Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

2011-08-03 Thread Sanku M
Sent: Wed, August 3, 2011 11:00:30 AM Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP On 4/08/2011 1:51 AM, Sanku M wrote: Hi Mark and Justin, > I did investigate on the rvdw=rlist issue. But, I found even if I >make rvdw < rlist and still keep t

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

2011-08-03 Thread Mark Abraham
ark *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Tue, August 2, 2011 10:16:17 PM *Subject:* Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP Sanku M wrote: > Hi Justin, >I did calculate the average temperature u

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

2011-08-03 Thread Sanku M
nku From: Mark Abraham To: Discussion list for GROMACS users Sent: Tue, August 2, 2011 11:46:21 PM Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP On 3/08/2011 2:23 PM, Sanku M wrote: > >Finally, I achieved the desired 300K

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

2011-08-02 Thread Mark Abraham
:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Tue, August 2, 2011 10:16:17 PM *Subject:* Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP Sanku M wrote: > Hi Justin, >I did calculate the average temperature using last 2 ns of the 8ns data.

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

2011-08-02 Thread Sanku M
as time-step. From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Tue, August 2, 2011 10:16:17 PM Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP Sanku M wrote: > Hi Justin, >I did calculate the a

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

2011-08-02 Thread Justin A. Lemkul
ture. -Justin *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Tue, August 2, 2011 9:55:40 PM *Subject:* Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP Sanku M wrote: > OKK, But, before, I have tried using md as integrator where I start th

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

2011-08-02 Thread Sanku M
Hi Justin, I did calculate the average temperature using last 2 ns of the 8ns data. It is still same 303K. From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Tue, August 2, 2011 9:55:40 PM Subject: Re: [gmx-users] Problem with temperature

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

2011-08-02 Thread Mark Abraham
se you're going to damage the stability of the system. > > -Justin > > > gen-vel                  = yes > >> >  gen-temp                = 300 > >> >  gen-seed                = -1 > > > > ------------------------ > > *From:*

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

2011-08-02 Thread Justin A. Lemkul
Sanku M wrote: OKK, But, before, I have tried using md as integrator where I start the initial velocity as 280K ( which makes sense as the minimized configuration is essentially at low temperature) and have used Nose-hoover at 300K and I never had problem in getting the desired 300K after ru

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

2011-08-02 Thread Sanku M
: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Tue, August 2, 2011 8:40:21 PM Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP Sanku M wrote: > Hi Justin, > So, do you suggest that after minimization, I should generate the velocity >

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

2011-08-02 Thread Justin A. Lemkul
*Sent:* Tue, August 2, 2011 8:26:16 PM *Subject:* Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP Justin A. Lemkul wrote: > > > Sanku M wrote: >> Hi Justin, >> I first performed two minimization using steep and l-bfgs as the method on the solvate

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

2011-08-02 Thread Sanku M
___ From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Tue, August 2, 2011 8:26:16 PM Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP Justin A. Lemkul wrote: > > > Sanku M wrote: >> Hi Justin, >> I first performed t

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

2011-08-02 Thread Justin A. Lemkul
Justin A. Lemkul wrote: Sanku M wrote: Hi Justin, I first performed two minimization using steep and l-bfgs as the method on the solvated system for each lambda. Then I ran a 500ps NVT simulation on minimized system ( for each lambda) where essentially same .mdp file was used except the

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

2011-08-02 Thread Justin A. Lemkul
reciated. Jagannath *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Tue, August 2, 2011 8:08:20 PM *Subject:* Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP Sanku M wrote: &

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

2011-08-02 Thread Sanku M
ust 2, 2011 8:08:20 PM Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP Sanku M wrote: > Hi, > I am trying to calculate the solvation free energy using thermodynamic >integration(TI) method . I am using gromacs 4.0.7 . But, I am having a problem >in

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

2011-08-02 Thread Justin A. Lemkul
Sanku M wrote: Hi, I am trying to calculate the solvation free energy using thermodynamic integration(TI) method . I am using gromacs 4.0.7 . But, I am having a problem in getting accurate average temperature . The following is what I did: I found that when doing TI, grompp recommends u