Hi
You should compile your fftw with --enable-shared if you want to link
your gromacs installation to shared libraries (which is the default in
the latest versions). Check the installation instructions in the website.
Javier
El 11/01/12 08:20, Anik Sen escribió:
Im having problems
Dear prof.
I used a piece of python code that reverses a trajectory named xtcrev.py
((c)2011 Tsjerk A. Wassenaar), I have one problem when I ran it as following:
./xtcrev.py 1a.xtc 1a-rev.xtc
it's error is:
Traceback (most recent call last):
File ./xtcrev.py, line 54, in module
n = 92
Dear gromacs users,
I have a problem regarding the simulation of Fe4S4 cluster attached to CYS of a
protein using opls ff. I editted the aminoacids.rtp file as like this.
[ SF4 ]
... [ atoms ]
FE1 opls_966 2.500 1
FE2 opls_967 2.500 1
FE3 opls_968 2.500 1
FE4 opls_969 2.500 1
S1 opls_970 -2.000
Hi Mark,
Please, I did not state that the groups should be coupled separately.
I suggested checking the temperatures of the subgroups of a combined
T-coupling group. So 'moot ..., because T-coupling group ...' is not
really in place.
Cheers,
Tsjerk
On Wed, Jan 11, 2012 at 6:29 AM, Mark Abraham
Hi Sara,
That can only happen if the input file is empty.
But I now see that the output file should be given as second argument,
so it should be
./xtcrev.py input.xtc output.xtc
rather than
./xtcrev.py input.xtc output.xtc
The latter will actually result in an empty xtc file. Maybe that's
Dear List
I'm newbie to gromacs (sigh). I'm simulating the interaction between two
proteins(chrystallographic structures) following the spider toxin tutorial.
I'm able to correctly minimize ( E1000) and equilibrate (400 ps ) the
system. No error message appears to me and I'm quite sure that my
Hi Tsjerk,
Thank you very much from your reply. Yes, you're right, I corrected that, but
now it gave me this error:
Traceback (most recent call last):
File ./xtcrev.py, line 68, in module
o = open(sys.argv[2],w)
IndexError: list index out of range
May I ask you to help me, please?
Hi Sara,
If you give two arguments, it shouldn't do that. './xtcrev.py
input.xtc output.xtc' should work fine. Of course I could've clogged
the script with checking the number of input files and such, and maybe
I will later, but for now it's just a nifty hack :p
Cheers,
Tsjerk
On Wed, Jan 11,
Hi,
running a md simulation with the same tpr file ( using Gromacs 4.5.3 ) on three
different platforms ( A: HP xw8600 Workstation; B: PC with Intel CORE 2 DUO
processor; C: IBM Power6 cluster ), I obtained the following results:
on A and B platforms the run is fine,
on C the run crashes at
Hi Tsjerk,
Thank you very very much from your help about xtcrev.py script, I did it till
end according to you said me before, but unfortunately my first problem about
view of 2 micelles was not solved and monomers are dispersed during
simulation!!! I don't know why!!!
You helped me very much
Hi Sara,
You have to understand what is happening. You don't have a static
system. Using -pbc nojump, in combination with xtcrev.py may help you
get a view in which the molecules seem to settle on a specific view or
clustering of your systems, in which you have the micelles. But they
will be
For checking the id of the last frame contained
in a trajectory, I usually apply ugly command line
hacks like:
echo 0|trjconv -dump 1e10 -o /tmp/x.gro 21/dev/null|perl -lne 'print $1
if /t=(\d+)$/'
which might look awe-inspiring first but is of course tiresome.
Did I overlook the appropriate
On 11/01/2012 8:16 PM, Tsjerk Wassenaar wrote:
Hi Mark,
Please, I did not state that the groups should be coupled separately.
I suggested checking the temperatures of the subgroups of a combined
T-coupling group. So 'moot ..., because T-coupling group ...' is not
really in place.
Right,
I have already done that but the problem persisits.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Javier Cerezo [j...@um.es]
Sent: Wednesday, January 11, 2012 1:56 PM
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] (no
On 11/01/2012 6:15 PM, Dialing Pretty wrote:
Dear All,
I am trying to install GROMACS 455. I got a series of error message in
the MAKE step. Will you please take a look at the following MAKE
screen file to see on how to make the installation successful?
