> > "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"
> wrote:
> >
> > > dear users,
> > >
> > > I am performing 500ps mdrun in vacuum for
> > polypeptide(formed
> > > by 10-residues leuci
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?
--
gmx-users mailing listgmx-users@gromacs.or
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"
wrote:
dear users,
I am performing 500ps mdrun in vacuum for
polypeptide(formed
by 10-residues leu
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 t
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 (pdb2
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
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 counter ions in to my sys
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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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gm
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 a
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 (solvat
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=parmbsc0&ns=main&path=) is
the parmbsc0 force field.
Please help me
Sincerely
Kiana
--
gmx-
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 wrote:
> 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 run
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=parmbsc0&ns=main&path=) is
the parmbsc0 for
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 unfolded
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 , 1
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 gives me 444.5 which is correct but when I run the
script
editconf -c -f A.gro
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 md_
Aah yes of course. Thanks James.
On Mon, Oct 28, 2013 at 3:16 PM, 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 submit script for job 4
> w
You're welcome
On 28 Oct 2013, at 20:03, Pavan Ghatty wrote:
> Aah yes of course. Thanks James.
>
>
>
> On Mon, Oct 28, 2013 at 3:16 PM, 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
>>
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 coulom
On Mon, Oct 28, 2013 at 7:56 PM, Xu Dong Huang wrote:
> 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 (den
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 bette
On Mon, Oct 28, 2013 at 7:53 PM, Pavan Ghatty wrote:
> 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 suggested -maxh, so you ca
On Mon, Oct 28, 2013 at 8:04 PM, Hari Pandey 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 gives me 444.5 w
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 wrote:
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 name
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 sit
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