Hello:
Does anybody have any idea how to run g_tune_pme in a cluster? I
tried many times with following command:
g_tune_pme_d -v -s npt_01.tpr -o npt_01.trr -cpo npt_01.cpt -g
npt_01.log -launch -nt 24 log
but it always failed.
Option Type Value Description
Dear ALL:how to install DSSP in Gromacs4.5.7I followed someone replies mail
still can not use do I do right ?DSSP
website-miscellaneous-distribution-dsspold-linux distribution then get
dsspcmbibut Gromacs can not recoginz this index gromacs index is do_dssp ?and
DSSPagain , how to install
On Thu, Apr 26, 2012 at 04:19, mu xiaojia muxiaojia2...@gmail.com wrote:
e.g, I want to make an HN group of both H and N from my 2nd residue,
There are multiple ways to achieve what you want with g_select.
Probably the easiest is
resnr 2 and name H N,
or if you need the atoms in a different
Hi
I am having problems installing gromacs on cygwin using autoconf so I used
cmake instead.
I used the following option with cmake:
cmake GMX_PREFER_STATIC_LIBS=ON ../gromacs-4.5.4
followed by make and make install. Gromacs installed finally without
complaints.
gromacs installs but I
Hi ALL,
I have prepared a step-wise tutorial for running a MD simulation of a GPCR
protein inserted in a lipid bilayer. I sincerely hope it will help people
who are new to such simulations and the GROMACS community in general. This
tutorial is adapted from the membrane protein tutorial prepared
Hi ALL,
I have prepared a step-wise tutorial for running a MD simulation of a GPCR
protein inserted in a lipid bilayer. It can be found at the following URL:
https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial
I sincerely hope it will help people who are new to such simulations and
Hi ALL,
I have prepared a step-wise tutorial for running a MD simulation of a GPCR
protein inserted in a lipid bilayer. It can be found at the following URL:
https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial
I sincerely hope it will help people who are new to such simulations and
hello:
it can find mdrun correctly. and it is only give me the log file as I
mentioned in previous thread.
thank you very much
On 04/26/2012 09:53 AM, Carsten Kutzner wrote:
Hi,
what output does g_tune_pme provide? What is in log and in
perf.out?
Can it find the correct mdrun / mpirun
it seesm to be good.
just one pieces of advices, why not use CHARMM36 for this tutorial ?
since it is the best FF for lipids currently.
On 04/26/2012 11:14 AM, Anirban Ghosh wrote:
Hi ALL,
I have prepared a step-wise tutorial for running a MD simulation of a
GPCR protein inserted in a lipid
Hello Albert,
Thanks.
Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS 4.5.5
provides only the option for CHARMM27 FF and I found that ff43a1 very well
preserves the characters of both the protein as well as the lipids for
fairly long simulation time, hence I used that FF in
You set the environment variable DSSP to the absolute path to your dssp
executable. Then do_sddp can make use of it. Is that clear?
Erik
26 apr 2012 kl. 09.33 skrev 李 麗花:
Dear ALL:
how to install DSSP in Gromacs4.5.7
I followed someone replies mail still can not use
do I do right ?
DSSP
On Apr 26, 2012, at 11:37 AM, Albert wrote:
hello:
it can find mdrun correctly. and it is only give me the log file as I
mentioned in previous thread.
What files are produced by g_tune_pme?
Is there a benchtest.log? Can you cat its contents?
Carsten
thank you very much
On 04/26/2012
Hello Anirban:
thanks for kind comments.
How long did you mean fairly long simulation time ? does 1u ns
belongs to this range? CHARMM36 ff is available in gromacs website and
we can download it and put them into top directory and then it works. It
is not need to make any modification by
yes, here is the contents for it:
:-) G R O M A C S (-:
GRowing Old MAkes el Chrono Sweat
:-) VERSION 4.6-dev-20120423-25c75 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert
Dear colleagues,
I came across a puzzling behaviour when simulating graphene sheets
(periodic in xy).
When running a simulation of just one position restrained graphene sheet
in a large vacuum slab with periodic_molecules=yes and pbc=xyz, I found
a static deformation of the boundaries of
Hello Albert,
Good to know that!
I have carried out simulations using this FF in the range of 600 ns.
Regards,
Anirban
On Thu, Apr 26, 2012 at 3:47 PM, Albert mailmd2...@gmail.com wrote:
Hello Anirban:
thanks for kind comments.
How long did you mean fairly long simulation time ? does
Dear Gromacs users,
I am here requesting your help with regards to the editing of the
OPLS-AA force field, and more specifically, the choice of the atom types.
I have added an entry for the molecule CABP to the .rtp and .hdb files.
I can run pdb2gmx, genbox and editconf without getting any
Hi Anirban:
how many ns/day for your simulations? Did you use PME?
best
Albert
On 04/26/2012 12:59 PM, Anirban Ghosh wrote:
Hello Albert,
Good to know that!