You should provide the command lines
Dear all:
I want to do a simulation using a dimer, but the system is connected by 2
disulfide bonds between A-chain and B-chain. I have produced topology file for
protein with pdb2gmx using AMBER99SB forcefield. In order to bond disulfide
bonds I using flag -ss. If I do not delete the TER
On 11/01/2012 5:27 PM, Nirmal Prasad wrote:
Dear Mark,
I am facing problem in creating Heme topology...prodrg server is
showing error ,
This is a GROMACS mailing list, so we're generally unable to help with
that. We certainly can't help if you don't tell us details about the error.
can
On 11/01/2012 10:11 PM, Xianwei Wang wrote:
Dear all:
I want to do a simulation using a dimer, but the system is connected
by 2 disulfide bonds between A-chain and B-chain. I have produced
topology file for protein with pdb2gmx using AMBER99SB forcefield. In
order to bond disulfide bonds I
Dear all:
I want to do a simulation using a dimer, but the system is connected by 2
disulfide bonds between A-chain and B-chain. I have produced topology file for
protein with pdb2gmx using AMBER99SB forcefield. In order to bond disulfide
bonds I using flag -ss. If I do not delete the TER
On 11/01/2012 10:07 PM, Anik Sen wrote:
I have already done that but the problem persisits.
Get a clean tarball of FFTW3 and follow
http://www.gromacs.org/Downloads/Installation_Instructions#Details_for_building_the_FFTW_prerequisite.
Probably you have a mess of previous configure commands,
On 11/01/2012 9:32 PM, Mirco Wahab wrote:
For checking the id of the last frame contained
in a trajectory, I usually apply ugly command line
hacks like:
echo 0|trjconv -dump 1e10 -o /tmp/x.gro 21/dev/null|perl -lne
'print $1 if /t=(\d+)$/'
which might look awe-inspiring first but is of
On 11/01/2012 9:18 PM, Ester Chiessi wrote:
Hi,
running a md simulation with the same tpr file ( using Gromacs 4.5.3 )
on three different platforms ( A: /HP xw8600 Workstation; B: PC with
//Intel CORE 2 DUO processor; C: /IBM Power6 cluster ), I obtained the
following results:
on A and B
On 11/01/2012 8:35 PM, Guido Leoni wrote:
Dear List
I'm newbie to gromacs (sigh). I'm simulating the interaction between
two proteins(chrystallographic structures) following the spider toxin
tutorial. I'm able to correctly minimize ( E1000) and equilibrate
(400 ps ) the system. No error
Dear Users,
Am running a shell script for the command g_mindist=
#!/bin/bash
groups=`grep ^\[ -o index.ndx | wc -l`
for ((i=0; i$groups; i++))
do
echo $((i++)) 3393 | g_mindist -f md.xtc -s md.tpr -od $i.xvg -o
atm-pair$i.out -d 0.8 -e 5000 -n index.ndx
done
here the index file has 3393
On 11/01/2012 7:14 PM, Suman Nandy wrote:
Dear gromacs users,
I have a problem regarding the simulation of Fe4S4 cluster attached to
CYS of a protein using opls ff. I editted the aminoacids.rtp file as
like this.
[ SF4 ]
... [ atoms ]
FE1 opls_966 2.500 1
FE2 opls_967 2.500 1
FE3 opls_968
Anik Sen wrote:
Dear nirmal,
try prodrg server for generating the topology file
for the said pdb file. Here is the link.
http://davapc1.bioch.dundee.ac.uk/prodrg/
PRODRG will be unable to handle this type of molecule, since it contains iron.
What's more, PRODRG
use -chainsep interactive option in pdb2gmx.
Suman
On Wed, 11 Jan 2012 16:42:12 +0530 wrote
Dear all:
I want to do a simulation using a dimer, but the system is connected by 2
disulfide bonds between A-chain and B-chain. I have produced topology file for
protein with pdb2gmx using AMBER99SB
You need to post how did you exactly installed fftw and gromacs in order
to get more help. It seems to me that the problem is related to the
shared fftw libraries. Could you compile the gromacs binaries with
--disable-shared?
Javier
El 11/01/12 12:07, Anik Sen escribió:
I have already done
Dear Mr Suman:
Thank you very much for your help !
Sincerely yours
Xianwei Wang
At 2012-01-11 19:42:24,Suman Nandy nandy.su...@rediffmail.com wrote:
use -chainsep interactive option in pdb2gmx.
Suman
On Wed, 11 Jan 2012 16:42:12 +0530 wrote
Dear all:
I want to do a simulation using a dimer,
Hi Tsjerk,
I have a good news!!! That was corrected!!!
Thank you very much from your help.
Best Regards
Sara
From: Tsjerk Wassenaar tsje...@gmail.com
To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Sent:
Dear all,
my colleague would like to calculate free energy profile for a single
virtual particle in 2D case given the arbitrary analytical potential
defined in x and y positions of the particle.
