How many protein atoms do you have? How many eigenvectors? The program is not
going to calculate the normal modes of the water molecules.
Peter
Sent from my iPhone
> On May 16, 2017, at 8:53 AM, luca maggi wrote:
>
> Hi Peter,
>
> Thanks for your answer...but my system is composed by a p
Hi Peter,
Thanks for your answer...but my system is composed by a protein and a
membrane plus the water. The Calphas are just 438, so I don't think that
number is referred to alpha carbons. Moreover I didn't set my calculation in
order to calculate the Calpha eigenvectors...
Hi,
What use are you making of constraints? Justin suggested sharing a full mdp
file, which I think may help. We discovered last year that you can get
equipartition failure for (IIRC) all-bonds constraints for moieties like
-CH2Cl, and latest grompp now detects this.
Mark
On Tue, 16 May 2017 01:
Hello Diana,
You may try using the -conc flag in genion program to specify your salt
concentration, along with -nname and -pname flags.
Best wishes,
Saumyak
On 16 May 2017 at 10:18, diana p wrote:
> Dear gmx users,
> I want to simulate 0.6M CaCL2 aqueous solution. To add the ions I use
> genio
Dear gmx users,
I want to simulate 0.6M CaCL2 aqueous solution. To add the ions I use
genion command and add 720 CL and 360 Ca ions respectively to the system of
pure 12568 water molecules.But on running the command genion I get error
message:
Program genion, VERSION 4.6.5
Source code file: /build
Hello,
The last thread was getting too big, and the conversation evolved to a
topic different from my original question, so I decided to start a new
thread.
We were discussing thermodynamic integration, and why the mass_lambdas
would have any contribution to the derivative of the Hamiltonian.
I
Dear Gromacs users,
I have an HII phase made of one inverted cylinder (and waters inside) in a
triclinic box with 90, 90, 60 angles. After running the simulation, this
cylinder become bent like a curve. I.e. is not a perfect cylinder anymore.
As a result, some water molecules and lipids pass the b
Perhaps just the eigenvectors for the Calpha atoms.
Peter
Sent from my iPhone
On May 15, 2017, at 9:30 PM, luca maggi
mailto:maggi_l...@hotmail.it>> wrote:
Dear Gromacs Users,
I have performed a normal mode analysis with gromacs. I have calculated the
hessian matrix and the related eigenval
Hi,
The moleculetype sections are intended to be combined in the system
directive, with your favourite text editor. This is even quicker than
combining gro files ;-)
Mark
On Mon, 15 May 2017 22:07 Alex wrote:
> Hello gromacs user,
>
> I have for peptides, each have a .gro file and a topol file
Hello gromacs user,
I have for peptides, each have a .gro file and a topol file. Using the
"cat" command I can easily merge their .gro file to have a box contains
four separated peptides (means I do not want to make a new big peptide but
seprated), but merging their topol files is not a easy task
Thank you very much Stéphane, I will certainly investigate this possibility.
Best regards,
João
On Mon, May 15, 2017 at 5:12 PM, ABEL Stephane wrote:
> Hello,
>
> You could write a proposal to have access to the supercomputers of the
> PRACE consortium |1]. The access to the machines is free,
>
Dear Gromacs Users,
I have performed a normal mode analysis with gromacs. I have calculated the
hessian matrix and the related eigenvalues and eigenvectors. At this point I
needed to extract some elements from the eigenvectors and using the dump tool
of gromacs I wrote the first of them in
Dear Gromacs Users,
I would like to hear your advice on scaling 1,4-interactions for both
classical and
QM/MM molecular dynamics simulations. I am using CHARMM27 force field.
Firstly, for classical MD, according to this post
https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=10
Hi,
Convergence times depend on system type and size, of course, but an
equilibration on an inhomogeneous system should probably run for more than
a few nanoseconds. That might help expose whether the issue is the system,
or the protocol, or the applied force.
Mark
On Mon, 15 May 2017 18:25 Kamp
Dear GMX users,
I am struggling with understanding my systems behaviour.
I have a semi-isotropic system where my bottom and upper plane are
composed of gold FCC plates. In between is a fluid, which during
equilibration is stationary (no acceleration). I equilibrate the
system with a Berendsen baro
Hello,
You could write a proposal to have access to the supercomputers of the PRACE
consortium |1]. The access to the machines is free,
[1] http://www.prace-ri.eu/
Stéphane
--
Message: 3
Date: Mon, 15 May 2017 14:45:00 +0200
From: Jo?o Henriques
To: gmx-us...@gr
Hi all,
I'm trying to add ligands into a simulation box without being a part of a
complex. I'm not sure how to calculate the number of ligand molecules I need to
achieve my specific concentration? Do I go according to the box volume? Could
anyone tell me how I should go about this?
