Hi,
I was wondering if there is an option or a way to use the algorithm SHAKE
for the water molecules (instead of SETTLE).
Thanks!
Guillaume
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On 10/30/13 12:00 PM, Guillaume Chevrot wrote:
Hi,
I was wondering if there is an option or a way to use the algorithm SHAKE
for the water molecules (instead of SETTLE).
Never tried it, but I would assume
define = -DFLEXIBLE
constraint-algorithm = shake
would do the trick. Of course,
Hi,
2013/10/30 Justin Lemkul jalem...@vt.edu
On 10/30/13 12:00 PM, Guillaume Chevrot wrote:
Hi,
I was wondering if there is an option or a way to use the algorithm SHAKE
for the water molecules (instead of SETTLE).
Never tried it, but I would assume
define = -DFLEXIBLE
Dear Gromacs users,
Please somebody help .
editconf computs the incorrect value of mass of input. I tried to resolve
this problem but failed. Previously I was doing AOt but now I just found that
the molecule OS1 =O2L showing error . Here I posted my A.pdb, RM.rtp
atomtypes.atp. The mass of
Dear Gromacs users,
Please somebody help .
editconf computs the incorrect value of mass of input. I tried to resolve
this problem but failed. Previously I was doing AOt but now I just found that
the molecule OS1 =O2L showing error . Here I posted my A.pdb, RM.rtp
atomtypes.atp. The mass of
On 10/30/13 2:34 PM, Hari Pandey wrote:
Dear Gromacs users,
Please somebody help .
editconf computs the incorrect value of mass of input. I tried to resolve
this problem but failed. Previously I was doing AOt but now I just found that the
molecule OS1 =O2L showing error . Here I posted my
On 10/30/13 1:46 PM, Guillaume Chevrot wrote:
Hi,
2013/10/30 Justin Lemkul jalem...@vt.edu
On 10/30/13 12:00 PM, Guillaume Chevrot wrote:
Hi,
I was wondering if there is an option or a way to use the algorithm SHAKE
for the water molecules (instead of SETTLE).
Never tried it, but I
Michael, thanks for taking the time to comment and have a look.
The real issue I am having is a bit deeper into the topic than that, my last
reply was just an observation on something else. Will summarise what I have
been doing etc.
I have a molecule that are calculating the Gibbs energy of
I likely won't have much time to look at it tonight, but you can see
exactly what the option is doing to the topology. run gmxdump on the
tpr. All of the stuff that couple-intramol does is in grompp, so the
results will show up in the detailed listings of the interactions, and
which ones have
Dear Users,
I have a system consisting of peptides and a linear carbohydrate.
Initially I tried to simulate these peptides using virtual sites and
it worked. I can use pdb2gmx for building virtual sites on protein
whereas I have an itp file for the carbohydrate. Is it possible to
apply virtual
On Oct 29, 2013 1:26 AM, Pavan Ghatty pavan.grom...@gmail.com wrote:
Now /afterok/ might not work since technically the job is killed due to
walltime limits - making it not ok.
Hence use -maxh!
Mark
So I suppose /afterany/ is a better
option. But I do appreciate your warning about spamming
On 10/29/13 2:21 AM, Neha Gandhi wrote:
Dear Users,
I have a system consisting of peptides and a linear carbohydrate.
Initially I tried to simulate these peptides using virtual sites and
it worked. I can use pdb2gmx for building virtual sites on protein
whereas I have an itp file for the
Hi GMX Users,
I am using Gromacs (Version 4.5.5) to do constant-force pulling of
ubiquitin and it's a implicit model. My mdp file for pulling is shown as
following.
integrator = md
dt = 0.001; ps !
nsteps = 50 ; total 500 ps.
nstxout
Dear Mark
Very thanks for your reply
To make this clear, center the trajectory on the water and watch the
time evolution in some visualization program.
