Hi,
You need to perform the NVT and NPT equilibration at 353.1 K and then use
your equilibrated system for the production run.
On Wed, Jul 16, 2014 at 10:55 AM, bharat gupta bharat.85.m...@gmail.com
wrote:
Hi,
I first simulated my protein system at 300 K. Now I want to simulate the
same
Thanks ..
On Wed, Jul 16, 2014 at 4:28 PM, rajat desikan rajatdesi...@gmail.com
wrote:
Hi,
You need to perform the NVT and NPT equilibration at 353.1 K and then use
your equilibrated system for the production run.
On Wed, Jul 16, 2014 at 10:55 AM, bharat gupta bharat.85.m...@gmail.com
Thanks for the reply and the helpful suggestion, Justin. I have now used
g_x2top, changed the necessary parameters to match the CHARMM36 cgenff
(graphene carbon as CG2R61). When I run a minimization with the graphene sheet
defined as a freeze group, I receive the following error:
WARNING:
Hi,
it is not directly clear what problem you mean.
If you refer to the binary being compiled for SSE4.1 and the
hardware being capable of AVX instructions, then simply recompile
with -DGMX_CPU_ACCELERATION=AVX_256 added to your cmake line.
Carsten
On 16 Jul 2014, at 04:02, Andy Chao
hello gromacs users
i am working on protein complex with popc membrane
at the time of minimization and shrinking steps my protein complex is out
of the lipid membrane protein is in the lipid membrane till inflate.gro but
after that it is out
i used the minimization script
; minim.mdp - used as
On 7/16/14, 1:42 AM, Sarath Kumar Baskaran wrote:
Dear all,
I was using PRODRG for my protein ligand Simulations,
Later, I came across the issues of PRODRG topologies on atom charges, and i
have been tryiing to correct these problems.
I couldnt use ATB since it gives topopology only for
On 7/16/14, 6:51 AM, Dawid das wrote:
Dear Justin,
In this case may I use Ryckaert-Bellemans dihedral (func. type 3) for one
part of the new residue and proper dihedral (multiple) (func. type 9) for
the rest? Is this mixing allowed?
No. Force fields are self-consistent entities; even what
On 7/16/14, 3:43 AM, Timothy Click wrote:
Thanks for the reply and the helpful suggestion, Justin. I have now used
g_x2top, changed the necessary parameters to match the CHARMM36 cgenff
(graphene carbon as CG2R61). When I run a minimization with the graphene sheet
defined as a freeze group,
On 7/16/14, 6:53 AM, RINU KHATTRI wrote:
hello gromacs users
i am working on protein complex with popc membrane
at the time of minimization and shrinking steps my protein complex is out
of the lipid membrane protein is in the lipid membrane till inflate.gro but
after that it is out
This
On Mon, Jul 14, 2014 at 12:51 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/13/14, 8:41 PM, Rasoul Nasiri wrote:
On Mon, Jul 14, 2014 at 1:02 AM, Justin Lemkul jalem...@vt.edu wrote:
On 7/13/14, 7:11 PM, Rasoul Nasiri wrote:
On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul
Hi,
I don't see anything obviously wrong with your setup; there are two
peculiarities that I suggest looking into:
- you seem to be running in a virtualized environment (at least the
hostname indicates this); check if the flags /proc/cpuinfo contains
rdtscp and if it does not try setting
That's what I thought. Thank you for your help.
Best regards,
Dawid
2014-07-16 12:53 GMT+01:00 Justin Lemkul jalem...@vt.edu:
On 7/16/14, 6:51 AM, Dawid das wrote:
Dear Justin,
In this case may I use Ryckaert-Bellemans dihedral (func. type 3) for one
part of the new residue and proper
My exact command was
g_x2top -f gra.gro -o gra.top -name GRA -nexcl 3 -ff charmm36 -kb 255224 -kt
334.72 -kp 12.9704
Cordially,
柯明 Timothy H. Click, Ph.D.
Department of Biological Science and Technology
Institute of Bioinformatics and Systems Biology
National Chiao Tung University
208 Lab
Dear all,
I wonder if there is anywhere I can know the details of mdp files used for
normal mode analysis.
