Dear community.
Thanks to all, finally I could resolve my problem, with the option
"-setttime", it was vital, then "c" (continue).
Now I have two questions,
1) In which case the option "l" could be useful? I did not understand very
well the aplicability.
2) Could you please recommend me an arti
ts of gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Re: scaling non-bonded interactions (Da-Wei Li)
> 2. question about trajcat command: Merge files (Miguel Quiliano Meza)
> 3. Re: Re: scaling non-bonded interactions (Justin A. Lemkul)
> 4. Re: scaling non-bond
Dear community,
I have a couple of doubts, please help me to clarify.
I performed 4 MD simulations using Gromacs (each one of 1ns, 2ns, 3ns ,4ns)
, they are only a continuation of the last, because of I was explored the
rmsd variation along the time. Now I want to merge all the trajectories to
do
Dear Community.
I am a beginner user of Gromacs for this reason I would like to consult my
case.
Nowadays, I am studying a protein which folding process has experimental
data (especially for a mutant). Structural information about how a mutant
destabilizes secondary structure was recently publish
make[2]: Entering directory `/share/apps/src/fftw-3.2.2/m4'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/share/apps/src/fftw-3.2.2/m4'
make[1]: Leaving directory `/share/apps/src/fftw-3.2.2'
What could be the problem? please advices.
Miguel Quiliano.
t; >>
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Dear community.
I have been trying to install gromacs 4.5.4 in my rocks cluster version 5.4
but unfortunately the system showed "configure: error: Cannot find fftw3
library" after launch the ./configure (you can see below)
Really I do not understand because I did before this:
# export LDFLAGS="-
gmx-users-requ...@gromacs.org
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Dear Colleagues.
I have been searching information about "HOW TO INSTALL GROMACS in rocks
cluster?". Unfortunately, the information that I found is not clear.
Someone can help me with this question. Maybe there are basic but important
steps that I have to keep in mind. Could you please share your
Dear Users.
Maybe this question is easy for all, but i have problems, patience please.
I do not have experience with metals, now I have a protein (crystal) with
Fe+2, which is coordinating with three HISTIDINES, one D and two molecules
of water, when I try to run "pdb2gmx" the program tells me "R
Dear Users.
I am a relative new user of GROMACS and I have some doubts:
I would like to perform a energy minimization (with water and iones) of a
crystal in orden to re-build the H-bonds responsible of the secundary
structure, to achieve this goal I want to restraint the movement of the
protein (
Hi everyone.
Nowadays I am learning how to analyze my results after MD. I have been
reading the tutorial "GROMACS Tutorial for Drug – Enzyme Complex" and all is
fine but I have a big doubt about g_rms. I know that g_rms compares two
structures by computing the root mean square deviation (RMSD). In
roup SOL is not continuous
> To: Discussion list for GROMACS users
> Message-ID: <4b5f5edf.4080...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Miguel Quiliano Meza wrote:
> > *Hi everyone.
> >
> > I have a prob
*Hi everyone.
I have a problem when I try to run GENION, GROMACS says:
*
WARNING: turning of free energy, will use lambda=0
Reading file 1x8a_solvatada.tpr, VERSION 3.3.3 (single precision)
Using a coulomb cut-off of 0.9 nm
Will try to add 0 Na ions and 15 NA+ ions.
Select a continuous group of so
Hi everyone.
I am a relative new user of GROMACS. I have performed some short simulations
but now I want to something big. I have been reading on the web site and
found that mdrun -.cpt option is used to generate checkpoints, I am using
GROMACS 3.3.3 but I don't find -cpt option when I call mdrun
Dear gromacs users
I am running a molecular dynamics calculation, all is fine but the time of
calculation is big, I would like to know if I can stop the calculation
without lose the information generated until that point.
thanks in advance.
Miguel Quiliano.
__
Dear all.
I am a new user of GROMACS, I have read the user book and free tutorials in
the WEB, but now when I try to do a simulation, appears FAD no topology, I
have been reading that PRODRG server is a way to achieve that goal, I tried
but the output format is different, it means old version (for
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