Dear all,
I am trying to simulate virus hollow capsid using gromos54a7 forcefield.
Since the capsid is hollow, I don't want water inside the capsid. But the
"gmx solvate" command solvates the hollow region of capsid also. So, every
time I manually remove the water located inside the capsid as foll
Hello,
My system is blowing up for the protein carbohydrate solvent complex. I
have attached the mdp file below. The NPT and NVT were in good accordance
to tutorial listed by Justin. 'Please help me solve the issue.
title = CD44 complex MD simulation
; Run parameters
integrator = md
Hi,
Just to make sure if I understood correctly: if I create energy groups as (i)
Calpha, (ii) Cbackbone, (iii), Nbackbone, (iv) everything else, I should be
able to achieve what I want, right?
Best,
Irem
On Jul 12, 2016, at 5:35 PM, Mark Abraham
mailto:mark.j.abra...@gmail.com>> wrote:
Hi,
Dear gromacs-users,
Doing simulations on lipid HII phase, I came to a question which I could
not get happy with my answer. I appreciate your opinion in advance:
Imagine you have a cylinder made of lipids with waters only inside the
cylinder, which is long enough and can be run for enough time so
On 7/12/16 9:47 AM, xy21hb wrote:
Dear all,
I am pulling the saturated and unsaturated chains of a lipid bilayer to
"simulate" its gel phase transition by pull code. It ends with the expected
extended structure.
But when I continue with zero pulling rate
to maintain the extended structur
The output frequency is far too large for normal usage. Reduce the output
frequency by increasing the values of nstxout and nstvout, or simply set them to
zero to suppress .trr writing (it's not useful for most normal quantities).
-Justin
On 7/12/16 12:38 PM, Tapash, Arifuzzaman wrote:
Hi
Hi all,
I'm very new in Gromacs. I have completed the Lysozyme in water tutorial (by
Justin A. Lemkul) successfully. Now I'm doing the KALP-15 in DPPC.
I have successfully done the equilibration stage (both temperature and
pressure). I have a question about the npt.trr file.
After completing
Hi,
The "only" thing you can do is define energy groups, and have a table per
kind of interaction between atoms from each energy group.
Mark
On Tue, Jul 12, 2016 at 11:15 PM Irem Altan wrote:
> Hi,
>
> Thanks. If I want to do this for only a subset of protein atoms (backbone
> atoms, for insta
Hi,
4.5.3 is really old version of GROMACS. You might have a better time with a
more recent version, perhaps with better docs. Or maybe you don't need to
write code at all if you ask people first. :-)
Mark
On Tue, Jul 12, 2016 at 9:56 PM MURILO GABARDO KRAMAR <
murilokra...@alunos.utfpr.edu.br>
Hi,
Thanks. If I want to do this for only a subset of protein atoms (backbone
atoms, for instance), what happens when calculating interaction between a side
chain protein atom (with default LJ format) and a backbone atom? Is it possible
to have the backbone atoms interact with the truncated LJ
Hello,
I've managed to solve the inclusion problem by adding it to the .pc files
inside pkgconfig folder.
Now I'm trying to implement the above mentioned, but I can't really do
that. I'm trying to update the 'selstr' field inside
'gmx_ana_selcollection_t *sc' and then calling
'gmx_ana_selcollecti
Hi,
Ok, that's starting to sound like either a code bug or hardware setup bug.
Please try with 5.1.2 (but it looks like maybe you have already) and/or
open an issue at https://redmine.gromacs.org and add your tpr file. I'll
try it on some hardware setups we know we trust. ;-)
Mark
On Tue, 12 Jul
Hi,
In short, this works for every combination. But with the big disadvantage
of being very slow and not using our precious little gpu´s.
Thanks for your fast reply Mark.
> Hi,
>
> What happens in your failing cases (or even all of them) when adding -nb
> cpu, to force the run off the GPU?
>
> M
Hi,
What happens in your failing cases (or even all of them) when adding -nb
cpu, to force the run off the GPU?
Mark
On Tue, 12 Jul 2016 19:02 Yannic Alber wrote:
> Dear all,
>
> we struggle to get a TI on our computer running. The specifications are
> listed below. As you can see, its a two s
Dear all,
we struggle to get a TI on our computer running. The specifications are
listed below. As you can see, its a two socket, two graphics cards
machine. Therefore, the plan is to run two simulations in parallel. But we
can't get a single one to run.
Running on 1 node with total 20 cores, 20
On 12/07/16 16:17, Morten wrote:
Hi,
I am trying to decide which computer to buy. I am primarily running all
atom simulations and MARTINI CG simulations with approximately 20 or
1 atoms, respectively. I care manly about through-put and run single
precision. The computers I am considering
Hi,
mdrun can't know what your visualization preference will be, and then VMD
doesn't know how to guess either. See
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
for
tips.
Mark
On Tue, Jul 12, 2016 at 4:35 PM Yeganeh Entezari
wrote:
> Hi,
> I have a problem afte
Hi,
You should likely start with a careful reading of
http://dx.doi.org/10.1002/jcc.24030
Mark
On Tue, Jul 12, 2016 at 4:17 PM Morten wrote:
> Hi,
>
> I am trying to decide which computer to buy. I am primarily running all
> atom simulations and MARTINI CG simulations with approximately 20
Hi,
I have a problem after this step:
grompp -f em.mdp -c sol_ions.gro -p topol.top -o em.tpr
mdrun -v -deffnm em
I achieved the ligand parameters from ANTECHAMBER that are usable for
GROMACS software.
