Hello,
This time I tried sesiisotropic scaling with Berendsen Barostat. The
compressibility was set to zero in Z-direction allowing scaling only in X
and Y. The NPT simulation was run for 10ns.
The result did not look good and the average pressure was ~36 bar
(reference pressure is 1 bar).
The simplest explanation would be that you've appended to a previous 5ns
trajectory, not run a new trajectory. Check the .log file and the length of
time you expected this job to run (wall and simulation).
Mark
On Fri, Mar 14, 2014 at 9:02 AM, sujithkakkat . sujithk...@gmail.comwrote:
Hello,
Hello Mark,
I guess you were asking whether I ran the simulation as a
continuation to a previous 5ns run?
But the results I got are from a continuous 10ns simulation.
Sujith.
On Fri, Mar 14, 2014 at 4:28 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
The simplest explanation would be
Hello,
After a while I got back to the problem posted here. This issue was the
large value for average pressure(~25 bar against the reference pressure of
1 bar) in NPT simulations with parrinello rahman barostat. The system
studied is cyclohexane-water system with an interface.
The forcefield
On 3/12/14, 7:51 AM, sujithkakkat . wrote:
Hello,
After a while I got back to the problem posted here. This issue was the
large value for average pressure(~25 bar against the reference pressure of
1 bar) in NPT simulations with parrinello rahman barostat. The system
studied is
your average pressure is the pressure you should report in the
publication. if you got 5 bars instead of 1 bar, you should write
I simulated the system at 5 bars
Dr. Vitaly V. Chaban
On Tue, Feb 25, 2014 at 6:01 AM, sujithkakkat . sujithk...@gmail.com wrote:
On Mon, Feb 24, 2014 at 5:37 AM,
No full solutions to this problem -- I'll write a few notes.
* With large systems run for relatively small amounts of time, the
ensemble could be statistically indistinguishble from the true
distribution even if the averages don't line up correctly. See:
On Tue, Feb 25, 2014 at 3:57 PM, Michael Shirts mrshi...@gmail.com wrote:
No full solutions to this problem -- I'll write a few notes.
* With large systems run for relatively small amounts of time, the
ensemble could be statistically indistinguishble from the true
distribution even if the
On 2/23/14, 11:37 PM, sujithkakkat . wrote:
Hello,
Thank you both for the comments. I am using gromos96 forcefield . I read
a little bit and as you said the nonbonded cutoff has to be higher.
The tau_p=5ps was chosen , since the manual mentions that the value has to
be raised by 4-5
Dear GROMACS users,
I am new to GROMACS, and recently started using the version 4.6.5.
I have seen a lot of NPT related issues raised earlier in this forum, but in
my case the error looks much more severe.
I am following Justin Lemkul's tutorial
On 2/23/14, 8:30 AM, sujith wrote:
Dear GROMACS users,
I am new to GROMACS, and recently started using the version 4.6.5.
I have seen a lot of NPT related issues raised earlier in this forum, but in
my case the error looks much more severe.
I am following Justin Lemkul's tutorial
Hello,
Thank you both for the comments. I am using gromos96 forcefield . I read
a little bit and as you said the nonbonded cutoff has to be higher.
The tau_p=5ps was chosen , since the manual mentions that the value has to
be raised by 4-5 times on going from berendsen to parrinello-rahman
Hello,
Thank you both for the comments. I am using gromos96 forcefield . I read
a little bit and as you said the nonbonded cutoff has to be higher.
The tau_p=5ps was chosen , since the manual mentions that the value has to
be raised by 4-5 times on going from berendsen to parrinello-rahman
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