Re: [gmx-users] random seed in molecular dynamics

2013-05-06 Thread Mark Abraham
Google knows a lot more about that one than me ;-) Mark On Mon, May 6, 2013 at 9:16 AM, Preeti Choudhary < preetichoudhary18111...@gmail.com> wrote: > hey thanks Mark > What do you mean by -the random seed is in a different variable.Can you > please explain "the random seed" > > > > On Fri,

Re: [gmx-users] random seed in molecular dynamics

2013-05-06 Thread Preeti Choudhary
hey thanks Mark What do you mean by -the random seed is in a different variable.Can you please explain "the random seed" On Fri, May 3, 2013 at 1:32 PM, Mark Abraham wrote: > gen_vel controls the generation of random velocities. grompp follows it > (but I'd have to check the code to see wha

Re: [gmx-users] random seed in molecular dynamics

2013-05-03 Thread Mark Abraham
gen_vel controls the generation of random velocities. grompp follows it (but I'd have to check the code to see what it does if you use grompp -t). tprconv does not follow it. The random seed is in a different variable, but only does anything if gen_vel=yes. I am not sure what the basis of your co

Re: [gmx-users] random seed in molecular dynamics

2013-05-03 Thread Erik Marklund
If I recall correctly it uses the seed provided in the mdp file. If no seed is provided it uses the process id for seeding. The manual explains the details. Erik On 3 May 2013, at 08:00, Preeti Choudhary wrote: > hey this is regarding random seed used in md.this is when it selects the > intia

[gmx-users] random seed in molecular dynamics

2013-05-02 Thread Preeti Choudhary
hey this is regarding random seed used in md.this is when it selects the intial velocity and selects from maxwell-istribution.but is it selects only once or selects this random seed every time when grompp makes .tpr file.really confused about this random seed concept.can u clear my confusion?? -th