I understand from the maunal that it needs steepest descent, conjugate
gradient, l-bfgs, nm in md options consecutively,
but I am not sure about other parameters set in these different
On 7/16/14, 10:27 AM, Timothy Click wrote:
My exact command was
g_x2top -f gra.gro -o gra.top -name GRA -nexcl 3 -ff charmm36 -kb 255224 -kt
334.72 -kp 12.9704
Use -alldih. It's off by default, but should almost certainly be used for
systems like this.
-Justin
--
I added the -alldih, readjusted the parameters to match the desired distances,
etc., and if I don’t freeze anything, I receive the following error upon a
minimization attempt.
Steepest Descents:
Tolerance (Fmax) = 1.0e+03
Number of steps=5
There were 4490
On 7/16/14, 10:58 AM, Timothy Click wrote:
I added the -alldih, readjusted the parameters to match the desired distances,
etc., and if I don’t freeze anything, I receive the following error upon a
minimization attempt.
Steepest Descents:
Tolerance (Fmax) = 1.0e+03
Number of
My exact command was
g_x2top -f gra.gro -o gra.top -name GRA -nexcl 3 -ff charmm36 -kb 255224 -kt
334.72 -kp 12.9704
Cordially,
柯明 Timothy H. Click, Ph.D.
Department of Biological Science and Technology
Institute of Bioinformatics and Systems Biology
National Chiao Tung University
208 Lab
Dear Gromacs experts
i simulated protein ligand complex by gromacs 4.6.3
I get following results for pressure in npt equilibration step:
Energy Average Err.Est. RMSD Tot-Drift
---
Pressure
dear justin
Thank you sincerely for your good advice
Good luck
On Wednesday, July 16, 2014 8:18 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/16/14, 11:18 AM, Mahboobeh Eslami wrote:
Dear Gromacs experts
i simulated protein ligand complex by gromacs 4.6.3
I get following results for
Dear GROMACS Users,
I have a question regarding the Neighbor searching, I used group scheme
when I used 4.5 and now I found that there is verlet in version 4.6. When I
compare the trajectories, For verlet simulation I found that the atoms of
water molecules are separated and it caused the long
Dear GROMACS Users,
I have a question regarding the Neighbor searching, I used group scheme
when I used 4.5 and now I found that there is verlet in version 4.6. When I
compare the trajectories, For verlet simulation I found that the atoms of
water molecules are separated and it caused the long
On 7/16/14, 2:21 PM, leila salimi wrote:
Dear GROMACS Users,
I have a question regarding the Neighbor searching, I used group scheme
when I used 4.5 and now I found that there is verlet in version 4.6. When I
compare the trajectories, For verlet simulation I found that the atoms of
water
Dear GROMACS Users,
I have a question regarding the Neighbor searching, I used group scheme
when I used 4.5 and now I found that there is verlet in version 4.6. When I
compare the trajectories, For verlet simulation I found that the atoms of
water molecules are separated and it caused the long
Thanks Justin.
On Wed, Jul 16, 2014 at 8:42 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/16/14, 2:21 PM, leila salimi wrote:
Dear GROMACS Users,
I have a question regarding the Neighbor searching, I used group scheme
when I used 4.5 and now I found that there is verlet in version 4.6.
hi dear Gromacs User,
i was wondering if you could help me with something,
I made a set of Umbrella sampling simulation of a Drug passing through a
POPC membrane, i use Gromacs 5.0 rc1, i use the geometry direction ,
when i use
g_wham -it tpr-files.dat -if pullf-files.dat -unit kCal -ac
Most probably this has nothing to do with the cut-off scheme. Please
read this page:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
--
Szilárd
On Wed, Jul 16, 2014 at 8:44 PM, leila salimi leilasal...@gmail.com wrote:
Dear GROMACS Users,
I have a question
Dear All,
I am running simulations of BMP2 protein and graphite sheet using
implicit solvent model (mdp file is pasted below). The graphite atoms
are frozen in the simulation and BMP2 is free to translate.
I got an error Step 1786210: The domain decomposition grid has
shifted too much in the
That is not possible.
Turn on the periodic image in the direction in which it appears to you that the
protein is out. Even turn on all six, play with them all, on and off in
different combinations, to see what it shows. The PBC is an important concept
that you need to get your head around.
Hello,
I am trying to simulate a peptide-membrane system on GPU using gromacs
4.6.1 . However whenever I invoke the mdrun command I get an error as *srun:
error: coe3: task 0: Segmentation fault (core dumped)*. Can anybody please
suggest me what might be the problem?
*Script file used to submit
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