Good evening here,
I get a segmentation fault with my GROMACS 5.1 install only for replica exchange
simulations right at the first successful exchange on a multi-node run. Normal
simulations across multiple nodes work fine, and replica exchange simulations on
one node work fine.
I've reproduced t
I am looking for the energy of solvation. The g_mmpbsa tool could help me for
it ?
> To: gmx-us...@gromacs.org
> From: jalem...@vt.edu
> Date: Thu, 29 Oct 2015 18:38:58 -0400
> Subject: Re: [gmx-users] There is no error message but the dynamic don´t show
> the correct number of frames
>
>
>
>
On 10/29/15 6:21 PM, Mishelle Oña wrote:
I attached the .mdp file I usedCould you tell me if there is a better form to
The mailing list does not accept attachments.
calculate the free energy of my polimer?And how can I do normal convergence
I would run a much longer simulation (20 ns cert
I attached the .mdp file I usedCould you tell me if there is a better form to
calculate the free energy of my polimer?And how can I do normal convergence
checks of the dynamics?
ThanksMishelle
> To: gmx-us...@gromacs.org
> From: jalem...@vt.edu
> Date: Thu, 29 Oct 2015 18:11:20 -0400
> Subject:
On 10/29/15 6:08 PM, Mishelle Oña wrote:
Well, I am trying to calculate the Solvation free energy of my molecule, I am
following the Hands-on tutorial
Solvation free energy of ethanol of Sander Pronk. Using trjconv I cut one
frame from this trajectory and make all the steps of the tutorial.
Well, I am trying to calculate the Solvation free energy of my molecule, I am
following the Hands-on tutorial
Solvation free energy of ethanol of Sander Pronk. Using trjconv I cut one
frame from this trajectory and make all the steps of the tutorial. When I do
g_bar to calculate the free energ
Ok. I misunderstood your intention to be to run a single calculation with
three MPI domains sharing its work. To simply get three independent non-MPI
calculations you could indeed use your approach. It sounds like you ran
into some behaviour where only one of the three calculations got the stdin,
b
On 10/29/15 5:46 PM, Mishelle Oña wrote:
Hi Justin, Thanks for your reply. I used gmxcheck to verify the trajectory and
it didn´t have errors. I got this:
Item#frames Timestep (ps)Step 400010.5Time 40001
0.5Lambda 400010.5Coords 400010.5Veloc
Hi Justin, Thanks for your reply. I used gmxcheck to verify the trajectory and
it didn´t have errors. I got this:
Item#frames Timestep (ps)Step 400010.5Time 40001
0.5Lambda 400010.5Coords 400010.5Velocities 40001
0.5Forces 0Box
On 10/29/15 4:50 PM, Mishelle Oña wrote:
Hi!I am simulating a polimer of Polylactic acid with 30 monomers in a water
system. For equilibrate the system I have made NVT, NPT and Process dynamics.
The fiinal dynamic should have 40 000 frames but when I load it in VMD it has
only 12 186 frames. A
Hi!I am simulating a polimer of Polylactic acid with 30 monomers in a water
system. For equilibrate the system I have made NVT, NPT and Process dynamics.
The fiinal dynamic should have 40 000 frames but when I load it in VMD it has
only 12 186 frames. Also the confout.gro file that result from
Hi!I am simulating a polimer of Polylactic acid with 30 monomers in a water
system. For equilibrate the system I have made NVT, NPT and Process dynamics.
The fiinal dynamic should have 20 000 frames but when I load it in VMD it has
only 12 186 frames. Also the confout.gro file that result from
Oh, I see. So the -contact flag calculates all contacts within the cutoff
distance and does not care if an atom is a donor or acceptor.
-Dina
On Thu, Oct 29, 2015 at 4:07 PM, Dina Mirijanian
wrote:
> Hi Erik,
>
> Thank you for the suggestion. But, will this not only give me H-bond
> contacts o
Hi Erik,
Thank you for the suggestion. But, will this not only give me H-bond
contacts only? I am looking for any contact. The only way I can see to make
this work is to make all atoms donors and acceptors, and I do not know how
to do this. Am I missing something or is there a simple way to do t
On 10/28/15 9:57 AM, Joan Clark Nicolas wrote:
Dear gmx users,
I am trying to run MD calculations on a protein-ligand system using Virtual
Sites, but as I generate my protein and ligand topologies separately (with
pdb2gmx and acpype, respectively), the VS for the ligand are not generated.
