On 8/22/17 5:28 AM, morpheus wrote:
Thanks!
Is this also just a note or is there a problem?
"
WARNING 1 [file md_vsIonDod.mdp]:
The sum of the two largest charge group radii (18.373196) is larger than
rlist (1.40)
"
I found this on the gromacs webpage:
"A similar error ("The
On 8/21/17 5:25 PM, farial tavakoli wrote:
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Hi justin
Thank you so much for replyingAccording to the gromacs tuturial, i am
Dear All,
I am using g_cluster. I am wondering what two groups used for?
group 1 for fit and RMSD calculation
group 2 for output
is g_cluster use RMSD values for clustering based on group 1 or group 2?
Any suggestions?
Thanks
Nikolai
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Hi Mark,
I’ll look in more detail the literature regarding this situation.
Thanks a lot for your reply.
Best,
Carlos
--
Carlos Navarro Retamal
Bioinformatic Engineering. PhD
Postdoctoral Researcher in Center for Bioinformatics and Molecular
Simulations
Universidad de Talca
Av. Lircay S/N, Talca,
Hi,
I don't understand whether you think diglycine is your solvent or your
solute.
Mark
On Tue, Aug 22, 2017 at 8:40 AM Dilip H N wrote:
> Hello,
> 1] it is the solute+Diglycine which is the constituting the mixture...
> 2] the method to create the system for both
Hi,
That functionality would be convenient for you, but hasn't been written. I
suggest using gmx check to report on the details of the last frame, and use
that to construct input to trjconv.
Mark
On Tue, Aug 22, 2017 at 4:58 PM CLARK NICOLAS Joan
wrote:
> Dear gmx
Hi,
The "1" selects the first index group, which is the whole peptide. If you
want to select the first residue, you have to use some other syntax.
Mark
On Tue, Aug 22, 2017 at 6:50 PM Dilip H N wrote:
> Hello,
> I have a Diglycine peptide in .gro file as:-
> 1GLY
Hi,
Please don't start new work with software that's no longer support and is
missing over four years worth of performance and correctness fixes. Some of
your problems relate to using commands that use the gmx wrapper binary,
which did not emerge until version 5.0.
Mark
On Wed, Aug 23, 2017 at
Hi,
The emails have been arriving, but you're asking a complicated series of
questions. You need to find some literature that shows these protein and
lipid force fields were parameterized in a compatible way, and even then
you may need to show that you in fact get a physically reasonable result.
Dear gmx users,
This is the third time I’m sending this email, but for some reason is not
been accepted.
I’m trying to set up a system consisting in a protein embebed into a
bilayer. The whole system contains approximately ~40 atoms, so to speed
up the simulation I'm using virtual sites.
I
Hi,
Check your log file, where it likely says that energy groups are not
supported on GPUs. Do a rerun on your traj you want to compute these things.
Mark
On Wed, 23 Aug 2017 12:08 Sergio Manzetti
wrote:
> Hi, when running gmx energy on a simulation ouput, I
Hi, when running gmx energy on a simulation ouput, I get:
---
1 Bond 2 Angle 3 Proper-Dih. 4 Ryckaert-Bell.
5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR)
9 Disper.-corr. 10 Coulomb-(SR) 11 Coul.-recip. 12 Potential
13 Pres.-DC
Well it seams that you compiled Gromacs with mpi support so now you should run
it with sth. like that: mpirun -np 1 /opt/apps/gromacs/4.6.6/bin/gmx
pdb2gmx_mpi -f 1aki.pdb -o 1AKI_processed.gro -water spceRun:man mpirunfor more
details.
On Wednesday, August 23, 2017, 10:42:47 AM GMT+3, Kashif
dear sir
after installing gromacs on server, I could not able to run the simulation.
It always shows "-bash: command not found".
when I tried to locate the pdb2gmx, it showed the path as-
/opt/apps/gromacs/4.6.6/bin/pdb2gmx_mpi
When I run the following command by using the path as
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