I did your suggestion (center the trajectory on the water). Again, drug
molecule is in region (1)in some frames and is in region (4) in other
Hi GMX Users,
I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin
and it's a implicit model. My mdp file for pulling is shown as following.
integrator = md
dt = 0.001; ps !
nsteps = 50 ; total 500 ps.
nstxout
On Tue, Oct 29, 2013 at 5:02 PM, shahab shariati
shahab.shari...@gmail.comwrote:
Dear Mark
Very thanks for your reply
To make this clear, center the trajectory on the water and watch the
time evolution in some visualization program.
I did your suggestion (center the trajectory on the
You want to switch to sd instead of md.
On Oct 29, 2013, at 17:43, Vivian ww...@bu.edu wrote:
Hi GMX Users,
I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin
and it's a implicit model. My mdp file for pulling is shown as following.
integrator =
Hello gromacs users,
I´m currently tring to calculate S2 order parameters for comparison with
nmr data and other simulations.
When i try the command for the NH vector:
g_rotacf -s ../protein.tpr -d -P 2 -n nh.ndx -f ../protein_fit.xtc -w
-noaver
It gives me the only half of the residues (NH
On Tue, Oct 29, 2013 at 2:21 AM, Neha Gandhi n.gandh...@gmail.com wrote:
Dear Users,
I have a system consisting of peptides and a linear carbohydrate.
Initially I tried to simulate these peptides using virtual sites and
it worked. I can use pdb2gmx for building virtual sites on protein
I dont know how well v-rescale works with pulling. It could be after removing some restraints it still had not reached a good equilibrium (ie let it run a while/nanosecound or 5, before pulling it), or maybe generating velocities on start causes more caos than the proteins or system can handle,
Greeting
I'm working on a MD of a ligand-protein complex during 40 ns
i want to analyses ligand-protein interaction hydrogen bonds
My first question :
Should i analyses a minimized frame from clustering of the trajectory
or should i analyses hydrogen bond occupancy over trajectory ?
On 10/29/13 12:02 PM, shahab shariati wrote:
Dear Mark
Very thanks for your reply
To make this clear, center the trajectory on the water and watch the
time evolution in some visualization program.
I did your suggestion (center the trajectory on the water). Again, drug
molecule is in
On 10/29/13 4:02 PM, Tiago Gomes wrote:
Hello gromacs users,
I´m currently tring to calculate S2 order parameters for comparison with
nmr data and other simulations.
When i try the command for the NH vector:
g_rotacf -s ../protein.tpr -d -P 2 -n nh.ndx -f ../protein_fit.xtc -w
-noaver
It
On 10/29/13 5:46 PM, larif sofiene wrote:
Greeting
I'm working on a MD of a ligand-protein complex during 40 ns
i want to analyses ligand-protein interaction hydrogen bonds
My first question :
Should i analyses a minimized frame from clustering of the trajectory
or should i
Hi,everyone, I'm a newcomer, i want to simulate partially hydrolized
polyacrylamide in solutions,please give me some suggestions,how to build the
polymer pdb structure and how to opitimize the structure, thank U!
Qu Guangmiao
qugm...@126.com--
gmx-users mailing listgmx-users@gromacs.org
Just want this to make another pass, just in case those in the know missed it.
Using couple-intrmol = yes the resulting dH/dl plot actually looks like that at
lamba = 1 it is actually equal to couple-intramol = no with lambda = 0.
Should that be the case?
Catch ya,
Dr. Dallas Warren
Drug
I think the grammar got a little garbled there, so I'm not sure quite
what you are claiming.
One important thing to remember; 1-4 interactions are treated as
bonded interactions right now FOR COUPLE intramol (not for lambda
dependence of the potential energy function), so whether
couple-intramol
Not working is too vague a symptom for anyone to guess what the
problem
is, sorry.
Mark
On Oct 24, 2013 9:39 AM, Santu Biswas santu.biswa...@gmail.com
wrote:
dear users,
I am performing 500ps mdrun in vacuum for
polypeptide(formed
by 10-residues leucine)
Hi all,
I'm trying to run a vacuum simulation of my protein which has a non-zero charge.
