan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posti