Hi,
Gro format doesn't support fields for forces. Either write out.g96 file, or
use gmx traj (better)
Mark
On Thu., 20 Feb. 2020, 16:43 Justin Lemkul, wrote:
>
>
> On 2/20/20 12:34 AM, 고연주 wrote:
> >
> >
> >Hello!
> >
> >I have a question about gmx trjconv -force option because it
On 2/20/20 11:36 AM, hind ahmed wrote:
Dear All,
I want to calculate the free energy of two different types of molecules in the
same system. Is there a way to do this in gromacs?
couple-moltype = CHOL DPPC
Did not find any molecules of type 'CHOL DPPC' for coupling,
You can only
On 2/20/20 4:49 PM, Sadaf Rani wrote:
Dear Justin, thank you for your reply. I have also tried adding ACE and
NME as below but it didn't work.
Please provide your full command and entire screen output, including any
applicable errors. Saying something "didn't work" is impossible to
Dear Justin, thank you for your reply. I have also tried adding ACE and
NME as below but it didn't work.
1ACE HC1 0.000 0.000 0.000 0. 0. 0.
1ACE CT2 0.000 0.000 0.000 0. 0. 0.
1ACE HC3 0.000 0.000 0.000 0.
Dear Gromacs users
I am doing a test calculation in MD simulation between ligand and a protein
residue for bond angle and dihedral restraints. I have set them in my
topology file as below:-
; distance restraints
[ bonds ]
;ij type r0A r1A r2AfcAr0B r1B
r2B
Hi again,
It seems including our openmp module was responsible for the issue the
whole time. When I submit the job only loading pmix and gromacs, replica
exchange proceeds.
Thank you,
Dan
On Mon, Feb 17, 2020 at 9:09 AM Mark Abraham
wrote:
> Hi,
>
> That could be caused by configuration of
Dear All,
I want to calculate the free energy of two different types of molecules in the
same system. Is there a way to do this in gromacs?
couple-moltype = CHOL DPPC
Did not find any molecules of type 'CHOL DPPC' for coupling,
Regards,
Hind
--
Gromacs Users mailing list
* Please
On 2/20/20 8:30 AM, Peter Mawanga wrote:
My apologies, this can be achieved easily with the command below:
gmx trjconv -s -f -n
-split -o .
It's even easier. You can just use gmx trjconv -sep (with -b/-e as
needed to define a time interval).
-Justin
On Thu, Feb 20, 2020 at 2:15
On 2/20/20 12:34 AM, 고연주 wrote:
Hello!
I have a question about gmx trjconv -force option because it seems to work at all.
I'm using GROMACS-5.1.5 version and I want to extract forces using gmx trjconv command.
So I tried.
gmx trjconv -f
On 2/19/20 10:45 AM, Maryam wrote:
Dear gmx users,
I am trying to generate topology for small ligands using cgenff . I will
like to confirm if the Charmm to gmx script available on the Mackerell
website is compatible with all versions of charmm forcefield or can only
be used with Charm36
On 2/19/20 6:29 AM, Sadaf Rani wrote:
Thank you, Alessandra, for your reply.
I have tried TER in the PDB file but it doesn't work. It requires an N and
C terminal for amino acid residue. I have prepared residue in avogadros and
used these coordinates.
ATOM 1 N PHE A 1 0.000
On 2/18/20 3:57 PM, Sadaf Rani wrote:
Dear Gromacs users
I am getting the following message while running an energy minimization:-
There is no domain decomposition for 32 ranks that is compatible with the
given box and a minimum cell size of 1.85723 nm
I am not using any distance restraint,
On 2/18/20 2:28 PM, Adarsh V. K. wrote:
Dear all,
While suing CGENFF server for " *.str " file generation, Few of the
penalties were found to be higher than 50. How to do
validation/optimization.? Is there any recommended softwares / servers
available for
I suggest you read the 2010 JCC
Dear Gromacs-users,
I have a question that may not be directly Gromacs-related. I want to
calculate the potential of mean force (PMF) for a solute that is pulled
away from a crystal surface. The issue is that the fluid phase is
inhomogeneous, as it consists of water and cluster-forming ions.
My apologies, this can be achieved easily with the command below:
gmx trjconv -s -f -n
-split -o .
On Thu, Feb 20, 2020 at 2:15 PM Peter Mawanga
wrote:
> Hello everyone
>
> Is it possible to output different frames of a .trr trajectory as single
> .gro files without supplying an index
Hello everyone
Is it possible to output different frames of a .trr trajectory as single
.gro files without supplying an index (.ndx) file each time?
In VMD this can be achieved with:
set mol [molinfo top]
set sel [atomselect $mol all]
set n [molinfo $mol get numframes]
for {set i 0} {$i < $n}
Hi,
There is not much information to go with, but I can give some general remarks.
Could this not suggest that either your reaction coordinate is not suited,
driving the system into a region of very high potential energy, from where it
can escape though the reaction you consider unreasonable.
Hi
You have said correctly...you can use trjconv for that..
On Thu 20 Feb, 2020, 4:30 PM Peter Mawanga,
wrote:
> Thanks a lot Bratin for your help.
>
> It worked and I was able to get the RMSD values. However, there is no
> option to change the reference frame (from the input trajectory) for
Thank you, Quyen. I will look into this paper.
Qing
At 2020-02-20 18:45:58, "Quyen V. Vu" wrote:
>Hi,
>you can think about employed multi-dimensional umbrella sampling and used
>3D-WHAM to derived the PMF as professor Pander did in this paper: Petrone,
>P. M., Snow, C. D., Lucent, D., &
Thanks a lot Bratin for your help.
It worked and I was able to get the RMSD values. However, there is no
option to change the reference frame (from the input trajectory) for the
RMSD calculation.
As a workaround, I was thinking about extracting the different frames of
the ligand as separate .gro
Hi,
you can think about employed multi-dimensional umbrella sampling and used
3D-WHAM to derived the PMF as professor Pander did in this paper: Petrone,
P. M., Snow, C. D., Lucent, D., & Pande, V. S. (2008). Side-chain
recognition and gating in the ribosome exit tunnel. *Proceedings of the
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