Re: [gmx-users] Regarding using random seed

On 3/10/16 3:21 AM, neha chaudhary wrote: Hello Sir, Thanks for your help. I need to clear one more doubt, if I am performing MD simulations with the mentioned parameter set but using same initial structures then will it affect the reproducibility of the results. Actually, I have repeated MD

Re: [gmx-users] Regarding using random seed

Hello Sir, Thanks for your help. I need to clear one more doubt, if I am performing MD simulations with the mentioned parameter set but using same initial structures then will it affect the reproducibility of the results. Actually, I have repeated MD simulations for my protein-ligand complex

Re: [gmx-users] Regarding using random seed

Right! T. On Mar 9, 2016 12:24 PM, "neha chaudhary" wrote: > Hi, > > So all I have to do is to extract different configurations from my already > performed MD simulation. Then I have to prepare a new system using that > configuration with the following parameters and

Re: [gmx-users] Regarding using random seed

Hi, So all I have to do is to extract different configurations from my already performed MD simulation. Then I have to prepare a new system using that configuration with the following parameters and rerun the simulations: continuation = no gen_vel = yes gen-seed = -1 Right? Best Regards,

Re: [gmx-users] Regarding using random seed

Hi Neha, Set continuation = no gen_vel = yes (check http://manual.gromacs.org/online/mdp_opt.html#vel) Best, Tsjerk On Wed, Mar 9, 2016 at 11:16 AM, neha chaudhary wrote: > Thanks Tsjerk for replying, > > I want to ask one more question that to start with new

Re: [gmx-users] Regarding using random seed

Thanks Tsjerk for replying, I want to ask one more question that to start with new velocities, what changes I have to make and in which .mdp file? Best Regards, *Neha* Research Scholar, Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal

Re: [gmx-users] Regarding using random seed

Hi Neha, You can perform a simulation first, and then extract configurations, which you simulate with new starting velocities. Alternatively, you can generate a number of different starting structures using elastic-network modeling, like with the ElNemo server. Mind to first energy minimize the

[gmx-users] Regarding using random seed

Hello there, Can anyone tell me how can I start my MD simulations with different starting structure (random seed) for my protein-ligand complex. Can I start with different sets of coordinates and velocities? If yes, how? Thanks, *Neha* Research Scholar, Centre for Computational Biology and