Hi Suniba,
For the first part, look up 'periodic boundary conditions' (my oh my, there
should be a keyboard shortcut for that term). For the second part, it seems
you have loaded two files, and you should see two objects in the right side
panel of Pymol. You can turn visualization off by clicking
Hello everyone
I have completed two independent 100 ns simulations of two differnt proteins in
water. One is monomer and the other is trimer. Both simulations were allowed to
run for 50 ns intially, after visulation, trajectories were 'correct' and then
extended the simulation to 100 ns. Now aft
On 4/21/16 4:30 PM, Pedro Lacerda wrote:
Hi Mark,
I starting converting from AMBER (according to the paper) to GROMACS and
comparing the results.
Please explain in more words what this constant of two mean or how can I
handle it. Ignoring it and just converting the units, I got these results
Thanks everyone. For your quick reply and support.
On Thu, Apr 21, 2016 at 10:37 PM, Justin Lemkul wrote:
>
>
> On 4/21/16 9:35 AM, Sotirios Dionysios I. Papadatos wrote:
>
>> Hi, in my case gmx is only needed for certain commands. For example
>> pdb2gmx is working if I use it solo, not with gmx
hi Gmx experts
i want to calculate Volume corresponding to the one molar standard state. is
there any tool in gromacs to do that. i read about gmx density.
Background: i have Protein-ligand complex simulation and i need to find energy
of restraints which requires Volume.
Thanks in advance
Sa
Hi Stéphane,
Did you see the following or similar output from running
/path/to/cuda/samples/1_Utilities/deviceQuery/deviceQuery when GROMACS wasn't
able to detect GPU?
./deviceQuery Starting...
CUDA Device Query (Runtime API) version (CUDART static linking)
cudaGetDeviceCount returned 35
Le 21/04/2016 03:54, treinz a écrit :
Hi,
Can you also explain why the function calls to cudaDriverGetVersion() and
cudaRuntimeGetVersion() both return 0, as in
>>CUDA driver:0.0
>>CUDA runtime: 0.0
Thanks,
Tim
Hi all,
As I already posted on the list, it seems the combination of g
Hi Mark,
I starting converting from AMBER (according to the paper) to GROMACS and
comparing the results.
Please explain in more words what this constant of two mean or how can I
handle it. Ignoring it and just converting the units, I got these results
AMBER (table 2a)
Rmin/2 (Å) epsilon (kcal/mo
Dear Gmx-Users
Currently i'm having this kind of sticky warning when i am doing gmx solvate or
gmx editconf (ff was charmm and oplsa). However i copied vdwradii.dat in my
working directory, or use -vdwread flag still get this warning..Please how to
get rid off of this Warning!
WARNING: Masses
Dear Gmx-Users
Currently i'm having this kind of sticky warning when i am doing gmx solvate or
gmx editconf (ff was charmm and oplsa). However i copied vdwradii.dat in my
working directory, or use -vdwread flag still get this warning..Please how to
get rid off of this Warning!
WARNING: Mas
On Thu, Apr 21, 2016 at 3:54 AM, treinz wrote:
> Hi,
>
>
> Can you also explain why the function calls to cudaDriverGetVersion() and
> cudaRuntimeGetVersion() both return 0, as in
Not really, but it is the normal behavior on hosts where the runtime
is not compatible with the driver or there is s
Hi Mark,
many thanks.
At the end it is really just a question if the user has flexibility
over how to visualise the communications. I'm happy to hear that the
old-fashioned email way would still have (some) support :-)
I hope you get sufficient feedback and support from the community.
Cheers,
On 4/21/16 9:35 AM, Sotirios Dionysios I. Papadatos wrote:
Hi, in my case gmx is only needed for certain commands. For example pdb2gmx is
working if I use it solo, not with gmx. It's worth a shot.