How to deal with this charge? Can I add counter ions in to my system?
Would it be energetically stable?
How can one bring a protein to its isoelectric point?
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On 10/28/13 3:30 AM, Santu Biswas wrote:
Not working is too vague a symptom for anyone to guess what the
problem
is, sorry.
Mark
On Oct 24, 2013 9:39 AM, Santu Biswas santu.biswa...@gmail.com
wrote:
dear users,
I am performing 500ps mdrun in vacuum for
Dear Users,
Whenever i convert a protein.pdb file using the following command (pdb2gmx
-f protein.pdb -o protein.gro/pdb -water spc) and thereafter visualise the
output with either vmd or pymol, i get the first amino acid residue
breaking from the main chain.
Would anyone help me understand why
Hi Musyoka,
I would guess that that is related to the input coordinates. A bit of EM
should fix it.
Cheers,
Tsjerk
On Mon, Oct 28, 2013 at 11:20 AM, MUSYOKA THOMMAS
mutemibiochemis...@gmail.com wrote:
Dear Users,
Whenever i convert a protein.pdb file using the following command (pdb2gmx
If in vacuum, I would add hydrogens via covalent bonds.
Dr. Vitaly V. Chaban
On Mon, Oct 28, 2013 at 10:29 AM, Richa Singh
richa.s.rathor...@gmail.com wrote:
Hi all,
I'm trying to run a vacuum simulation of my protein which has a non-zero
charge.
How to deal with this charge? Can I add
Hello dears
I would liked to know which of the tutorials presented by Gromacs for binding
free energy analysis (http://www.gromacs.org/Documentation/Tutorials) are
based on LIE method?
regards,
Sajad
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On 10/28/13 8:02 AM, Sajad Ahrari wrote:
Hello dears
I would liked to know which of the tutorials presented by Gromacs for binding
free energy analysis (http://www.gromacs.org/Documentation/Tutorials) are
based on LIE method?
I would suggest you read them and see. I suspect none of them
Dear GROMACS users and developers,
We are very pleased to announce that PLUMED2 is available at
www.plumed-code.org.
Version 2.0 is a complete rewrite, so there is no way to write a complete set
of differences with respect to PLUMED.
Here is a summary of the major differences:
- The input is
Dear Gromacs Users
I would like to suggest a project in free energy calculations which can be in
cooperation.
The project is to demonstrate a novel and interesting method to calculate free
energy differences between two solvation/binding processes.
The first simulations are rather simple
Hi GMX users
I want to use parmbsc0 force field for G-quadruplex structures MD simulation,
but I'm not sure, the amber99sb_parmbsc0.ff.tgz in the gromacs
site(http://www.gromacs.org/Special:Search?search=parmbsc0ns=mainpath=) is
the parmbsc0 force field.
Please help me
Sincerely
Kiana
--
I have need to collect 100ns but I can collect only ~1ns (1000steps) per
run. Since I dont have .trr files, I rely on .cpt files for restarts. For
example,
grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15
This runs into a problem when the run gets killed due to walltime limits.
On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty pavan.grom...@gmail.comwrote:
I have need to collect 100ns but I can collect only ~1ns (1000steps) per
run. Since I dont have .trr files, I rely on .cpt files for restarts. For
example,
grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o
On 10/28/13 10:06 AM, kiana moghaddam wrote:
Hi GMX users
I want to use parmbsc0 force field for G-quadruplex structures MD simulation, but I'm
not sure, the amber99sb_parmbsc0.ff.tgz in the gromacs
site(http://www.gromacs.org/Special:Search?search=parmbsc0ns=mainpath=) is
the parmbsc0
Hi gromacs users:
I use gromacs 4.5.6 for energy minimization with steepest descent method
for ubiquitin pulling simulation with pulling step for applying
displacement. For that simulation, I should repeat pulling and minimization
process. I need 10^4 pulling step calculation to get fully
Mark,
The problem with one .tpr file set for 100ns is that when job number (say)
4 hits the wall limit, it crashes and never gets a chance to submit the
next job. So it's not really automated.
Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5
till job 4 ends. But the PBS
Hello,
I have couple objectives as part of an analysis of my simulated system. And I
would like some opinions on the tools to use to achieve it.
I have the following interest in my system:
1) Find the probability distribution (density) of bond angle on my molecule
between (i.e atom 12, 2,3 ,
No this isn't a problem. You can use job names under the -hold_jid flag.
As long as you change the job name in the submit script between
submissions this isn't a problem. You could have a submit script for job 4
with -N md_job4 and -hold_jid md_job3 then change these to -N md_job5 and
-hold_jid
Aah yes of course. Thanks James.
On Mon, Oct 28, 2013 at 3:16 PM, jkrie...@mrc-lmb.cam.ac.uk wrote:
No this isn't a problem. You can use job names under the -hold_jid flag.
As long as you change the job name in the submit script between
submissions this isn't a problem. You could have a
You're welcome
On 28 Oct 2013, at 20:03, Pavan Ghatty pavan.grom...@gmail.com wrote:
Aah yes of course. Thanks James.
On Mon, Oct 28, 2013 at 3:16 PM, jkrie...@mrc-lmb.cam.ac.uk wrote:
No this isn't a problem. You can use job names under the -hold_jid flag.
As long as you change the
DearGromacs users
I have encountered something strange. I have installed Red
Hat Enterprise Linux 6.1 6.2 on two machines recently and then lam 7.1.4,
fftw 3.3.2 and Gromacs 4.5.5 .
During linux installation, everything went well I didn`t
face any complain or receiving any error, as well as in
Greetings,
I would also be interested in an example of using REST via Hamiltonian REMD
in the current gromacs build. I'm particularly interested in enhanced
conformational sampling of 160-270 residue proteins. As it stands, I've
been unable to achieve any appreciable exchange probability in
Hi,
Hard to know. LAM was discontinued over 4 years ago. You could have a flaky
file system. Unless you're trying to run a jobsover both machines over
network like Infiniband, you don't even want to use an external MPI library
- single-node performance with built-in thread-MPI will give much
On Mon, Oct 28, 2013 at 7:53 PM, Pavan Ghatty pavan.grom...@gmail.comwrote:
Mark,
The problem with one .tpr file set for 100ns is that when job number (say)
4 hits the wall limit, it crashes and never gets a chance to submit the
next job. So it's not really automated.
That's why I
On Mon, Oct 28, 2013 at 8:04 PM, Hari Pandey hariche...@yahoo.com wrote:
Dear Gromacs Users,
First, I would like to thank Dr. Lemkul for reply.
My problem description is as follows:
I am using CHARMM36 forcefield to equilibrate of AOT. when I add the mass
of all atoms from topology, it
On 10/28/13 1:59 PM, Gwonchan Yoon wrote:
Hi gromacs users:
I use gromacs 4.5.6 for energy minimization with steepest descent method
for ubiquitin pulling simulation with pulling step for applying
displacement. For that simulation, I should repeat pulling and minimization
process. I need 10^4
Thank you so much Mark.
I still did not understand. More detaily. Atomtypes are only following:
atomtypes.atp::
H 1.00800 ; polar H
DUM 0.0 ; dummy atom
HAL1 1.008000 ; alphatic proton
HAL2 1.008000 ; alphatic proton
HAL3 1.008000
On 10/28/13 7:41 PM, Hari Pandey wrote:
Thank you so much Mark.
I still did not understand. More detaily. Atomtypes are only following:
atomtypes.atp::
H 1.00800 ; polar H
DUM0.0 ; dummy atom
HAL1 1.008000 ; alphatic proton
HAL2 1.008000
Many thanks to Dr.Lemkul
Yes mass is 444 in my .top file and I did -density 1000 because then it
will show the density also.
