Hi George,
I usually delete/move the molecules reported to have high force
values in the minimization steps. A better thing would be to start
with a box which has sufficient intermolecular distance again by
deleting molecules which are very close to each other (use the
g_mindist program)
Hi,
I am doing an energy minimization for a carbon nanotube (end capped
with hydrogen atoms) in a box of water. I get the following message:
" Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
Double precision normally
toma0052 wrote:
Hello,
I am looking to edit a little bit of the source code in Gromacs, and I
am having a little bit of a problem. Normally, I am using Gromacs that is
installed on a network, but I cannot edit this, so I also have Gromacs
installed on a personal windows machine running Cygw
Hello,
I am looking to edit a little bit of the source code in Gromacs, and I
am having a little bit of a problem. Normally, I am using Gromacs that is
installed on a network, but I cannot edit this, so I also have Gromacs
installed on a personal windows machine running Cygwin. The installat
toma0052 wrote:
Hello,
I am working with a DPPC lipid bilayer system in water, and I would like
to add a shear force to the bilayer. Preferably, this force would be a
function of the z coordinate and be maximal at the bilayer surface and decay
to zero at the box top and bottom. For this, I
WILLIAM R WELCH wrote:
Gromacsers
I have been running jobs successfully for a while, submitting them directly, but when I
submitt them to the q (qsub) I get an error from grompp that it can't find
"libXm.so.3". I recompiled with configure option --without-motif-include, but
that did not get
Elias santos wrote:
Hi, users of the Gromacs.
I have a question for you. I want to know which the meaning of the term
(14) in the energies Coulomb 14 and Lenard Jones 14.
thanks
chapter 4.
___
Robert Selwyne wrote:
Dear All
Is there any way of generating the distance restraints for a pdb file? Do
any of the gromacs command support this problem or it has to be filled out
manually?
Best wishes
Robert
what do you mean generating the distance restraints? from nMR data? in
that case ther
Gromacsers
I have been running jobs successfully for a while, submitting them directly,
but when I submitt them to the q (qsub) I get an error from grompp that it
can't find "libXm.so.3". I recompiled with configure option
--without-motif-include, but that did not get rid of the problem. How
Dear All
Is there any way of generating the distance restraints for a pdb file? Do
any of the gromacs command support this problem or it has to be filled out
manually?
Best wishes
Robert
___
gmx-users mailing listgmx-users@gromacs.org
http://www.grom
Hi, users of the Gromacs.
I have a question for you. I want to know which the meaning of the term (14)
in the energies Coulomb 14 and Lenard Jones 14.
thanks
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/
Hi Mark
I checked my mdp file, the flags for nstvout and nstfout are all zero, this
must be the problem.
Thank you for your suggestions!
Yours
Xin
On 4/18/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
liu xin wrote:
> Hi GMX users
>
> My 2ns simulation crashed accidentally, gmxcheck said my prev
liu xin wrote:
Hi GMX users
My 2ns simulation crashed accidentally, gmxcheck said my previous
simulation was stopped at 1400 ps, then I used the tpbconv to generate a
new tpr to restart it from the previous ending point:
"tpbconv -f -e -s -o new.tpr"
but I found the output message of tpbconv
Hi GMX users
My 2ns simulation crashed accidentally, gmxcheck said my previous simulation
was stopped at 1400 ps, then I used the tpbconv to generate a new tpr to
restart it from the previous ending point:
"tpbconv -f -e -s -o new.tpr"
but I found the output message of tpbconv said:
"100 step
Sergio Garay wrote:
Hi to all
I've checked all the answers in the gmx list about this item, but I still
don't know if it is possible to describe a dihedral behavior with more than
one potential function. In one answer I understood that it is posible, but
when I try to run grompp it does not p
Sergio Garay wrote:
Hi to all
I've checked all the answers in the gmx list about this item, but I still
don't know if it is possible to describe a dihedral behavior with more than
one potential function. In one answer I understood that it is posible, but
when I try to run grompp it does not p
Hi to all
I've checked all the answers in the gmx list about this item, but I still
don't know if it is possible to describe a dihedral behavior with more than
one potential function. In one answer I understood that it is posible, but
when I try to run grompp it does not process the topology, g
Joern Lenz wrote:
dear users,
i am simulating a complex of DNA and protein.
also i looked through the mailing list I did not find any solution to my
problem.
If you searched for advice about T-coupling groups you will have seen
the strongly-worded advice not to use more than two or three, and
kanin wichapong wrote:
Dear All,
In my MD system, I applied a time step just 1 fs and I didn't
apply bond constraints. I would like to know that is there will be any
problems with this parameter. Can I used this parameter for my MD
simulations?
Probably fine - see what other people
Luca Ferraro wrote:
Date: Tue, 17 Apr 2007 19:08:02 +0200 From: Erik Lindahl
<[EMAIL PROTECTED]> Subject: Re: [gmx-users] Preliminary report on
benchmark on Opteron Cluster Infiniband on current CVS version To:
Discussion list for GROMACS users Message-ID:
<[EMAIL PROTECTED]> Content-Type:
text/
From: Luca Ferraro <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: gmx-users@gromacs.org
Subject: [gmx-users] [Re]: Preliminary report on benchmark on Opteron
Cluster Infiniband on current CVS version
Date: Wed, 18 Apr 2007 11:53:00 +0200
Date: Tue, 17 Apr 2007 19:08:0
Dear All,
In my MD system, I applied a time step just 1 fs and I didn't apply
bond constraints. I would like to know that is there will be any problems
with this parameter. Can I used this parameter for my MD simulations?
All Regards,
Kanin
___
18 apr 2007 kl. 11.27 skrev David van der Spoel:
Joern Lenz wrote:
dear users,
i am simulating a complex of DNA and protein.
also i looked through the mailing list I did not find any solution
to my problem.
i am using make_ndx with:
make_ndx -f blah_ion -o blah_ion and in my mdp file i use
Date: Tue, 17 Apr 2007 19:08:02 +0200 From: Erik Lindahl
<[EMAIL PROTECTED]> Subject: Re: [gmx-users] Preliminary report on
benchmark on Opteron Cluster Infiniband on current CVS version To:
Discussion list for GROMACS users Message-ID:
<[EMAIL PROTECTED]> Content-Type:
text/plain; charset=US-ASC
Joern Lenz wrote:
dear users,
i am simulating a complex of DNA and protein.
also i looked through the mailing list I did not find any solution to my
problem.
i am using make_ndx with:
make_ndx -f blah_ion -o blah_ion
and in my mdp file i use:
tcoupl= berendsen
tau_t = 0.
dear users,
i am simulating a complex of DNA and protein.
also i looked through the mailing list I did not find any solution to my
problem.
i am using make_ndx with:
make_ndx -f blah_ion -o blah_ion
and in my mdp file i use:
tcoupl= berendsen
tau_t = 0.1 0.1 0.1 0.1
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