Does
On 10/28/15 1:40 PM, Irem Altan wrote:
Hi,
I am trying to run an MD simulation with tip5p, using amber99sb. When I look at
the folder amber99sb.ff, I see that there exists a tip5p.itp file. However,
when I do
pdb2gmx -f 1ytt_refine_001.pdb -ff amber99sb -o box.gro -p topol.top
I don’t see
On 10/29/15 12:16 AM, Chunlei ZHANG wrote:
Dear All,
I was trying to compiling Gromscs 5.1 on a cluster with with two 10-core
Intel Xeon E5-2600 v3(Haswell) on each node.
The command with cmake:
cmake .. -DCMAKE_C_COMPILER=mpiicc \
-DCMAKE_CXX_COMPILER=mpiicpc \
-DGMX_MPI=on -DGMX_OPENMP=on \
On 10/29/15 4:56 AM, badamkhatan togoldor wrote:
Dear GMX Users, I am simulating a free energy of a protein chain_A in water
by parallel. Then i got domain decomposition error in mdrun. Will use 15
particle-particle and 9 PME only ranksThis is a guess, check the performance
at the end of the lo
On 10/29/15 6:45 AM, Nikhil Maroli wrote:
Dear All,
i am following protein-Ligand tutorial for my protein and ligand .
when i run grompp i got this error
Group Protein_LIG referenced in the .mdp file was not found in the index
file.
Group names must match either [moleculetype] names or custom
after several days of trial and error, i was told only today that our
HPC indeed has one cluster/queue (40 core nodes SMP) that does not
require the use of aprun/mprun. so, after having compiled all the tools
again on that cluster, i am finally able to execute many processes per node.
(howev
Le 29/10/2015 04:24, Sana Saeed a écrit :
is it possible?
yes.
--
Assistant Professor, UFIP, UMR 6286 CNRS, Team Protein Design In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes
cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.u
I run 20ns simulation in 3.5hours and I assumed it is correct.
My system size is 2.5x2.5x12.5nm with 512 water and 50 organics molecules.
I do not use GPU.
On Thu, Oct 29, 2015 at 2:04 PM, Jorge Fernandez-de-Cossio-Diaz <
j.cossio.d...@gmail.com> wrote:
> Also check your time step size. A large t
Also check your time step size. A large time step can lead to numerical
errors, but you will run more ns/day
On Thu, Oct 29, 2015 at 8:56 AM, Smith, Micholas D.
wrote:
> A few clairfying questions:
>
> 1) What is the size of the system?
> 2) What is your frame saving rate?
> 3) Are you using a G
A few clairfying questions:
1) What is the size of the system?
2) What is your frame saving rate?
3) Are you using a GPU? What about MPI or OpenMP?
60ns a day (what 5ns/2hours) is not unheard of given a reasonable system size
and GPU acceleration. If you are curious about the performance you can
Hi,
As written on the website, g_mmpbsa does not directly support MPI. g_mmpbsa
does not include any code concerning OpenMP and MPI. However, We have tried
to interface MPI and OpenMP functionality of APBS by some mechanism.
One may use g_mmpbsa with MPI by following: (1) allocate number of
proce
Yes. It is formally possible.
I do not think that implicit solvation precludes PBC usage.
On Thu, Oct 29, 2015 at 9:40 AM, Анна Павловна Толстова <
tolst...@physics.msu.ru> wrote:
> Hello, gmx_users.
>
> Is that possible to simulate a protein adsorption on graphite sheet with
> implicit s
Hello, gmx_users.
Is that possible to simulate a protein adsorption on graphite sheet with
implicit solvent? It works good in vacuo and with explicit solvent with
periodic-molecules = yes. But implicit solvent requires no PBC so that
periodic molecules should be switched off too. Is there any idea
hi again,
3 answers are hidden somewhere below ..
Am 28.10.2015 um 15:45 schrieb Mark Abraham:
Hi,
On Wed, Oct 28, 2015 at 3:19 PM Vedat Durmaz wrote:
Am 27.10.2015 um 23:57 schrieb Mark Abraham:
Hi,
On Tue, Oct 27, 2015 at 11:39 PM Vedat Durmaz wrote:
hi mark,
many thanks. but can
Dear All,
i am following protein-Ligand tutorial for my protein and ligand .
when i run grompp i got this error
Group Protein_LIG referenced in the .mdp file was not found in the index
file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must sup
Dear GMX Users,
I am simulating a free energy of a protein chain_A in water by parallel. Then i
got domain decomposition error in mdrun.
Will use 15 particle-particle and 9 PME only ranksThis is a guess, check the
performance at the end of the log file
---
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