Yeping Sun,
Quoting Justin's answer for a similar question I had on how to repeat a
simulation say 10 times
" To run 10 independent simulations, I would run minimization once and start
from 10 new equilibration runs, each with a different set of initial velocities
(change gen_seed or simply se
On 1/2/20 10:07 PM, Sun Yeping wrote:
I guess I understand what you mean, but could you clarify it further? I
usually perform the simulations by the following process:
(1) energy minimization (EM); (2) NVT for 1 ns with heavy atom restraints;
(3) NPT for 1 ns with heavy atom restrains; (4) pr
I guess I understand what you mean, but could you clarify it further? I
usually perform the simulations by the following process:
(1) energy minimization (EM); (2) NVT for 1 ns with heavy atom restraints;
(3) NPT for 1 ns with heavy atom restrains; (4) production simulation
without restraints.
To
On 1/2/20 8:25 PM, Sun Yeping wrote:
Hello Justin,
Your reply is very helpful. I can understand the first method for proving
repeatablity: use a different initial configuration. But how to set the
different initial velocities with the same initial configuration if not
using the "gen-vel" opti
Hello Justin,
Your reply is very helpful. I can understand the first method for proving
repeatablity: use a different initial configuration. But how to set the
different initial velocities with the same initial configuration if not
using the "gen-vel" option in the .mdp file for the production sim
On Tue, Dec 31, 2019 at 12:22 PM Justin Lemkul wrote:
>
>
> On 12/30/19 11:11 PM, sunyeping wrote:
> > Hello Justin,
> >
> > Thank you for your reply.
> >
> > If I need to prove the repeatability of a phenonmenon (such as the
> > peptide folding pathway or a conformational transition) in
> > simu
On 12/30/19 11:11 PM, sunyeping wrote:
Hello Justin,
Thank you for your reply.
If I need to prove the repeatability of a phenonmenon (such as the
peptide folding pathway or a conformational transition) in
simulations, is it reasonable to run the production MD several times
and each time t
-users] What is the "gen-vel" used for?
On 12/30/19 10:14 PM, sunyeping wrote:
> Dear all,
>
> In the molecular dynamics parameters (.mdp option) section of the Gromacs
> user guide
> (http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html),
> there is
On 12/30/19 10:14 PM, sunyeping wrote:
Dear all,
In the molecular dynamics parameters (.mdp option) section of the Gromacs user guide
(http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html), there is an
introduction of the "gen-vel" option. According to the introduction,
Dear all,
In the molecular dynamics parameters (.mdp option) section of the Gromacs user
guide
(http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html),
there is an introduction of the "gen-vel" option. According to the
introduction, if set to "yes", it will generate velocit
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