Hi all
I have a single machine with multilpe processors. I want run mdrun with 8
processors and I use the options
% mdrun – np 8 -s toppl.tpr -v -N 8
I see in the system monitor that just one procesor is running, if I use
%mdrun_mpi -np 8 -s topol.tpr -v -N 8
I see the same in the system
Hi,
I am running simulations of gaseous molecules (CH4, C2H6, CO2, N2) in
a silica pore (4nm in diameter), cell dimensions, 46 x 44 x 37. This
in an infinite pore in the z direction.
I am interested in looking at diffusion but I am a bit concerned about
the shape of my MSD curves, for a 5
I am trying to run grompp using a pdb file of DNA duplex, a sucessfully
generated topology, and the steep.mpd from
http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/build.html#top
I am getting the fatal error:
Fatal error:
[ file spc.itp, line 37 ]:
Atom index (1) in bonds out of bounds (1-0).
Th
Dear Friends,
I have to make three covalent bonds between the protein and the heme group.
I have parameters for heme and the residues.
Do I have to make as if everything belongs to the same molecule? (as
it realy is)
Has anyone done something like this?
Thanks
Alberto
Dear GMXers,
For long time, I have had a puzzle: while the top file generally describe
interactions in a molecule, intermolecular interactions are not explicitly in
the top file. How are these intermolecular interactions described in GROMACS?
Thanks a lot for any reply.
Sincerely,
C
The group PROTEIN isn't very large as the group NONPROTEIN, therefore its
total kinetic energy fluctuates more.
--Omer.
On Wed, Sep 16, 2009 at 12:10, Stephane Abel wrote:
> tc-grps = Protein Non-Protein ; two coupling groups - more accurate
> tau_t = 0.4 0.4 ; time constant, in ps
> ref_t = 310
wuxiao wrote:
Dear GMXers,
For long time, I have had a puzzle: while the top file generally
describe interactions in a molecule, intermolecular interactions are not
explicitly in the top file. How are these intermolecular interactions
described in GROMACS? Thanks a lot for any reply.
S
Jarol E. Molina wrote:
Hi all
I have a single machine with multilpe processors. I want run mdrun with
8 processors and I use the options
% mdrun – np 8 -s toppl.tpr -v -N 8
I see in the system monitor that just one procesor is running, if I use
%mdrun_mpi -np 8 -s topol.tpr -v -N 8
I see
Original Message
Subject:free energy calculation
Date: Wed, 16 Sep 2009 11:34:25 -0400
From: Elio Cino
To: sp...@gromacs.org
Hello. Dr. van der Spoel. I have been waiting for an account to be made
on gmx-users so that i can post. Until the account is made, I
Hello everyone,
I have been struggling to find a way to supply initial coordinates and
initial velocities to a molecule like pentane. I want to add about 2500
molecules of pentane to a box, but all these molecules must have initial
positions and velocities. I have used ghemical to draw t
Dear GROMACS Gurus,
In order to correctly model an infinite graphene sheet using periodic
boundary conditions, should the box edges be located at the midpoints
between the atomic bonds?
Thanks.
Darrell
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Gunnar Widtfeldt Reginsson wrote:
I am trying to run grompp using a pdb file of DNA duplex, a sucessfully
generated topology, and the steep.mpd
from http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/build.html#top
I am getting the fatal error:
Fatal error:
[ file spc.itp, line 37 ]:
Atom i
You need to run MPI jobs with 'mpirun'. The correct command would be
mpirun -np 8 mdrun -s topol.tpr
(I don't know what the -N 8 does).
Sander
On 16 Sep 2009, at 18:03 , Jarol E. Molina wrote:
Hi all
I have a single machine with multilpe processors. I want run mdrun
with 8 processors and
Gunnar Widtfeldt Reginsson wrote:
I am trying to run grompp using a pdb file of DNA duplex, a sucessfully
generated topology, and the steep.mpd
from http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/build.html#top
I am getting the fatal error:
Fatal error:
[ file spc.itp, line 37 ]:
Atom ind
Is the RMSD given by g_energy -f -f2 in Joule or KJoule?
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Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (
Problem is solved. The atom needed to be called O not O2.
Thanks,
On Tue, Sep 15, 2009 at 11:29 PM, Justin A. Lemkul wrote:
>
>
> Gunnar Widtfeldt Reginsson wrote:
>
>> Hi. Can someone please help me.
