Dear Justin,
I have tried implicit solvent without pbc or barostat. The box was not
compressed but the molecules flew out of the box. I believe that it was because
of nopbc box. Would you please give more information on why implicit solvent is
used without pbc?
Thanks!
Regards,
Zhuo
--
Grom
First thing is that GROMACS measures things in nanometers, whereas VMD uses
Angstroms.
Other thing to check is whether the first and last atom in the index group
selected when using polystat is the same as the two atoms you selected in
VMD.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition
A visual artefact of the periodic boundary condition.
See https://twitter.com/dr_dbw/status/909559339366572032
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@mon
Hello Gromacs Developers/Users,
I'm trying to install Gromacs-2019.3 on Intel Xeon W-2175 with Intel
compilers (+MKL+MPI).
First I compiled cmake with Intel compilers. All output files are attached.
cmake, make seemed to go ok, but all check test failed. What do I do wrong?
https://drive.google.co
Dear Justin,
Thank you for your suggestions! So what I have done is right. For implicit
solvent, I just need turn on the options in .mdp file and no .itp file is
needed to be included in the topology file. (I have tried but get errors).
Thanks!
Regards,
Zhuo
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Gromacs Users mailing list
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On 10/7/19 3:30 AM, Olga Press wrote:
Dear all,
I would like to perform a simulation of protein on a membrane surface.
Following the placement of the protein on the DOPC surface I solvated the
system by the following command:
gmx_mpi solvate -cp min_dopc.gro -cs spc216.gro -o solvate.gro -p sy
On 10/7/19 11:12 AM, zhangzhu...@hotmail.com wrote:
Dear Paul,
Thanks for your advice. Since my system is acidic, I thought implicit solvent
would get better approximation as I read from the GROMACS website. So there was
no idea about my problem?
Implicit solvent is used without PBC and n
Hi
I am trying to calculate the shape of an aggregate which is cylindrical in
shape.
I have used the command
gmx polystat -f aggregate.pdb -s aggregate.tpr -o poly.xvg
The eigen values from gmx polystat of the aggregate for a particular
frame are 3.3566 0.8837 0.7660 but using VMD the distance
Dear Paul,
Thanks for your advice. Since my system is acidic, I thought implicit solvent
would get better approximation as I read from the GROMACS website. So there was
no idea about my problem?
Thanks!
Zhuo
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Gromacs Users mailing list
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http://www.gromacs.org
Hi, I am doing the aggregations of small peptides in implicit solvents.
However, it seems that there is no detailed tutorial on such subject and I just
turned on the 'implicit solvent' option in the .mdp file. However, I found that
the box was compressed during mdrun. It comes to me that the imp
Hello,
the implicit solvent functionality has been deprecated a while ago in
GROMACS and has been removed in the recent versions.
Can the simulations also be run in explicit solvents (that are a better
physical representation anyway)?
Cheers
Paul
On 07/10/2019 16:50, 张 卓 wrote:
Hi, I am
Hi, I am doing the aggregations of small peptides in implicit solvents.
However, it seems that there is no detailed tutorial on such subject and I just
turned on the 'implicit solvent' option in the .mdp file. However, I found that
the box was compressed during mdrun. It comes to me that the imp
Hi
Good point. The environment variable names changed.
Thus
$GMX_QM_MODIFIED_LINKS_DIR is what used to be DEVIL_DIR
The same for the others.
Gerrit
> Good 4. Re: Gromacs2019 + Gaussian09 QMMM (nikol...@spbau.ru)
>
>
> Dear Gerrit,
>
> Thank you very much for your answer.
> As I under
Dear all,
I would like to perform a simulation of protein on a membrane surface.
Following the placement of the protein on the DOPC surface I solvated the
system by the following command:
gmx_mpi solvate -cp min_dopc.gro -cs spc216.gro -o solvate.gro -p system.top
I made a local copy of vdwadii.dat
Thank you!
*Olga Press-Sandler*
Ph.D. student, Yifat Miller's lab
Department of Chemistry
Ben-Gurion University, Israel
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I've shared an item with you:
Solvation of protein on membrane surface .JPG
https://drive.google.com/file/d/1cdYTCn7PLrRrt4aUSHz40WTLG7QZ9xzP/view?usp=sharing&ts=5d9ae82d
It's not an attachment -- it's stored online. To open this item, just click
the link above.
Dear all,
I would like to sim
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