I have carried out simulations using this FF in the range of 600 ns.
Regards,
Anirban
--
gmx-users mailing list
On 4/26/12 7:45 AM, Delmotte, Antoine wrote:
Dear Gromacs users,
I am here requesting your help with regards to the editing of the OPLS-AA force
field, and more specifically, the choice of the atom types.
I have added an entry for the molecule CABP to the .rtp and .hdb files.
I can run
Hello Albert,
On our cluster I usually get around 25-30 ns/day running on 120 cores
(system size around 85K atoms) with PME.
Regards,
Anirban
On Thu, Apr 26, 2012 at 5:28 PM, Albert mailmd2...@gmail.com wrote:
Hi Anirban:
how many ns/day for your simulations? Did you use PME?
best
Hey Thomas,
The rhombic dodecahedron corresponds to the packing of a sphere.
Consequently, the difference in the distance between periodic images
over the shortest diameter and the longest diameter is pretty small.
That means that there isn't really an optimal orientation in a rhombic
-users/attachments/20120426/23d33012/attachment-0001.html
--
Message: 6
Date: Thu, 26 Apr 2012 14:24:53 +1000
From: Mark Abraham mark.abra...@anu.edu.au
Subject: Re: [gmx-users] How to increase the ratio of cell size to
constrain length per error message
Hi,
And even if not all orientations are exactly equal in this respect, bare in
mind that the solute might rotate during the simulation, taking it out of any
optimum.
Erik
26 apr 2012 kl. 14.36 skrev Tsjerk Wassenaar:
Hey Thomas,
The rhombic dodecahedron corresponds to the packing of a
Dear Anirban,
Thanks for the tutorial you have created for the newbies like me to follow.
I wonder the tutorial is only for the GPCRs not applicable for other
membrane proteins?
I also have another question about slecting a lipidbilayer, what is the
criteria is selecting it, for instance popc,
Hi Tsjerk and Erik,
Thanks for the comments. It's strange, because I get different minimum
distance for different orientations of the same protein structure using the
afore-mentioned command lines. I used a single step energy minimization for
speed (em_real.mdp). Below are the outputs of editconf
Hi Thomas,
Apologies, you are right. I was thinking of the distance to the wall.
If the protein is elongated, it will matter in the minimal distance
whether the protein major radius is oriented towards a face or towards
a corner. In addition, the shape of the protein plays a role. Yet it
doesn't
On 26/04/2012 10:47 PM, PAVAN PAYGHAN wrote:
Dear Mark,
Thanks a lot for the reply and highlighting the cause of error that I
was facing.
Still can it be possible to overcome the same error with the available
facility.
Unfortunately you're forcing me to guess the context for this
Dear All:
I am simulating a complex of protein and ligand, however, the ligand is
covalent bound to the protein. I have calculated the charges of the ligand and
the non-standard residue by QM method and trying to use the bond parameters in
the GROMOS force field. However, I don't know how to
Hi all,
I am carrying out energy minimization on bulk polymer system (N~2) with
integrator = l-bfgs in double precision gromacs 4.5.5. I am using
tabulated force-fields for bonded, and non-bonded interactions. In the
force field, the coulombic interaction is set to zero, hence, the output is
Hello all,
This is in reply to Michael shirts a while ago on a FEP of a R-CH3 to
an R-H group. Below is the orignal email. I recently tested out
mutating a CH3-CH3-(3dummy atoms) molecule on both sides in order to
test out that a peturbation would give you a total of 0. forcefield
used was
Dear Justin,
Many thanks for your response. I managed to reduce the number of errors
by trying other atom types, by looking at what seemed most likely to be
right from the ffnonbonded.itp and ffbonded.itp files.
Unfortunately, I did not manage to find a combination that both made
some
On 4/26/12 10:23 AM, mirc...@sjtu.edu.cn wrote:
Dear All:
I am simulating a complex of protein and ligand, however, the ligand is
covalent bound to the protein. I have calculated the charges of the ligand
and the non-standard residue by QM method and trying to use the bond
parameters in the
On 4/26/12 11:00 AM, Yongchul Chung wrote:
Hi all,
I am carrying out energy minimization on bulk polymer system (N~2) with
integrator = l-bfgs in double precision gromacs 4.5.5. I am using tabulated
force-fields for bonded, and non-bonded interactions. In the force field, the
coulombic
On 4/26/12 11:37 AM, Delmotte, Antoine wrote:
Dear Justin,
Many thanks for your response. I managed to reduce the number of errors by
trying other atom types, by looking at what seemed most likely to be right from
the ffnonbonded.itp and ffbonded.itp files.
Unfortunately, I did not manage to
Thank you very much for your answer. This has been very helpful. I think
I will follow your advice and try to find similar molecules to find the
parameters.
Could I just ask you if you know of a database where I could look for
the opls parameters which have calculated for other molecules?
