Dear All,
I want to opt for the rhombic dodecahedron box in my simulation of a
protein. I am using the following command to select the type of the
box
editconf -f test.gro -o test_box.gro -c -d 1.2 -bt dodecahedron
but after this if I'm seeing this protein system within the box in VMD
but its
On 17/07/2012 4:16 PM, tarak karmakar wrote:
Dear All,
I want to opt for the rhombic dodecahedron box in my simulation of a
protein. I am using the following command to select the type of the
box
editconf -f test.gro -o test_box.gro -c -d 1.2 -bt dodecahedron
but after this if I'm seeing this
Dear Gmx-users,
I created a box size 4 4 2 and named layer.gro. Then genconf was
used to doulble this box:
genconf -f layer.gro -o 2layers.gro -nbox 1 1 2 -dist 0 0 8
However, the copied box has the same direction as the original box.
Could you please help me to rotate 180 degrees the copied one?
HELLO
I want simulate gold-protein complex by Golp forcefield. but when I use pdb_gmx
I came across this error There is a dangling bond at at least one of the
terminal ends and the force field does not provide terminal entries or files.
Edit a .n.tdb and/or .c.tdb
file.
PLEASE HELP ME
Dear all,
I am running a 9000 atom system with GBSA (Gromacs 4.5.5) in a
Blue Gene/Q cluster. I got the speed 1.002 ns/day with 8 cores.
However, in my own workstation with 8 cores the same system can reach
nearly 10 ns/day (Intel(R) Xeon(R) CPU E5620 @ 2.40GHz). Can anyone
tell me what's
Hi Justin,
I have the following Notes during NPT equilibration.
NOTE 1 [file pr_NPT.mdp]:
nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 2 [file pr_NPT.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
On 17/07/2012 4:32 PM, cuong nguyen wrote:
Dear Gmx-users,
I created a box size 4 4 2 and named layer.gro. Then genconf was
used to doulble this box:
genconf -f layer.gro -o 2layers.gro -nbox 1 1 2 -dist 0 0 8
However, the copied box has the same direction as the original box.
Could you please
On 17/07/2012 5:00 PM, DeChang Li wrote:
Dear all,
I am running a 9000 atom system with GBSA (Gromacs 4.5.5) in a
Blue Gene/Q cluster. I got the speed 1.002 ns/day with 8 cores.
However, in my own workstation with 8 cores the same system can reach
nearly 10 ns/day (Intel(R) Xeon(R) CPU
Dear cuong nguyen..
I think use following commands.
Try editconf -rotate for rotaion angle along axis
along these use -center co-ordinate if you want to place canter of
box at particular position
Try editconf -translate For translation along axis
On Tue, Jul 17, 2012 at 2:07 PM, Mark
--
Message: 8
Date: Tue, 17 Jul 2012 18:40:05 +1000
From: Mark Abraham mark.abra...@anu.edu.au
Subject: Re: [gmx-users] why Blue Gene/Q is so slow?
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 500524e5.9050...@anu.edu.au
Content-Type:
On 7/17/12 4:05 AM, J Peterson wrote:
Hi Justin,
I have the following Notes during NPT equilibration.
NOTE 1 [file pr_NPT.mdp]:
nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
http://manual.gromacs.org/online/mdp_opt.html#out
Dear All,
I rephrase my question (for the original see below).
Is there any (easy) way to give gromacs (mdrun -rerun) accurate coordinates for
a single point calculation (to get accurate energy and forces)?
The accuracy of .pdb and .gro formats is not sufficient and .g96
format reading seems to
Hello,
I've been trying some time now to run a QMMM calculation with gromacs and
orca on a system of 5000 atoms with the QM system being ~300 atoms.
Setting up the calculation with bOpt = yes and 1 minim step in the .mdp file
produces some problems.
Orca does the calculation without taking
On 7/17/12 7:16 AM, Markus Kaukonen wrote:
Dear All,
I rephrase my question (for the original see below).
Is there any (easy) way to give gromacs (mdrun -rerun) accurate coordinates for
a single point calculation (to get accurate energy and forces)?
The accuracy of .pdb and .gro formats is
I have the following Notes during NPT equilibration.
NOTE 1 [file pr_NPT.mdp]:
nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 2 [file pr_NPT.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
What do
Dear gmxers,
I am trying to generate one polymer melt from one big enough box using
NPT MD in gmx. I find that the density of system varies very slow.
Could you please give me some hints about how to speed up this
process? Thanks a lot for any reply.