>>
>> I am new to Gromacs. I have a 20mer DNA duplex I want to do some MD on. I
>> start by mak
Just a work-around, force mpicc to point to cc.
alias mpicc=cc
Yang Ye
On Wed, Sep 16, 2009 at 5:35 PM, Mu Yuguang (Dr) wrote:
> No, even I do not use mpi , the error is still there.
>
>
>
> Regards
>
> Yuguang
>
>
> --
>
> *From:* gmx-users-boun...@gromacs.org [m
Hi,
In Linux, one can apparently set processor affinity (or, in this case
core affinity) with 'taskset'. The command is used like this:
taskset command
where is a hexadecimal bit mask with the cpus to use (in a
format like 0xff, where 0xff enables the first 8 cpus on a system).
For mdr
wuxiao wrote:
> Dear GMXers,
>by looking through the manual, I find that the tabluated interaction
> functions seem very flexible for performing MD simulations. But some
> questions puzzle me too much:
> for bonded interactions, as for bonds, angles, dihedrals, the f'(x)
> are the derivati
Lum Ngwagia wrote:
Hello everyone,
I have been struggling to find a way to supply initial
coordinates and initial velocities to a molecule like pentane. I want to
add about 2500 molecules of pentane to a box, but all these molecules
must have initial positions and velocities. I have
ds,
Yang Ye
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http:/
That is nearly correct.
For a single 4-core Intel Core I7 cpu, the first 4 cpu's (as well as the last 4)
cover all 4 physical cores.
Therefore the command line (under Linux) is:
mpirun -np 4 taskset 0xf mdrun
But you get 15% more performance using 8 processes (if your system is not too
small):
mp
Yes, you must put the heme and the protein in the same topology file (or
.itp file). The problem is you can only make bonds (angles, etc) between
atoms which are in the same [ moleculetype ] section.
Best is to write a simple script which merges the two topologies
together. You must only be aware t
Hi Darrell,
No, you just have to make sure that the bond lengths are correct in
the periodic system. The PBC are invariant under translation.
Cheers,
Tsjerk
On 9/17/09, Darrell Koskinen wrote:
> Dear GROMACS Gurus,
> In order to correctly model an infinite graphene sheet using periodic
> boun
Look in the manual for 'genbox', with this tool you can make a box with
as many molecules you like.
For the velocity generation look under *surprise* 'Velocity generation'.
The manual is your friend, look in it.
Greetings
Thomas
>
> Hello everyone,
>
>I have been struggling to find a way
0171398
> T-Protein 310 32.1134 32.1117 -4.10352e-05 -1.14898
> T-Non-Protein 310 2.47549 2.47548 8.55869e-07 0.0239643
>
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Dear Gromacs Users,
While I was runing the Justin's tutorial that is KALP-15 in DPPC , I have
some queries regarding the INFLATEGRO, Please have patience to read and
answer my queries:
1) does the system.gro should include the position restrained file of
KALP_newbox.gro after running genrestr,
ram bio wrote:
Dear Gromacs Users,
While I was runing the Justin's tutorial that is KALP-15 in DPPC , I
have some queries regarding the INFLATEGRO, Please have patience to read
and answer my queries:
1) does the system.gro should include the position restrained file of
KALP_newbox.gro a
Dear Justin,
Thanks for the suggestions.
will be back aftersome time as i am redoing it. Please check me for the
accuracy in steps in near future.
Ram
On Thu, Sep 17, 2009 at 8:20 PM, Justin A. Lemkul wrote:
>
>
> ram bio wrote:
>
>> Dear Gromacs Users,
>>
>> While I was runing the Justin's
I have installed Gromacs 4.0.5 on a 64 CPU Altix 3700 BX2 and when running
mdrun it just seems to spin there. It uses 100% of one CPU but doesn't finish.
