Dear Gromacs users&devs,
I just installed gromacs-4.5.7 in a Cray XE6m, the serial installation
went fine, however the mpi installation presents a problem. It
compiles fine, but the "make install" (or make install-mdrun) seems to
have problems copying the executable files to the installation
direc
ore even for those kernels not requiring SSE2.
>
> Roland
>
> On Tue, Dec 20, 2011 at 6:05 AM, Daniel Adriano Silva M <
> dadri...@gmail.com> wrote:
>
>> Hi Devs,
>>
>> Is this intended or just a typo:
>>
>> #nb_kernel_x86_64_sse/n
Hi Devs,
Is this intended or just a typo:
#nb_kernel_x86_64_sse/nb_kernel_x86_64_sse.c#
.:
211:fprintf(log,"Testing x86_64 SSE2 support...");
.:
##
instead of:
.:
211:fprintf(log,"Testing x86_64 SSE1 support...");
.:
The same thing appears in other "_sse.c" files.
Thanks,
Da
In the energy minimisation step, any "conformational rearrangement" taking
place is not a function of time, it is just an algorithm for reaching a
basin of minimum energy:
(http://www.gromacs.org/Documentation/Terminology/Energy_Minimisation),
hence there are not velocities in the atoms of the sy
Hi,
Is this your input? (a GRO file?). Can you paste the PDB corresponding to
the RNA nucleotide that you are interested on? I think the file may be small
enough to paste it here so someone can try to reproduce what is happening to
you.
Daniel
2011/3/22 maria goranovic
> Sorry for the incomple
Hi,
I think g_covar can calculate the average structure (take a look to the
manual). However note that average structure could be a non relevant
structure, i.e. the average could represent an imposible conformation. So
maybe you can also give a try to g_cluster and look for the central
conformatio
Dear gmx users and developers,
I am facing a problem that is new for me and I will appreciate advice from
your expertise. I am working with a big protein complex (around 100K atoms,
several subunits) and I used g_membed to embed it in a (aprox 24 14 nm)
pre-equilibrated POPC membrane, however afte
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test is incomplete for mpi, since some test does
not run with dd and others with pd. Please, are there any chance that
you have some tprs that could work as a test-set, with results that
can be compared
Thank you
Daniel
2009/10/30 Mark Abraham :
> Daniel Adriano Silva M wrote:
>>
) without any apparent errors, do you think that
there could be any way to check if these md-sims results are actually
wrong?
Thanks
Daniel
2009/10/30 Mark Abraham :
> Daniel Adriano Silva M wrote:
>>
>> Mark,
>>
>> Thank you!!! It was non directly MPI, since I tried the
booth with gcc and intel, booth compilations seems
to work. Do you think that it could be any problem at mix gcc-fftw and
intel mdrun??? I will continue the tests with the new gmx-tests and
other TPRs.
Thanks
Daniel
2009/10/30 Mark Abraham :
> Daniel Adriano Silva M wrote:
>>
>> Mar
/10/30 Mark Abraham :
> Daniel Adriano Silva M wrote:
>>
>> Dear Gromacs users,
>>
>> I am experimenting the next problem on an infiniband-cluster (8
>> intel-cores per node, GROMACS compiled with icc 11.1, all run through
>> mvapich2):
>>
>> I have
Dear Gromacs users,
I am experimenting the next problem on an infiniband-cluster (8
intel-cores per node, GROMACS compiled with icc 11.1, all run through
mvapich2):
I have a molecule (protein 498aa, solvated or in vacuum I get the same
problem at any box shape), when I try to SD minimize it with
= 4000
nstfout = 0
nstlog = 50
nstenergy = 50
energygrps = Protein non-protein
__
END of message
2009/9/4 Erik Lindahl :
> Hi,
>
> On Sep 3, 2009, at 4:52 AM, D
Mark,
Your are right. Thanks
Daniel
2009/9/24 Mark Abraham :
> Daniel Adriano Silva M wrote:
>>
>> Dear GROMACS users and developers.
>>
>> I don known if this issued had been previously addressed, but I found
>> that when I try to run a MD with time-step of
Dear GROMACS users and developers.
I don known if this issued had been previously addressed, but I found
that when I try to run a MD with time-step of 2fs and 25 steps
(yes 500us!!!) the dynamics aborts with the next message (64bit-LINUX
and icc 10 compiler):
WARNING:
Dear Gromacs users, (all related to GROMACS ver 4.0.x)
I am facing a very strange problem on a recently acquired supermicro 8
XEON-cores nodes (2.5GHz quad-core/node, 4G/RAM with the four memory
channels activated, XEON E5420, 20Gbs Infiniband Infinihost III Lx
DDR): I had been testing these nodes
Hi,
I answered a very similar question last week but it appears that
gmx-users is not online by now: try to use this script. And be aware
to re-wrap code lines as my mail splits it. Please comment if it
actually works for you.
Best.
Daniel
***
Usage notes:
- Just copy/and/paste the code
Hi,
This is a recurrent issue. I have figured a bash script that had
worked for every system which I had tested (i.e. protein,
protein-ligand, protein-DNA, protein-protein), but this is not a
warranty. It centers the protein on the box, and at the same time puts
waters inside the box ; however the
Serdar.
If the "real charge" of your system is not zero and you are using PME, then
PME code will take account for any non-zero charge on the system and
neutralize it with an uniform background charge (
http://wiki.gromacs.org/index.php/Errors).
If your system is composed by a protein, then try fi
Thanks David,
as you addressed, adding "NULL," at the end of the line 250 of
calcpot.c solved the compilation issue.
Daniel
2008/4/15 David van der Spoel <[EMAIL PROTECTED]>:
> Daniel Adriano Silva M wrote:
>
> > Hi there,
> >
> > I am tyring to com
Hi there,
I am tyring to compile CVS gromacs version "up-to-this-day", and I
always finish with the same error (on two different machines), this
error is recurrent even if I use gcc or pathscale:
# cc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/include/libxml2
-I../../include
-DGMXLIBDIR=\"/home/
> Hi,
> I have added missing atoms to my pdb file through servers of WHATIF,when I
> use the force field option then the following output comes in shell console:
> Fatal error:
> Residue 'GTP' not found in residue topology database
> and the following files are created:
> 2a5f.top 2a5f_A.itp 2a5
Hello,
I have three problems here. First, I'm trying to made FEP calculations
in order to calculate the DG of binding for a small ligand (aminoacid)
to a protein, but my ligand (arginine) have a net charge of +1e, so
when I "disappear" this ligand the system takes a total charge of -1e
and I get t
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