Yours sincerely,
Chaofu Wu.
--
gmx-users
Well,
the problem was solved at the end, please don't bother answering.
Following the advise of one of the Orca developers, Christoph, I changed
QMMMscheme to normal instead of ONIOM and disabled periodic boundary
conditions.
Now the files are extracted normally.
for further reference, one
Dear all,
I have a question about internal bond interactions within a molecule.
I understand that 1-4 interactions can be scaled with nbfunc. But I wonder:
1. What is the default for 1-5 and larger interactions in Gromacs? Are the LJ
and charge interactions included (i.e., not scaled)? I'm
A variabvle thermostat that increases from 180 K to 300 K over cycles of
100-1
Original-Nachricht
Datum: Tue, 17 Jul 2012 20:40:12 +0800
Von: Wu Chaofu xiaowu...@gmail.com
An: gmx-users@gromacs.org
Betreff: [gmx-users] How to speed up equilibrating the density of bulk
On 17/07/2012 7:06 PM, DeChang Li wrote:
--
Message: 8
Date: Tue, 17 Jul 2012 18:40:05 +1000
From: Mark Abraham mark.abra...@anu.edu.au
Subject: Re: [gmx-users] why Blue Gene/Q is so slow?
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
Convert the .g96 file to .trr format. Double precision may be necessary and
will certainly give the greatest possible accuracy.
-Justin
I try
trjconv -f gromacs.g96 -o test.trr
and get
Program trjconv, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/trxio.c, line: 693
Fatal
On 7/17/12 12:51 PM, Markus Kaukonen wrote:
Convert the .g96 file to .trr format. Double precision may be necessary and
will certainly give the greatest possible accuracy.
-Justin
I try
trjconv -f gromacs.g96 -o test.trr
and get
Program trjconv, VERSION 4.5.5
Source code file:
Hi,
You can scale the system with editconf to some density and energy
minimize, and equilibrate 1000 steps or so in NVT. Do this with small
scaling factors, repeating until tje density is correct. You might
want to run at a relatively high temperature.
Cheers,
Tsjerk
On Tue, Jul 17, 2012 at
Hi all,
I have a system that consists of two distinct reservoirs filled with
water+NaCl connected by a CNT. I want to measure the average number of
hydrogen bonds per water in each reservoir as a function of time, but
my current workflow for this is far too time-consuming to get any
significant
On 7/17/12 4:37 PM, Alex Marshall wrote:
Hi all,
I have a system that consists of two distinct reservoirs filled with
water+NaCl connected by a CNT. I want to measure the average number of
hydrogen bonds per water in each reservoir as a function of time, but
my current workflow for this is
Hi Justin,
I am just curious, do you have experience writing such a shell script to
iterate over the index files (one per frame)? I am just curious, because I
have been trying this, and I have found it very difficult to do using bash.
Do you use a different shell language?
Also, I wonder if
On 7/17/12 4:57 PM, Andrew DeYoung wrote:
Hi Justin,
I am just curious, do you have experience writing such a shell script to
iterate over the index files (one per frame)? I am just curious, because I
have been trying this, and I have found it very difficult to do using bash.
Do you use a
Thanks Justin, this is great.
On Tue, Jul 17, 2012 at 5:07 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/17/12 4:57 PM, Andrew DeYoung wrote:
Hi Justin,
I am just curious, do you have experience writing such a shell script to
iterate over the index files (one per frame)? I am just
Hi,
I tried again simulating the same peptide with OPLS FF for 2000 ns time
duration. I used VMD for the secondary structure analysis and trajectory
visualization. This time I was able to get folding events but the residues
that are should be beta strands were helical for most of the time during
and this did not happen with EM?
Did you add new atoms/FF parameters to the existing C36 set?
On 2012-07-13 02:05:47AM -0700, Shima Arasteh wrote:
Dear gmx users,
My system is composed of a protein and water. I am working with CHARMM36 and
the current version of Gromacs, 4.5.5.
For
I added a new residue by using defined atom types.
I did not get this error with EM. This error happened when I just entered the
command of #deffnm NVT.
Thanks in advance.
Sincerely,
Shima
From: Peter C. Lai p...@uab.edu
To: gmx-users@gromacs.org
Sent:
Has anyone been recently using the coupling feature of mdrun for
parameterising? I used it many versions ago and have just been trying to use
it today with 4.5.5, however I can't get it to work as it did previously.
Currently you can't couple more than one set of charges (seems a bit weird
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