I scanned through the list and found that I should try setting the
NOASSEMBLYLOOPS environment variable. By doing this it runs now and the
Hello. I am trying to run free energy calculations on a protein - protein complex. I believe that I have made all of the necessary changes to my topology, and the nonbonded parameters are set to 0 for state B. I am using the GROMOS96 53a6 ff. My system runs fine with free energy turned off, but giv
Hi Steve,
I made some tests on an Altix 4700 some time ago because I ran into
the same problem. If you use the fortran loops (--enable-fortran, which
is the default on sgi) you do not loose much performance. Here are
my benchmark results with a 8 atom protein+bilayer+water
simulation on a sin
2009/9/16 wuxiao
> Dear GMXers,
>
> For long time, I have had a puzzle: while the top file generally describe
> interactions in a molecule, intermolecular interactions are not explicitly
> in the top file. How are these intermolecular interactions described in
> GROMACS? Thanks a lot for any r
Hi
I have a silly question about the implementation of the Gromos forcefield
in gromacs, particularly about the exclusions. I have the gromos manual
and have seen that, for instance, for the residue MET there are only 1st
and 2nd neighbors exclusions defined for it. However, when I build a
protei
Hi,
I'm having some problems compiling the latest development build from the
git using fortran kernels.
The nb_kernel_f77_single.c file includes lot's of headers which are
incorrect
(e.g. "nb_kernel410_f77_single.h") the proper file name has no underline
after nb
("nbkernel410_f77_single.h"). I tr
actually it's the other way around,
it should be
"nb_kernel410_f77_single.h"
but the c file contains
"nbkernel410_f77_single.h"
Alex
aherz schrieb:
> Hi,
>
> I'm having some problems compiling the latest development build from the
> git using fortran kernels.
> The nb_kernel_f77_single.c file
On Thu, 17 Sep 2009, Carsten Kutzner wrote:
Hi Steve,
I made some tests on an Altix 4700 some time ago because I ran into
the same problem. If you use the fortran loops (--enable-fortran, which
is the default on sgi) you do not loose much performance. Here are
my benchmark results with a 8000
Steve Cousins wrote:
On Thu, 17 Sep 2009, Carsten Kutzner wrote:
Hi Steve,
I made some tests on an Altix 4700 some time ago because I ran into
the same problem. If you use the fortran loops (--enable-fortran, which
is the default on sgi) you do not loose much performance. Here are
my benchma
On Thu, 17 Sep 2009, Discussion list for GROMACS users wrote:
Since there is a 10% speedup by going back to version 3.3, is there any
reason *not* to use 3.3 instead on the Altix? I'm sure there are other
bug fixes and features since then but I don't know much about MD so I
don't know how impor
Ragnarok sdf wrote:
Is the RMSD given by g_energy -f -f2 in Joule or KJoule?
Units are described in section 2.2 of the manual. For g_energy, the
units will obviously depend on the quantity involved.
Mark
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Hi Everybody:
I am trying to perform a MD simulation of n-butane. But I cannot find the
gromacs paramaters for it. In the 2005 paper from Lange about Flooding in
GROMACS (J.Comp.Chem 21:1693.2006), the authors performed this simulation
before using the ffgmx united atom force field. But I canno
rvers...@ccny.cuny.edu wrote:
Hi Everybody:
I am trying to perform a MD simulation of n-butane. But I cannot find the gromacs paramaters for it. In the 2005 paper from Lange about Flooding in GROMACS (J.Comp.Chem 21:1693.2006), the authors performed this simulation before using the ffgmx unite
Hello everyone. I have seen a lot of post for the PULL function in Gromacs
4.0. ( I am using Gromacs 4.0.3)
I have also been trying to use this function and I had a question about the
Force output.
The system I am working with is a pair of Ionic Liquids in spc216 solution.
I want to fi
Hello everyone,
which one is used by default in case I do not provide any of them in the mdp
file for molecular dynamics?
Thanks!
---
Ricardo O. S. Soares , MsC.
Group of Biological Physics - Department of Physics & Chemistry
Faculty of Pharmaceutical Sciences at Ribeirão Preto - Univer
I tried to modify the spc.itp file, but wasn't successful. I decided not to
try any more and changed to the amber_tip4p water model in the .top file.
That solved the problem, no more error messages.
Thanks for your help.
On Wed, Sep 16, 2009 at 7:30 PM, Gunnar Widtfeldt Reginsson <
regins...@gma
Ricardo O. S. Soares wrote:
Hello everyone,
which one is used by default in case I do not provide any of them in the
mdp file for molecular dynamics?
You'll have to define "any of them," because if you do not specify the
"constraints" keyword in the .mdp file, then no constraints are use
>
> Ragnarok sdf wrote:
> > Is the RMSD given by g_energy -f -f2 in Joule or KJoule?
>
> Units are described in section 2.2 of the manual. For g_energy, the
> units will obviously depend on the quantity involved.