I am wandering how do I find that which atom name mismatched. The
forcefield folder is in my working directory and there are all files.
atomtypes.atp is there
On 10/28/13 8:07 PM, Hari Pandey wrote:
Many thanks to Dr.Lemkul
Yes mass is 444 in my .top file and I did -density 1000 because then it
will show the density also.
If you have one molecule in a box of a known size, you don't need any
command-line flags - you have a mass and a known
Now /afterok/ might not work since technically the job is killed due to
walltime limits - making it not ok. So I suppose /afterany/ is a better
option. But I do appreciate your warning about spamming the queue and yes I
will re-read PBS docs.
On Mon, Oct 28, 2013 at 5:11 PM, Mark Abraham
When performing free energy calculations using the expanded ensemble
method, there is a barker and metropolis option for lmc-stats. Are the
corresponding transition probabilities computed with or without the
weighting factors? That is, are these probabilities biased or not?
Thank you,
Andrew
Hi, Andrew-
The choice of lmc-stats only affects the calculation of the weights,
it does not affect the calculation of the transition matrix.
There are two possibilities for the transition matrix; the estimated
one (which is just called 'Transition Matrix' -- we should probably
have a better
You are not allowed to post to this mailing list, and your message has
been automatically rejected. If you think that your messages are
being rejected in error, contact the mailing list owner at
gmx-developers...
Sorry I was trying to post this to the Feature suggestion/request site on
Dear Justin
I want to study translocation of drug molecule in lipid bilayer.
My gro file after minimization is em2.gro.
After NPT-MD simulation, I obtained npt.gro and 0.xtc files.
When I see trajectory by vmd, there are some things abnormal.
I guess there is pbc problem.
I attached these 3
Please keep the discussion on the list.
On 10/27/13 5:09 AM, sunyeping wrote:
Dear professor Lemkul,
For warning 1:
I use the npt_umbrella.mdp file you provided in step 6 in the umbralla sampling
tutorial. You told us to start by running a brief NPT equilibration in each
window using this mdp
On 10/27/13 8:16 AM, shahab shariati wrote:
Dear Justin
I want to study translocation of drug molecule in lipid bilayer.
My gro file after minimization is em2.gro.
After NPT-MD simulation, I obtained npt.gro and 0.xtc files.
When I see trajectory by vmd, there are some things abnormal.
I
Dear Justin
Please check this trajectory file (1.xtc) being smaller than 0.xtc.
https://www.dropbox.com/s/9qd2l37qyfqvpox/1.xtc
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Hello All,
Is there a way to make mdrun put out .cpt file with the same frequency as a
.xtc or .trr file. From here
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts I see that we
can choose how often (time in mins) the .cpt file is written. But clearly
if the frequency of output of
Dear Justin
I attached images related to before (em2.gro) and after equilibration.
https://www.dropbox.com/s/yjkyj5ycshvp20u/images.docx
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Hi Shahab,
What about running trjconv -pbc mol with a .tpr as input file?
Cheers,
Tsjerk
On Sun, Oct 27, 2013 at 3:24 PM, shahab shariati
shahab.shari...@gmail.comwrote:
Dear Justin
I attached images related to before (em2.gro) and after equilibration.
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
--
发件人：Justin Lemkul jalem...@vt.edu
发送时间：2013年10月27日(星期日) 20:27
收件人：gromacs gmx-users@gromacs.org
主 题：Re: 答复: [gmx-users] error in umbralla sampling step 6
Please
On 10/27/13 9:37 AM, Pavan Ghatty wrote:
Hello All,
Is there a way to make mdrun put out .cpt file with the same frequency as a
.xtc or .trr file. From here
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts I see that we
can choose how often (time in mins) the .cpt file is written.
On 10/27/13 11:23 AM, sunyeping wrote:
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
--
发件人：Justin Lemkul jalem...@vt.edu
发送时间：2013年10月27日(星期日) 20:27
收件人：gromacs gmx-users@gromacs.org
主 题：Re: 答复: [gmx-users]
Dear Tsjerk Wassenaar
Very very thanks for your reply.