On 4/26/12 12:15 PM, Delmotte, Antoine wrote:
Thank you very much for your answer. This has been very helpful. I think I will
follow your advice and try to find similar molecules to find the parameters.
Could I just ask you if you know of a database where I could look for the opls
parameters
On 4/26/12 12:36 PM, Yongchul Chung wrote:
Well, actually it has a meaning in the simulation that I am carrying out.
Ah, I remember a discussion about this some time ago and was recalling the wrong
side of it ;) What you're doing is relying on the virial to dictate the
pressure then.
Dear All,
I am using CG-MD using MARTINI forcefield. The system contains Protein and
lipid bilayer. Although I used:
define = -DPOSRES
components in system were moving around and interact with each other. Then,
I cannot do NVT or NPT equilibration.
Could you please let me know how can I control
On 4/26/12 1:35 PM, Dariush Mohammadyani wrote:
Dear All,
I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid
bilayer. Although I used:
define = -DPOSRES
components in system were moving around and interact with each other. Then, I
cannot do NVT or NPT
Greetings,
I am trying to do electrostatics calculations for a protein system which
requires knowledge of the average dipole vector for an experimental probe.
I've previously obtained this average dipole vector by using umbrella sampling
with WHAM over the chi_2 dihedral angle of this probe,
Thanks dear Justin.
No, the protein is moving in right direction, but I am going to restrain
any changing the position and then monitory these movements during MD run.
I could see the Pos. Res. works in md.log file.
Regards,
Dariush
On Thu, Apr 26, 2012 at 1:38 PM, Justin A. Lemkul
I configure Amber1.5 and installed the Acpype compatible (the tests went
pretty well)
BUT when I tried to submit my own job by the line
acpype -i proteinname.mol2 -c user
i got the message:
==
=
|
On 4/26/12 1:59 PM, Dariush Mohammadyani wrote:
Thanks dear Justin.
No, the protein is moving in right direction, but I am going to restrain any
changing the position and then monitory these movements during MD run.
I could see the Pos. Res. works in md.log file.
Then I don't understand what
Hi Guys,
I have done the simulation. The total steps is 500. At around 90 steps,
the error information appear like the followings.
Please give me some suggestions to fix it.
Best wishes,
Desheng
--
Program mdrun, VERSION 4.5.5
I suppose I can calculate virial manually ... but thought there might be a
glitch in the code when making a transition from 4.0 to 4.5. I sent an
e-mail to gmx-developers.
Greg
On Thu, Apr 26, 2012 at 1:00 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 4/26/12 12:36 PM, Yongchul Chung wrote:
On 4/26/12 2:52 PM, Desheng Zheng wrote:
Hi Guys,
I have done the simulation. The total steps is 500. At around 90 steps,
the error information appear like the followings.
Please give me some suggestions to fix it.
Based on the comment that precedes the error call in the code:
Dear users,
In GROMACS, does CHARMM36 ff, calculate eventual 1-4 interactions that are
absent from the [pairtypes] section of the ffnonbonded.itp file?
I ask this because I'm converting cholesterol parameters from CHARMM36c to gmx
format, and several 1-4 values are absent in the last two
On 4/26/12 3:30 PM, Desheng Zheng wrote:
Thanks Justin!
about the Software inconsistency error: Inconsistent DD boundary staggering
limits!
I still have three concerts.
1. Is it ok, if i use grompp to generate the edr file in gromacs 4.5.5
environmentwith the gro file and top file which
Thanks for the reply!
On Thu, Apr 26, 2012 at 3:28 AM, Teemu Murtola teemu.murt...@cbr.su.sewrote:
On Thu, Apr 26, 2012 at 04:19, mu xiaojia muxiaojia2...@gmail.com wrote:
e.g, I want to make an HN group of both H and N from my 2nd residue,
There are multiple ways to achieve what you want
Thanks Justin!
about the Software inconsistency error: Inconsistent DD boundary staggering
limits!
I still have three concerts.
1. Is it ok, if i use grompp to generate the edr file in gromacs 4.5.5
environmentwith the gro file and top file which were builed under Gromacs
4.0.7 ?
2. In
http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
Looks I got to the party late (at a conference with limited time to do emails).
As a shameless self-plug, we recently published a soup-to-nuts protocol paper
for GPCR + POPC + ligand in Gromacs 4.5.x and CHARMM27/36/CGenFF.
Our timescales are on the order 100+ns.
20ns/day is possible on 100K
Hello Bala,
Yes, exactly as Justin said it represents just a workflow where a GPCR
protein (here B2AR) has been taken as an example. I mentioned it as a GPCR
tutorial because many often inquire about GPCR MD simulations only in the
forum. But it can be adapted for other membrane proteins as well.
Respected sir,
While i am running the gromacs software i am getting the
following error.Kindly tell me how to over come the error.
Fatal error:
Atom HA in residue LYS 1 was not found in rtp entry LYSH with 15 atoms
while sorting atoms.
SURYANARAYANA SEERA,
PhD student
--
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