Re: [gmx-users] High Initial generated Temp

2013-06-05 Thread Mark Abraham
On Wed, Jun 5, 2013 at 3:06 PM, tarak karmakar wrote: > One more query Justin. > Even if I don't use any sort of constraints in the final run, I'm not > getting the initial temperature as exactly 300 K. Initial part of the .log > file is as follows > > > Initial temperature: 297.694 K > > Started

Re: [gmx-users] High Initial generated Temp

2013-06-05 Thread tarak karmakar
One more query Justin. Even if I don't use any sort of constraints in the final run, I'm not getting the initial temperature as exactly 300 K. Initial part of the .log file is as follows Initial temperature: 297.694 K Started mdrun on node 0 Wed Jun 5 16:58:40 2013 Step Ti

Re: [gmx-users] High Initial generated Temp

2013-06-04 Thread Justin Lemkul
On 6/4/13 12:51 PM, tarak karmakar wrote: Yeah! It is indeed a silly point to generate a velocity distribution at 0 K. ( Maxwell-Boltzmann will be in trouble) After the warm up, now let say my protein is in 300 K, can't I generate a velocity distribution at 300 k (using the keyword gen_vel = ye

Re: [gmx-users] High Initial generated Temp

2013-06-04 Thread tarak karmakar
Yeah! It is indeed a silly point to generate a velocity distribution at 0 K. ( Maxwell-Boltzmann will be in trouble) After the warm up, now let say my protein is in 300 K, can't I generate a velocity distribution at 300 k (using the keyword gen_vel = yes, gen_temp = 300 K gen_seed = 173529 ) during

Re: [gmx-users] High Initial generated Temp

2013-06-04 Thread Justin Lemkul
On 6/4/13 12:17 PM, tarak karmakar wrote: Thanks Justin. Sorry for not uploading the full .mdp. Here it is, ; 7.3.3 Run Control integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps

Re: [gmx-users] High Initial generated Temp

2013-06-04 Thread tarak karmakar
I'm extremely sorry for copying the other '.mdp' file here. This is the modified one I just created after seeing your reply. In the previous case I didn't use 'continuation'. On Tue, Jun 4, 2013 at 9:47 PM, tarak karmakar wrote: > Thanks Justin. > Sorry for not uploading the full .mdp. Here it

Re: [gmx-users] High Initial generated Temp

2013-06-04 Thread tarak karmakar
Thanks Justin. Sorry for not uploading the full .mdp. Here it is, ; 7.3.3 Run Control integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps = system comm_mode = li

Re: [gmx-users] High Initial generated Temp

2013-06-04 Thread Justin Lemkul
On 6/4/13 8:07 AM, tarak karmakar wrote: Dear All, Although I have set gen_temp = 300, it is showing the initial temperature 445.7 K, generated at the very beginning of the run. gen_vel = yes ; velocity generation gen_temp= 300 gen_seed

[gmx-users] High Initial generated Temp

2013-06-04 Thread tarak karmakar
Dear All, Although I have set gen_temp = 300, it is showing the initial temperature 445.7 K, generated at the very beginning of the run. gen_vel = yes ; velocity generation gen_temp= 300 gen_seed= 93873959697 Is it because of a bad geo