I used trjconv -pbc mol.
pbc problem was solved only for lipid molecules.
When I see new trajectory by vmd, there are some problesm about drug
molecule.
https://www.dropbox.com/s/xq4s6az17buhvb8/images-2.docx
If I show my system as 4
On 10/27/13 12:05 PM, shahab shariati wrote:
Dear Tsjerk Wassenaar
Very very thanks for your reply.
I used trjconv -pbc mol.
pbc problem was solved only for lipid molecules.
When I see new trajectory by vmd, there are some problesm about drug
molecule.
(Please accept our apologies if you receive multiple copies of this CFP)
#
CALL FOR PAPERS
4th International Workshop on
Model-driven Approaches for Simulation Engineering
part of the Symposium on
Hi GROMACS users
can any body tell me how do I solvate fixed number of molecules in fixed
volume: for example 100 molecule water in 14*14*14 Aungstrom^3 box. eidt conf
and genbox never can do this.
One more question.
Please any body help me on following warning:
WARNING: masses and atomic
On 10/27/13 9:30 PM, Hari Pandey wrote:
Hi GROMACS users
can any body tell me how do I solvate fixed number of molecules in fixed
volume: for example 100 molecule water in 14*14*14 Aungstrom^3 box. eidt conf
and genbox never can do this.
genbox -maxsol 100 will put a block of no more
Hi,
Sorry for the late reply. I have tried all the possibilities with filename
extension as mentioned in the VMD molfile details. As said, VMD uses .crd
or .crdbox filename extensions for reading Amber trajectories. I have tried
with both the options ( ie. with .crd and .crdbox extensions) , but
Hi,
FYI, when I feed the coordinates in '.binpos' format, which I generated
after loading the same '.crd' file to VMD, could able to do the job. What I
infer from this is that the VMD molfile, for reading AMBER '.crd'
trajectories, has made for reading AMBER 7 '.crd' formatted trajectories
which
Dear Chris,
Thanks for your information. It is really helpful to me.
Mingjun
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Christopher Neale [chris.ne...@mail.utoronto.ca]
Sent: Friday, October 25, 2013 8:19 PM
To:
Hi,
Seems plausible, and it's good to know you have the plugins working for at
least one format! The question of whether the plugins are out of step with
the main VMD distribution would be best raised on the VMD mailing list (but
search first!). If you do, you might also suggest that the links in
Not working is too vague a symptom for anyone to guess what the problem
is, sorry.
Mark
On Oct 24, 2013 9:39 AM, Santu Biswas santu.biswa...@gmail.com wrote:
dear users,
I am performing 500ps mdrun in vacuum for
polypeptide(formed
by 10-residues leucine) using
Dear gromacs user,
I am doing umbralla sampling on a protein-ligand system following the gromacs
umbralla sampling turial. It seems that the first five steps go well, and I
select 23 gro files as the starting configurations of adjacent umbrella
sampling windows. However when I use grompp to
Dear gromacs user,
I am doing umbralla sampling on a protein-ligand system following the gromacs
umbralla sampling turial. It seems that the first five steps go well, and I
select 23 gro files as the starting configurations of adjacent umbrella
sampling windows. However when I use grompp to
On 10/26/13 10:45 AM, sunyeping wrote:
Dear gromacs user,
I am doing umbralla sampling on a protein-ligand system following the gromacs
umbralla sampling turial. It seems that the first five steps go well, and I
select 23 gro files as the starting configurations of adjacent umbrella
On Sat, Oct 26, 2013 at 2:07 PM, Santu Biswas santu.biswa...@gmail.comwrote:
Not working is too vague a symptom for anyone to guess what the problem
is, sorry.
Mark
On Oct 24, 2013 9:39 AM, Santu Biswas santu.biswa...@gmail.com
wrote:
dear users,
I am
Hi
Ive been looking for a sample input for a REST simulation but
so far have not been able to find one.
Does anybody have an example to share?
