[gmx-users] simulated annealing (SA)

Hi all Simulated annealing consists of heating and gradually cooling steps. What is maximum temperature that we can use for heating in SA simulation of protein. Any help will highly appreciate. -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] simulated annealing (SA)

shahab shariati wrote: Hi all Simulated annealing consists of heating and gradually cooling steps. What is maximum temperature that we can use for heating in SA simulation of protein. The better question is not if there is a maximum, but rather if whatever you're doing is

[gmx-users] simulated annealing

Hi gromacs users (1) Simulated annealing method is as two forms: single and periodic. I want to do Simulated annealing for obtaining global minimum in protein structure. Which one of them is better? (in point of view obtaining to global minimum). Thank you so much for any help! -- gmx-users

[gmx-users] mutation to/from proline

Hi, I want to calculate relative free energy associated to mutation of P1 (native protein) to p2 (mutated protein).In this mutation, Isolusine (in P1) is mutated to Proline(in P2). With using Thermodynamic cycle: Bilayer+P1= = = Bilayer-P1 delta G1

Re: [gmx-users] simulated annealing

On 25/04/2010 10:17 PM, leila karami wrote: Hi gromacs users (1) Simulated annealing method is as two forms: single and periodic. I want to do Simulated annealing for obtaining global minimum in protein structure. No procedure is assured of finding a global minimum with less than infinite

Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations

Dear Berk, First of all thanks very much for your kind patience and help. As a new user i am facing some problems and not clear about many options and how to use them. I was reading several messages of yours from mailing list which are very close to my problem. After reading several of them from

Re: [gmx-users] grompp error(Segmentation fault)

In continuation with my previous e-mail, I'm sorry to continue bothering you with this but after reevaluating, it seems that problem might just be with the amber forcefield after all as I manged to run grompp just fine and to start the minimization by applying the OPLS forcefield(with another

Re: [gmx-users] grompp error(Segmentation fault)

Arik Cohen wrote: In continuation with my previous e-mail, I'm sorry to continue bothering you with this but after reevaluating, it seems that problem might just be with the amber forcefield after all as I manged to run grompp just fine and to start the minimization by applying the OPLS

[gmx-users] segmentation fault in position restrained step

Dear Justin, 1- Could you please check if I have grouped atoms properly? Lastly, I could generate the tpr file for PR step. Since I am getting segmentation fault in the next step I though maybe there is sth wring with charge groups.. However, I have a funda,mental question. I am to compute

Re: [gmx-users] segmentation fault in position restrained step

Moeed wrote: Dear Justin, 1- Could you please check if I have grouped atoms properly? Lastly, I could generate the tpr file for PR step. Since I am getting segmentation fault in the next step I though maybe there is sth wring with charge groups.. I don't know how your labeling is set up.

[gmx-users] Segmentation fault with gromacs executables

Hi I am facing this strange problem of segmentation fault while executing mpi-enabled gromacs executables on remote server. I source GMXRC, so that I can access executables from any directory without specifying full path of gromacs/bin. And when I execute, say grompp, I get segmentation fault.

Re: [gmx-users] Segmentation fault with gromacs executables

On 26/04/2010 2:45 PM, Sikandar Mashayak wrote: Hi I am facing this strange problem of segmentation fault while executing mpi-enabled gromacs executables on remote server. I source GMXRC, so that I can access executables from any directory without specifying full path of gromacs/bin. And when

Re: [gmx-users] Segmentation fault with gromacs executables

On 26/04/2010 3:44 PM, Mark Abraham wrote: On 26/04/2010 2:45 PM, Sikandar Mashayak wrote: Hi I am facing this strange problem of segmentation fault while executing mpi-enabled gromacs executables on remote server. I source GMXRC, so that I can access executables from any directory without