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> On Apr 16, 2020, at 7:53 PM, Mohamed Abdelaal wrote:
>
> I have one more question please regarding the velocity.
No problem.
>
> What is the mean value for the velocity being generated by GROMACS ? Is it
> zero ?
Yes.
>
> I have also understood fr om the below
I have one more question please regarding the velocity.
What is the mean value for the velocity being generated by GROMACS ? Is it
zero ?
I have also understood fr om the below paragraph which is written in the
manual section 3.4.1, that the values generated are selected from the range
between 0
My knowledge is a bit old.
Tpr files are binary so you cannot read them without a special tool. In
gromacs 2018, there was a tool that would spit out the contents of a tpr file
in a readable format. Execute
“gmx dump -h” to learn more.
Justin is correct. There is no tool or file that will
Many thanks Dr. Erik for your reply :)
On Tue, Apr 14, 2020 at 11:15 PM Eric Smoll wrote:
> No problem.
>
> Now it is clear what you are trying to do. The previous description of
> your goals did not make much physical sense. The initial velocities are
> such that all three dimensions are
Many thanks for your quick reply :)
On Tue, Apr 14, 2020 at 11:09 PM Justin Lemkul wrote:
>
>
> On 4/14/20 4:55 PM, Mohamed Abdelaal wrote:
> > Sorry for writing again in the same topic but I couldn't solve
> > the velocity problem.
> >
> > I am trying to reproduce a paper written by: Claire
On 4/14/20 4:55 PM, Mohamed Abdelaal wrote:
Sorry for writing again in the same topic but I couldn't solve
the velocity problem.
I am trying to reproduce a paper written by: Claire Tonnel + , Martin
Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, Alpeshkumar
K. Malde, Paul L.
Sorry for writing again in the same topic but I couldn't solve
the velocity problem.
I am trying to reproduce a paper written by: Claire Tonnel + , Martin
Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, Alpeshkumar
K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and
Many thanks for your reply :)
All your language assumptions are true and that is exactly what I wanted to
communicate, next time I will try to be more precise and sorry for the
confusion
I will read section 3.4.1 again carefully.
Thanks again and sorry for the inconvenience.
Mohamed
On Thu,
On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal
wrote:
> Many thanks for your reply
>
> The limitation in the generate velocity using the .mdp file, is that while
> I can generate the velocity from Maxwell distribution, I will have the
> same velocities in the x, y and z directions.
>
I
Many thanks for your reply
The limitation in the generate velocity using the .mdp file, is that while
I can generate the velocity from Maxwell distribution, I will have the
same velocities in the x, y and z directions.
On the other hand, generating the velocity from the .gro file will let me
On Tue, Apr 7, 2020 at 3:38 PM Mohamed Abdelaal
wrote:
> No, I use the generate velocity option in the .mdp files.
>
> However I want now to assign different velocities in the x,y,z directions.
> Which I thought it could only be done through the .gro file, but I don't
> know If I did that,
No, I use the generate velocity option in the .mdp files.
However I want now to assign different velocities in the x,y,z directions.
Which I thought it could only be done through the .gro file, but I don't
know If I did that, should I change the value of the generate velocity to
be = NO in the
On 4/6/20 12:16 PM, Mohamed Abdelaal wrote:
Hello everybody :)
Can I use the gmx insert-molecules to insert molecules in my box with
velocities by adding the velocities in the .gro file and insert the
molecules from this .gro file ?
Have you tried it?
-Justin
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