Ive seen the tutorial by Mark which mentions REST but I dont
see this included in the archived examples.
Am I missing something?
Thanks for any help
Hi, all-
Rest essentially scales the solute-solvent interactions, but maintains
the solute-solute interactions. This can be done solely with
Hamiltonian replica exchange, which is in 4.6. It's a bit tricky,
though. We plan on having something that does this automatically in
5.0 or 5.1, but it's
On Sat, Oct 26, 2013 at 06:06:59PM -0400, Michael Shirts wrote:
Hi, all-
Rest essentially scales the solute-solvent interactions, but maintains
the solute-solute interactions. This can be done solely with
Hamiltonian replica exchange, which is in 4.6. It's a bit tricky,
though. We plan on
Hi
I had tried using gromacs-4.6.1 to perform solute tempering. If you go
through terakawa's paper you have to describe the lambdas corresponding to
the temperatures. In your topology file define the params corresponding to
the two end states l=0 and l=1. Then define vdw, bonded and coulomb
Dear Rajat Desikan,
I recently ported the 54A8 to Gromacs format. However I did not have the time
yet to extensively test it or compare it to published results.
I did the porting by hand (the differences between 54A7 and 54A8 are modest),
which is of course more error prone.
I'll send you the
Thank you so much, Djurre.
I will do some tests with protein-membrane systems in mind and share it
with the community. I will see if I can reproduce the results in the 54A8
paper.
On Fri, Oct 25, 2013 at 1:01 PM, Djurre de Jong-Bruinink
djurredej...@yahoo.com wrote:
Dear Rajat Desikan,
I
Hi,
I am relatively new to the gromacs environment and would like to optimize
performance for my mac pro (osx 10.6.8)
with 8 cores (16 in hyper-theading). I´ve read that one can use
the g_tune_pme, i guess with np = 16. Don´t know if using mpirun or gromacs
compiled mpi
would be faster. I guess
Hi everyone!
I'm new to Gromacs and trying to
simulate a membrane system with two walls, one at the bottom of my
box at z=0 and one at the top, using the gromos53a6 forcefield
(GROMACS version 4.5.5).
My testing system consists of a
membrane in the middle, water and sodium ions (40)
unfortunately not. It will be done eventually though: to follow the progress of
that feature, check out: http://redmine.gromacs.org/issues/1346
If you have to do that, there is a patch that I posted on that same redmine
page (posts 8 and 9) to allow this in gromacs 4.0.5.
Chris.
-- original
On Fri, Oct 25, 2013 at 11:19 AM, Tiago Gomes tiagogome...@gmail.comwrote:
Hi,
I am relatively new to the gromacs environment and would like to optimize
performance for my mac pro (osx 10.6.8)
with 8 cores (16 in hyper-theading). I´ve read that one can use
the g_tune_pme, i guess with np =
Dear prof.,
i want install gromacs on a multi-core workstation with a GPU(tesla c2075),
should i install the openmpi or mpich2?
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On Oct 25, 2013, at 4:07 PM, aixintiankong aixintiank...@126.com wrote:
Dear prof.,
i want install gromacs on a multi-core workstation with a GPU(tesla c2075),
should i install the openmpi or mpich2?
If you want to run Gromacs on just one workstation with a single GPU, you do
not need to
Dear Xavier,
2013/10/12 XAvier Periole x.peri...@rug.nl
Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one?
FYI, I tried 10 and 1 and the energy drift is exactly the same.
Similar flags apply to temperature and pressure and I believe might
seriously affect
Hello dears
searching through literature, many cases of LIE method application for BFE
calculation of small molecules are on hand . but I couldn't find any report of
using this method for interaction of small peptides and proteins. I wanted to
know if the protocol prepared in Justin tutorial
On 10/25/13 11:07 AM, Sajad Ahrari wrote:
Hello dears
searching through literature, many cases of LIE method application for BFE
calculation of small molecules are on hand . but I couldn't find any report of
using this method for interaction of small peptides and proteins. I wanted to
know
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