>
> Mark
>
> Well, that is the reason of my question. My FEP step when analysed with
"
Justin A. Lemkul wrote:
Ricardo O. S. Soares wrote:
Hello everyone,
which one is used by default in case I do not provide any of them in
the mdp file for molecular dynamics?
You'll have to define "any of them," because if you do not specify the
"constraints" keyword in the .mdp file, th
hi everyone,
I want to analyze the gromacs trajectories using vmd, is there a quick way
of doing so ? Is there a reference for this?
Thank you
Amit
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Pl
I just thought I'd mention some troubles and fixes I had with trying to
get Gromacs 4.0.5 to configure with --with-fft=mkl on a SGI Altix 3700
BX2 system. I did:
export CC=icc
export F77=ifort
export CFLAGS="-O3 -ip -ftz"
export FFLAGS="-O3 -ip -ftz"
export LDFLAGS="-O3 -ip -ftz -L/opt/intel
Amit Choubey wrote:
hi everyone,
I want to analyze the gromacs trajectories using vmd, is there a quick
way of doing so ? Is there a reference for this?
Depends on what you want to analyze, but probably the VMD tutorials and manual
will be the right place to start.
-Justin
Thank you
Steve Cousins wrote:
I just thought I'd mention some troubles and fixes I had with trying to
get Gromacs 4.0.5 to configure with --with-fft=mkl on a SGI Altix 3700
BX2 system. I did:
export CC=icc
export F77=ifort
export CFLAGS="-O3 -ip -ftz"
export FFLAGS="-O3 -ip -ftz"
export LDFLAGS="-O3
Hello,
Are there any links on how we can merge two simulation boxes to make a
single configuration? What technicalities should be considered?
Payman
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Paymon Pirzadeh wrote:
Hello,
Are there any links on how we can merge two simulation boxes to make a
single configuration? What technicalities should be considered?
Define "merge". There's a whole pile of issues depending what you mean.
Why can't you build initial coordinates up from scratch,
I have a box of crystal (from another simulation) and a box of solvated
protein. Now I want to put the protein close to my crystal.
Payman
On Fri, 2009-09-18 at 09:04 +1000, Mark Abraham wrote:
> Paymon Pirzadeh wrote:
> > Hello,
> > Are there any links on how we can merge two simulation boxes
Paymon Pirzadeh wrote:
I have a box of crystal (from another simulation) and a box of solvated
protein. Now I want to put the protein close to my crystal.
Throw the water away, so you have two coordinate files, one of protein
and one of crystal each in the same format. You can translate and ro
Paymon Pirzadeh wrote:
I have a box of crystal (from another simulation) and a box of solvated
protein. Now I want to put the protein close to my crystal.
Use editconf to define a box for your new system, use -center on each component
as appropriate, and cat the two .gro files together (rem
Mauricio Carrillo Tripp wrote:
Dear Justin,
could you please tell me the right way of creating the index file to use
with g_order v4.0.5?
I found a discussion about it at
http://www.mail-archive.com/gmx-users@gromacs.org/msg19885.html
however, the following link has been down for a while:
h
hi everyone,
I had a question about the purpose of chain identifier character in pdb.
What does it mean for Gromacs, i mean what does gromacs do with it? I
actually have a "bad" pdb file which has *different* chain identifiers for
first few molecules of the same type and then there exists none for
If you just want to a visual inspection of the trajectory then the easiest
way is to type:
vmd X.gro Y.xtc
Where X is the name of your structure file and Y the name of your trajectory
Tom
--On Thursday, September 17, 2009 14:51:57 -0700 Amit Choubey
wrote:
hi everyone,
I want to analyz
HI
Can Gromacs produce the data from NMR?
Thank you
Lin
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Please don't post
Hi,
> Anybody have any real-world comparisons of using MKL vs. FFTW3?
>
http://www.quantumespresso.org/user_guide/node16.html says:
Axel Kohlmeyer suggests the following (April 2008): "(I've) found that Intel
is now turning on multithreading without any warning and that is for example
why their
Chih-Ying Lin wrote:
HI
Can Gromacs produce the data from NMR?
No, if my guess at what "data" you mean is right. Why don't you ask a
full question? :-)
Mark
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Hi,
The only program that really uses chain identifiers is pdb2gmx.
It uses chain identifiers to recognize different protein (or DNA)
molecules that appear sequentially in pdb files.
All other programs will read chain identifiers and write them out again.
Also Gromacs will add chain identifiers f
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