This is true for versions in the 5.0.x series; they can be called via gmx or
through the old
Hi, in my case gmx is only needed for certain commands. For example pdb2gmx is
working if I use it solo, not with gmx. It's worth a shot.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Email Gmail
Pribadi
Sent: Thursday, April 21,
Le 21/04/2016 04:24, bharat gupta a écrit :
Dear Gmx Users,
I am interested in calculating cremer-pople parameters for a trisachharide
ligand from its simulation docked with a protein. I found one tool
g_puckering for calculating the parameters but it was written for Gromacs
version 4.0.x and I
On 4/21/16 7:29 AM, David Newman wrote:
Hi,
So on Gromacs 4.6.5, I'm using the make_ndx command to try to create a custom
index of a binding pocket on my protein of interest, I want to group 5
non-contiguous residues, I can index them separately and tried to group them
with & but that creates
Hi,
So on Gromacs 4.6.5, I'm using the make_ndx command to try to create a custom
index of a binding pocket on my protein of interest, I want to group 5
non-contiguous residues, I can index them separately and tried to group them
with & but that creates an empty group error because I guess it i
On 4/21/16 6:57 AM, Tuhin Samanta wrote:
please check it...
[ moleculetype ]
; molname nrexcl
HOD 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_116 1HOD OW 1 -0.8476
2 opls_117 1HOD HW
please check it...
[ moleculetype ]
; molname nrexcl
HOD 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_116 1HOD OW 1 -0.8476
2 opls_117 1HOD HW 1 0.4238
3 opls_805 1HOD
Hi,
Indeed, Link atoms have to be added to the .gro file. The atom indexing in the
.gro file is not used, so no need to renumber. A simple editconf can do that
for you if too, if you would like to have the numbering correct. However, you
need to adjust the total number of atoms at the top of t
On 4/20/16 3:56 PM, Jayant James wrote:
Hi!
All I have been running into some trouble with CA2+ recognition in GMX
5.1.1.
So some back ground..I have a protein that I am trying to simulate that
has three chains.First chain is 161 amino acids long, second one is about
200AA and the third one
On 4/21/16 3:00 AM, Divya Dube wrote:
Dear all,
How to calculate number of urea molecules required for a box size of 294.68
nm^3 for 2.1 M urea solution
You have a volume, you have a desired concentration, C = n/V.
-Justin
--
==
Justin A. L
On 4/21/16 3:32 AM, Tuhin Samanta wrote:
The topology file for my system - HOD System like that ---
#include "oplsaa.ff/forcefield.itp"
; Include hod topology
#include "hod.itp"
[ system ]
;Name
HOD
[ molecules ]
; Compound#mols
HOD102
.mdp file is lik
On 4/21/16 4:56 AM, Jason Loo Siau Ee wrote:
Hi all,
I'm trying to simulate a protein-ligand complex in POPC membrane using the CHARMM36 forcefield,
which I got from the Mackerell site and included in /share/gromacs/top/. Now when I run grompp I
get the error "Fatal error: No such moleculety
Hi all,
I'm trying to simulate a protein-ligand complex in POPC membrane using the
CHARMM36 forcefield, which I got from the Mackerell site and included in
/share/gromacs/top/. Now when I run grompp I get the error "Fatal error: No
such moleculetype SOD" despite the fact that I have #include
"
Hi Hannes,
Yes, previous discussion has identified this as a likely key feature, and
thanks for adding confirmation of that. Discourse can be integrated with
functionality for replying to threads from email to suit people who want
that kind of small change to their workflows; that will indeed suit
Dear GMX Users,
I am trying to perform QM/MM simulation for my system and I need to define
LA for the boundary between QM and MM region. I have the boundary regions
but I don't know how to add them in the gro file. Do I have to manually
modify the .gro file, if that's the case, adding, them manual
On Thu, 21 Apr 2016 07:11:42 +
Mark Abraham wrote:
> Hi people,
>
> As part of the new BioExcel project (http://bioexcel.eu/) that
> supports biomolecular research with codes including GROMACS, we're
> exploring migrating the gmx-users mailing list to the Discourse
> format. You can see an e
The topology file for my system - HOD System like that ---
#include "oplsaa.ff/forcefield.itp"
; Include hod topology
#include "hod.itp"
[ system ]
;Name
HOD
[ molecules ]
; Compound#mols
HOD102
.mdp file is like that -
(FOR Energy minimization)
; mi
Hi people,
As part of the new BioExcel project (http://bioexcel.eu/) that supports
biomolecular research with codes including GROMACS, we're exploring
migrating the gmx-users mailing list to the Discourse format. You can see
an example at http://try.discourse.org! This has a number of immediate
ad
Dear all,
How to calculate number of urea molecules required for a box size of 294.68
nm^3 for 2.1 M urea solution
regds
Divya
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