Many thank
Hi,
I can't, since I only know in vague terms how LIE is intended to work.
Sounds like you should start by reading the paper that introduced LIE.
Mark
On Mon, May 15, 2017 at 4:28 PM Varvdekar Bhagyesh Rajendra <
bhagyesh.varvde...@research.iiit.ac.in> wrote:
> Hi Mark,
>
> Thank you for replyi
Hi Mark,
Thank you for replying.
I would be grateful if you could please answer the doubts I have asked in my
previous emails.
Thank you,
Bhagyesh
- Original Message -
From: "Mark Abraham"
To: gmx-us...@gromacs.org
Sent: Monday, May 15, 2017 7:25:43 PM
Subject: Re: [gmx-users] Doubts a
Hi,
Unfortunately, I don't know how/whether this worked in software that is a
decade old. Not too much has changed, however, so you may have better luck
(or error messages) with the most recent version, and thereby learn how to
get the topology to work.
Frankly, any force field that purportedly o
Hi,
On Sat, May 13, 2017 at 5:18 PM Varvdekar Bhagyesh Rajendra <
bhagyesh.varvde...@research.iiit.ac.in> wrote:
> Dear all,
>
> I have tried to find Delta G of Binding using g_lie and g_bar from the
> following systems (Protein+Ligand with ligand = chain B):
> PDB Ids: 1CDL, 1CKK, 1NIW, 2L7L, 2o
Dear Users
I am tryjng to simulate protein ligand complex using charmm36ff for 100ns.
I found the ligand moving away from the protein around 55ns. I don't think
it s a pbc effect. Is there anything I have done wrong or Should I add any
additional commands.?
Await your valuable advice.
PS: Will th
On 5/15/17 2:45 AM, abhisek Mondal wrote:
On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul wrote:
On 5/11/17 9:21 AM, abhisek Mondal wrote:
On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal
wrote:
Hi,
Thank you for the explanation. It really cleared some concepts. But I'm
still having m
Dear users and developers,
Our research group is having trouble finding enough computational resources
to run our GROMACS simulations and it was decided that I would be in charge
of finding new alternatives. I know this topic is not 100% GROMACS related
in a strict sense, but I've seen threads abo
On 5/14/17 9:43 AM, Mohammad Roostaie wrote:
Hi GROMACS users,
I want to model a graphene sheet. I used the instruction stated in link
http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube. I put the
cnt_oplsaa.ff folder in the directory where I want to run the rest of the work.
On 5/12/17 3:01 PM, Ali Shomali wrote:
Dear Justin thanks for your answer
actually I'm trying to reproduce other constant surface tension simulations
of bilayers to make sure my method is right. they calculate area per lipid
for different surface tensions from approximately 0 to 100 dyn/cm and
On 5/12/17 2:52 PM, Dan Gil wrote:
I ran equilibrium simulations, and then a longer simulations with the
recommended sd integrator. Still, the mass_lambda dH/dL is nonzero and
sometimes it is the dominant contribution at certain lambdas. I don't think
it is a convergence issue because there are
Dear all,
I have tried to find Delta G of Binding using g_lie and g_bar from the
following systems (Protein+Ligand with ligand = chain B):
PDB Ids: 1CDL, 1CKK, 1NIW, 2L7L, 2o60.
I have encountered following 2 doubts while doing so:
1. This doubt may have been answered in the past threads but I
Hi Mark,
The complete story was to add a manually capped residue for VAL and I named
it as VAT. NH2 capped was borrowed from NH2 in residue ASN. I hope to
borrow the parameters from ASN to VAT too but then the error comes.
To add the new residue VAT, I have included it in aminoacids.dat
(gromacs3
Hi,
It's hard to tell from this fragment. Are your include files all what you
think they are? Does grompp terminal output all make sense?
Mark
On Mon, May 15, 2017 at 10:43 AM Simon Kit Sang Chu
wrote:
> Hi everyone,
>
> I need to add a new residue in my forcefield and borrow the atoms and
> p
Hi everyone,
I need to add a new residue in my forcefield and borrow the atoms and
parameter from another existing residue. I encounter missing parameter
warning for a number of bonds. However, if I check in .itp, the parameters
exist. Is there something I missed?
Here is an example I encounter.
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