After using this command line :
$AMBERHOME/exe/ambpdb -p lig.prmtop < lig.inpcrd > lig.pdb
Hi,
I am trying to decide which computer to buy. I am primarily running all
atom simulations and MARTINI CG simulations with approximately 20 or
1 atoms, respectively. I care manly about through-put and run single
precision. The computers I am considering are:
i7-6700K with GTX970 or
Dear all,
>>
>> I am pulling the saturated and unsaturated chains of a lipid bilayer to
>> "simulate" its gel phase transition by pull code. It ends with the expected
>> extended structure.
>>
>> But when I continue with zero pulling rate
>> to maintain the extended structur
Concerning to the harmonic restraints, in step 1. is just something inside
the molecule (as said applying restraints to the H and O atoms in HCOO-)
but in step 3 is restraint between waters molecules and surface, but my
question is in general how I should apply the harmonic restraint? If it is
by t
How's that related to what Mark and I said?
--
Szilárd
On Mon, Jul 11, 2016 at 4:02 PM, Albert wrote:
> yes.
>
> But the job failed from to time:
>
> vol 0.87! imb F 34% step 33600, will finish Sat Jul 23 17:26:12 2016
>
> ---
> Program gmx mdr
On Tue, 12 Jul 2016 12:44:10 +0200
Alexander Alexander wrote:
> Yes, Fig.6 comes from the different step in Fig.1. I think the
> easiest way here is to have 6 different "topol-mdp" files
> corresponding to each step. Although unlike the amino acid, defining
> the [ moleculetype ] for ion and a li
On 12/07/16 13:47, Justin Lemkul wrote:
On 7/11/16 9:52 AM, ALEXANDER DHALIWAL wrote:
Dear GROMACS users,
I am pioneering the use of GROMACS in my lab to supplement some of our
experimental research. I have generated some topologies from the
Automated
Topology Builder (ATB), but I am unsure w
On 7/11/16 9:52 AM, ALEXANDER DHALIWAL wrote:
Dear GROMACS users,
I am pioneering the use of GROMACS in my lab to supplement some of our
experimental research. I have generated some topologies from the Automated
Topology Builder (ATB), but I am unsure whether or not to trust the files
provided
On 7/12/16 6:54 AM, David van der Spoel wrote:
On 12/07/16 10:12, 王珍 wrote:
Hi all,
I want to calculate the dihed torsion energy(for example the dihed of
o3'-p-o5'-c5') using gromacs, how can i define the exergy_groups and how can I
extract the energy?
Thank you very much.
You can not in
On 12/07/16 10:12, 王珍 wrote:
Hi all,
I want to calculate the dihed torsion energy(for example the dihed of
o3'-p-o5'-c5') using gromacs, how can i define the exergy_groups and how can I
extract the energy?
Thank you very much.
You can not in a simple manner. You would have to modify the to
Yes, Fig.6 comes from the different step in Fig.1. I think the easiest way
here is to have 6 different "topol-mdp" files corresponding to each step.
Although unlike the amino acid, defining the [ moleculetype ] for ion and a
limited number of water molecules out of thousand of water molecules in th
Hello:
I noticed that my GPU job under 5.1.2 often failed with messages:
step 52400, will finish Mon Jul 25 12:04:59 2016
---
Program gmx mdrun, VERSION 5.1.2
Source code file:
/home/albert/Downloads/gromacs/gromacs-5.1.2/src/gromacs/mdlib/nbn
On Tue, 12 Jul 2016 10:29:04 +0100
Hannes Loeffler wrote:
> On Tue, 12 Jul 2016 10:16:24 +0200
> Alexander Alexander wrote:
>
> > Hi,
> > Thanks for your response.
> > I want to calculate the binding free energy of a single amino acid
> > to a solid surface in aqueous solution by FEP, alchemica
On Tue, 12 Jul 2016 10:16:24 +0200
Alexander Alexander wrote:
> Hi,
> Thanks for your response.
> I want to calculate the binding free energy of a single amino acid to
> a solid surface in aqueous solution by FEP, alchemical
> transformation, where perturbations applying on different species in
>
Hi,
Thanks for your response.
I want to calculate the binding free energy of a single amino acid to a
solid surface in aqueous solution by FEP, alchemical transformation, where
perturbations applying on different species in ordered steps. For instance:
Step.1 applying harmonic restraints to the O
Hi all,
I want to calculate the dihed torsion energy(for example the dihed of
o3'-p-o5'-c5') using gromacs, how can i define the exergy_groups and how can I
extract the energy?
Thank you very much.
--
Gromacs Users mailing list
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http://www.gromacs.org/Support/
On Tue, 12 Jul 2016 07:35:00 +0100
Hannes Loeffler wrote:
> On Tue, 12 Jul 2016 01:56:42 +0200
> Alexander Alexander wrote:
>
> > I was wondering that how I can have for example two different
> > "couple-moltype" in free energy part of my *.mdp file in FEP,
> > alchemical transformation? The re
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