Is it possible to calculate such special simulation in Gromacs? Or how
Gromacs should be hacked to be
Dear GMX users,
I am trying to compile templete.c in template directory of gromacs-.4.5.3.
However, when I type make, I got the following errors with termination of
compiling:
gcc -L/home/h1y//lib -L/home/h1y/fftw3s/lib -o template template.o -lmd
-lgmx -lfftw3f -lxml2 -lnsl -lm
Dear Gromacs users,
I defined tree beads for aniline consists of SC4, SC4 and SNd as following:
[moleculetype]
; molname nrexcl
DRG 1
[atoms]
; id type resnr residu atom cgnr charge
1 SNd 1 DRG NH2 1 0
2 SC4 1 DRG
Dear All,
I've been reading the manual (v4.5.4) and could use a small amount of
clarification. On p117 it says:
pdb2gmx sets the number of exclusions to 3, which means that
interactions between atoms connected by at most 3 bonds are excluded.
Pair interactions are generated for all pairs of
Hi,
I am trying to run a REMD of a peptide. But while executing the following
command after nvt and npt equilibration , I am getting the following error:-
mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot
enable
Dear all,
Has anyone here have idea on how one can compute heat of mixing for a
binary mixture? Thank you. :)
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On 12/01/2012 11:54 AM, bharat gupta wrote:
Hi,
I am trying to run a REMD of a peptide. But while executing the
following command after nvt and npt equilibration , I am getting the
following error:-
mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
mdrun_mpi: error while loading shared
Dear Sir,
I want to unscribe there emails, thank.
Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
--- 12年1月12日，周四, Mark Abraham mark.abra...@anu.edu.au 写道：
On Thursday 12,January,2012 09:36 AM, yp sun wrote:
Dear Sir,
I want to unscribe there emails, thank.
http://lists.gromacs.org/mailman/listinfo/gmx-users
at the bottom, fill in your email address and click Unsubscribe.
Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology Immunology
On Thursday 12,January,2012 08:54 AM, bharat gupta wrote:
Hi,
I am trying to run a REMD of a peptide. But while executing the
following command after nvt and npt equilibration , I am getting the
following error:-
mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
mdrun_mpi: error while
Thanks for the advice I re-complied everything again with static libraries
and the installation went fine. But while executing the following command I
am again getting error :-
mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 500 -v
Fatal error:
The number of nodes (1) is not a multiple of
On 12/01/2012 5:29 PM, bharat gupta wrote:
Thanks for the advice I re-complied everything again with static
libraries and the installation went fine. But while executing the
following command I am again getting error :-
mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 500 -v
Fatal error:
hello sir,
I did dynamics for 5ns for my protein. i submitted my run in cluster.. i
got my output.. when i go for rmsd and gyrate analysis i got plot for only
1.2ns out of 5ns..
i dono what is the problem..
is this because of low runtime in cluster..
even i gave 200hours in cluster..
i
fftw-3.3 installation:
first gone to the fftw3.3 folder
./configure --enable-threads --enable-float --enable-sse --enable-shared
--prefix /home/ganguly/Gromacs/fftw3.3
.
.
.
make
.
.
.
make install
Then gromacs 4.5.5 is being installed.
installation:
first gone to the gromacs-4.5.5 folder
On 12/01/2012 5:45 PM, bharat gupta wrote:
It says that The number of cores must be a multiple of the number of
replicas (given with |-multi|, which must equal the number of .tpr
http://www.gromacs.org/Documentation/File_Formats/Topology_%28.tpr%29_File
files i.e., 10 for the above general
On 12/01/2012 5:44 PM, Anik Sen wrote:
fftw-3.3 installation:
first gone to the fftw3.3 folder
./configure --enable-threads --enable-float --enable-sse
--enable-shared --prefix /home/ganguly/Gromacs/fftw3.3
.
.
.
make
.
.
.
make install
Then gromacs 4.5.5 is being installed.
installation:
On 12/01/2012 5:39 PM, priya thiyagarajan wrote:
hello sir,
I did dynamics for 5ns for my protein. i submitted my run in cluster..
i got my output.. when i go for rmsd and gyrate analysis i got plot
for only 1.2ns out of 5ns..
i dono what is the problem..
is this because of low runtime in
The command I used this time :-
mdrun_mpi mdrun -s prefix_.tpr -multi 5 -replex 100
Here's the error that I got :-
Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (5)
For more information and tips for troubleshooting, please check the GROMACS
website at
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