Hi Paul,
Thank you for your e-mail. I forgot to note that without the plumed patch,
the situation remains still problematic. The vanilla versions produce the
same errors (segmentation faults), even without any specific input files.
Just running the command e.g. gmx(_mpi) grompp, or gmx(_mpi) trjcon
Dear all,
Could one kindly let me know how $i should come in gmx gangle used in a for
loop to avoid syntax errors?
I tested different flavors like "$i", "${i}", ..., and still the problem is
here.
#!/bin/bash/
for i in {1..1000}
do
gmx gangle -g1 vector -group1 'group $i and name C10 plus
On 11/5/19 7:53 PM, Dave M wrote:
Hi Justin,
Will appreciate any suggestions about the error am getting with
distance_restraints.
Aside from using the pull code rather than this approach, I have no
other suggestions.
-Justin
Thanks.
regards,
Dave
On Thu, Oct 31, 2019 at 1:39 AM Dave M
Hi Justin,
Will appreciate any suggestions about the error am getting with
distance_restraints.
Thanks.
regards,
Dave
On Thu, Oct 31, 2019 at 1:39 AM Dave M wrote:
> Hi Justin,
>
> Thanks, not sure [distance_restraints] also does not work for me. Though
> pull code works (like shared by other
Hi,
I'm coming late, but I may add a few words. The GROMOS force fields have
been parameterized with the GROMOS software using a twin-range cutoff
(0.8/1.4), but this option is no longer available in recent versions of
GROMACS. However, in a recent study
(https://doi.org/10.1021/acs.jctc.8b007
Hello,
could you try running first with an unmodified version of GROMACS, so we
can check if the PLUMED modifications are responsible for the crashes
(unlikely for the tools, but we need to make sure)?
If the vanilla versions are still crashing, can you supply us with some
log files and input
Dear all,
I am running Mac OS Catalina 10.15.1 (Xcode 11.2 11B52). I have
successfully compiled several versions of Gromacs (5.1.5, 2018.8, or
2019.4) patched with plumed (v.2.4.6 for 5.1.5, or v.2.5.3 for 2018/2019
versions). The compilations are completed without any errors, employing the
configu
On 11/5/19 11:55 AM, Najamuddin Memon wrote:
You may use Amber99sb force field for DNA-protein simulation and also put
residue type.dat file in your folder. It will work
The nucleic acid parameter sets packaged with these GROMACS ports are
wildly outdated. I suggest finding better paramet
Residue type.dat file having definition of nucleotides
On Tue, Nov 5, 2019, 9:55 PM Najamuddin Memon
wrote:
> You may use Amber99sb force field for DNA-protein simulation and also put
> residue type.dat file in your folder. It will work
>
>
> On Tue, Nov 5, 2019, 6:59 PM Paul bauer wrote:
>
>>
You may use Amber99sb force field for DNA-protein simulation and also put
residue type.dat file in your folder. It will work
On Tue, Nov 5, 2019, 6:59 PM Paul bauer wrote:
> Hello,
>
> the error states that you are missing parameters for your system. Did
> you check that the forcefield contain
Hi,
SLURM and OpenMPI do different things. SLURM is a resource manager, from
which you might request multiple compute nodes. OpenMPI is a parallelism
library that allows a program to run on those nodes. GROMACS is the
program, and it doesn't care which MPI library is in use, or which resource
mana
Hello,
the error states that you are missing parameters for your system. Did
you check that the forcefield contains all the special parameters you
need for the conjugate molecule?
Also, I would recommend to not use a prehistoric version of GROMACS for
new studies, if there are no specific reas
Researchers,
Is slrum required to run GROMACS on multiple computers or OpenMPI is fine?
Thank you
Shradheya
DBT-BIF University of Rajasthan
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Hi all,
i am preparing system of DNA-protein complex, downloaded it from RCSB website,
by using GROMACS-version 4.5.5; force field AMBER03WS with water Model TIP4P
(2005). The DNA chain contains DA, DT, DG, DC atom type.
but the problem is that when i use command for energy minimization the
foll
So the answer is yes, you can, but I'm not sure you should.
Assuming you have a mid to high end gaming laptop - say something like a
i7-8750H with a Nvidia MaxQ 1070 (i.e. a Gigabyte Aero 15x or equivalent; I'm
just going with what I have), you will get decent performance (I can get circa
80 ns
Hi all,
i am preparing system of DNA-protein complex, downloaded it from RCSB website,
by using GROMACS force field AMBER03WS with water Model TIP4P (2005). The DNA
chain contains DA, DT, DG, DC atom type.
but the problem is that when i use command for energy minimization the
following error has
Den 2019-11-05 kl. 01:59, skrev Mijiddorj B:
Dear Prof. David van der Spoel,
Thank you very much for your reply and sending an amazing work.
I am sorry for asking further questions. Can you give me an advice to use
the parameters which were considered in the ref#44 in this work?
Ref#44 uses the
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