Hi,
If you feel you must install software that is three years old and no longer
supported, please at least get the latest bug-fix version of it (4.6.7).
You should consider carefully one of the more recent, faster and less buggy
versions.
I can't tell what your problem is, but my guess is that yo
Dear all
I am trying to simulate 3M urea in a water box.when i do the mdrun of pr ,
i get too many LINCS warning and also segmentation fault(core dumped).
I am pasting my em.mdp and pr.mdp file below-
em.mdp
;
;User spoel (236)
;Wed Nov 3 17:12:44 1993
;Input file
;
cpp
Hi,
The default name for that file is confout.gro, which it will be unless you
chose a different name with
gmx mdrun -c nvt.gro
or
gmx mdrun -deffnm nvt
However, you can sometimes
get slightly better results by using
gmx grompp -c whatever -p topol -t nvt.cpt -f npt -o npt
because now the bo
Hi,
The list does not accept attachments, unfortunately. However, your problem
is probably solvable via the advice at
http://www.gromacs.org/Documentation/Terminology/Blowing_Up. There's also
probably no reason to do a run with position restraints for urea in water,
since there's little that is sp
Dear all
I am trying to simulate 3M urea in a water box.when i do the mdrun of pr ,
i get too many LINCS warning and also segmentation fault(core dumped).
I am attaching my em.mdp and pr.mdp file below-
Thanks in advance
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I had restarted my crash run for NVT equilibration using* gmx mdrun -s
nvt.tpr -cpi nvt.cpt -v *, the simulation restarted and finished fine, but
at the end of the simulation I did not get my nvt.gro, which I needed to do
further NPT equilibration. Where is nvt.gro ? Did I do something wrong, or
th
Greetings!
I was performing an EM run with an array of dioxane molecules, for which I had
produced co-ordinates from PRODRG. I got the co-ordinates, and made an array of
it, using the gmx genconf module, and corrected my topology file. Then, I
thought I should minimize the energy of this array b
Please don't reply to digests or unrelated threads when starting a new topic; it
creates a mess in the archive.
On 10/2/16 6:11 PM, Nash, Anthony wrote:
Hi all,
I had a homology/de-novo model .pdb converted into .gro, solvated,
neutralised and now I¹m going through a series of energy minimis
Hi all,
I had a homology/de-novo model .pdb converted into .gro, solvated,
neutralised and now I¹m going through a series of energy minimisation
steps. Unfortunately, during energy minimisation I get LINCS WARNINGS
(angle relative constraint deviation). The the naked eye, the atoms
involved don¹t
Mark,
I understand your concern.
I need to have the hydrogens for my final answer, so an all-atom force
field is definitely inevitable. Justification for choosing OPLS over the
other all-atom force fields is a little more tricky, but I have found
literature where they used OPLS-aa for similar purp
Hi,
Did you start with
http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-features.html#running-a-membrane-protein-embedding-simulation?
Mark
On Sun, 2 Oct 2016 17:13 Sophia Kuriakidi wrote:
> Hi again to all of you!
> I am trying to run at last this membrane simulation. I am trying
Hi again to all of you!
I am trying to run at last this membrane simulation. I am trying to use the
-membed option but I can't figure out how to. Can anyone provide me with an
example input line? e.g. gmx mdrun -membed -input file -n index.ndx -p
topol.top -o output file etc ? And also, can anyone
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