Hi Mark and Justin,
I did investigate on the rvdw=rlist issue. But, I found even if I make rvdw
rlist and still keep time step 0.002, the average temperature goes to 303 K.
Only reducing the time step does help ( even if rvdw=rlist) to get average
temperature to 300K.
Sanku
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 time step 0.002, the average
temperature goes to 303 K.
Only reducing the time step does help ( even if rvdw=rlist) to get
average
Yes. I did check the tau_t issue. I used tau_t=2ps as recommended in the manual.
Again here, the simulation with 0.002 ps step gives rise to 303K. But, from now
on, as per your( and Justin's) recommendation, I am going to use the tau_t=2ps
and rvdwrlist in conjunction with 0.001 ps time step
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
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
following change:
gen-vel
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 following change:
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
Hi Justin,
So, do you suggest that after minimization, I should generate the velocity at
300K instead ?
i.,e for equilibration,should following the set-up?
gen-vel = yes
gen-temp= 300
gen-seed= -1
From:
Sanku M wrote:
Hi Justin,
So, do you suggest that after minimization, I should generate the
velocity at 300K instead ?
i.,e for equilibration,should following the set-up?
You should always equilibrate under the desired conditions. Never make sudden
changes, or else you're going to
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 running a short NVT
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
On 03/08/11, Sanku M msank...@yahoo.com wrote:
!-- DIV {margin:0px;} --
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
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 jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tue, August 2, 2011 9:55:40 PM
Subject: Re:
Sanku M wrote:
Hi Justin,
I did calculate the average temperature using last 2 ns of the 8ns
data. It is still same 303K.
Going back to the original .mdp file, I can see that you're using some incorrect
settings. You've set rlist=rvdw even though you're using a shifted potential
Finally, I achieved the desired 300K average temperature using sd
integrator
. I had to reduce the time step from 0.002 ps to 0.001 ps and then running the
NVT could produce 300K as average temperature.
Still Not sure why md integrator still could 300K average temperature using
0.002 ps
On 3/08/2011 2:23 PM, Sanku M wrote:
Finally, I achieved the desired 300K average temperature using sd
integrator . I had to reduce the time step from 0.002 ps to 0.001 ps
and then running the NVT could produce 300K as average temperature.
Still Not sure why md integrator still could 300K
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