Hello everyone,
I am trying to do normal mode analysis for a protein using Gromacs.
Can anyone point me out towards a sample mdp file that I could edit for this
purpose?
Thanks
Ajit B.
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the log file just lists all the parameters of the simulation, following is a
part of it
parameters of the run:
integrator = md
nsteps = 4000
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm
- Original Message -
From: Amit Choubey
Date: Saturday, February 20, 2010 10:25
Subject: Re: [gmx-users] domain decomposition and load balancing
To: Discussion list for GROMACS users
> Hi Mark and Justin,
> I am using a box of size (20nm)x(20nm)x(60nm)..system is open along z ie
> (60
Hi Mark and Justin,
I am using a box of size (20nm)x(20nm)x(60nm)..system is open along z ie
(60nm) side.
I tried using only two nodes, it gives the same error
There is no domain decomposition for 2 nodes that is compatible with the
given box and a minimum cell size of 0.889862 nm
Change the num
- Original Message -
From: "Justin A. Lemkul"
Date: Saturday, February 20, 2010 10:13
Subject: Re: [gmx-users] domain decomposition and load balancing
To: Discussion list for GROMACS users
>
>
> Amit Choubey wrote:
> >Hi Mark,
> >
> >I am not using PME calculation.
> >
> >I was hoping
Amit Choubey wrote:
Hi Mark,
I am not using PME calculation.
I was hoping mdrun will do the cell allocation itself.
It will, unless it can't, which is exactly your problem. Mark's point stands,
regardless of whether or not you're using PME. DD requires certain minimum size
requirements
Hi Mark,
I dont think i need to play with npme at all.
Amit
On Fri, Feb 19, 2010 at 2:41 PM, Amit Choubey wrote:
> Hi Mark,
>
> I am not using PME calculation.
>
> I was hoping mdrun will do the cell allocation itself.
>
> Thanks,
> Amit
>
>
> On Fri, Feb 19, 2010 at 2:27 PM, Mark Abraham wrot
Hi Mark,
I am not using PME calculation.
I was hoping mdrun will do the cell allocation itself.
Thanks,
Amit
On Fri, Feb 19, 2010 at 2:27 PM, Mark Abraham wrote:
> - Original Message -
> From: Amit Choubey
> Date: Saturday, February 20, 2010 8:51
> Subject: [gmx-users] domain decompo
- Original Message -
From: Amit Choubey
Date: Saturday, February 20, 2010 8:51
Subject: [gmx-users] domain decomposition and load balancing
To: Discussion list for GROMACS users
> Hi Everyone,
> I am trying to run a simulation with the option "pbc=xy" turned on. I am
> using 64 processo
Hi Everyone,
I am trying to run a simulation with the option "pbc=xy" turned on. I am
using 64 processors for the simulation. The mdrun_mpi evokes the following
error message before starting the md steps
There is no domain decomposition for 64 nodes that is compatible with the
given box and a min
Chih-Ying Lin wrote:
Hi
From Gromacs Manual:
* Backbone: all protein backbone atoms (C-alpha, N, C)
* MainChain: backbone atoms, plus the carbonyl oxygens
The following is part of .gro file.
I listed the atom number, are those all correct ?
C-alpha: 161,170,179
These are not C
Hi
>From Gromacs Manual:
- Backbone: all protein backbone atoms (C-alpha, N, C)
- MainChain: backbone atoms, plus the carbonyl oxygens
The following is part of .gro file.
I listed the atom number, are those all correct ?
C-alpha: 161,170,179
N:158,163, 172
C: ??? what does this "C" rep
Hello !
I would like to have some information about how to set the coefficients
for tabulated potentials.
I'm using coulombtype ewald and vdwtype user so I have to define tables
for each pair of atoms (and/or one table all the rest of them) :
table.xvg
table_Si_O.xvg
table_Si_Si.xvg
table_O_O.xvg
- Original Message -
From: Maurício Menegatti Rigo
Date: Friday, February 19, 2010 22:28
Subject: Re: [gmx-users] Help with Segmentation fault!!!
To: Discussion list for GROMACS users
> But what is the real problem about the use of -DFLEXIBLE? Will I get wrong
> calculations from MD if
But what is the real problem about the use of -DFLEXIBLE? Will I get wrong
calculations from MD if I define it? Or it is just a matter of time
(DFLEXIBLE = take longer) ??
2010/2/18 Tsjerk Wassenaar
> Hi Deisy,
>
> > define = -DFLEXIBLE
> > integrator = md
>
> We
Hi E R Azhagiya singam,
You first have to ask yourself whether you're up to it. This is considered
an advanded topic. In particular for groups like these. To start with, do
you know the protonation state of the Zn(Cys)4 group in your case?
Cheers,
Tsjerk
On Fri, Feb 19, 2010 at 9:14 AM, babu go
shaya...@post.tau.ac.il skrev:
Hello Parthiban,
Can you elaborate more on the 'wrong answer'?
Perhaps the following link can shed some light on the 'wrong' answer:
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040276.html
[Deals with g_dist and PBC]
Regards,
-Shay
Quoting parthi...@n
Hello Parthiban,
Can you elaborate more on the 'wrong answer'?
Perhaps the following link can shed some light on the 'wrong' answer:
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040276.html
[Deals with g_dist and PBC]
Regards,
-Shay
Quoting parthi...@ncbs.res.in:
Hello,
Can anyone
Hello,
Can anyone tell, how to index two specific atoms, (one form protein and
one from ligand)
eg; 440th atom of protein & 450th atom of small molecule or OED of small
molecule.
My second question is:
how to calculate the distance b/w these two atoms.
i tried g_dist by including the indexed fil
Hello John,
How large was the force after EM? Large forces often results in systems that
explode during the simulation. Also, did you minimise with or without
solvent? You assessment seems correct - the initial structure wasn't
minimised and the tools of the trade are trying different conforma
If you are new to Gromcs you must study all the documentation/tutorials/HowTo's
first, in particular this one about parametrization of new molecules:
http://www.gromacs.org/Documentation/How-tos/Parameterization
Andreas
---
From: gmx-users-boun...@gromacs.org [mailto:gmx-us
Dear all
I would like to simulate the molecule which consist of a zn atom coordinated to
four CYS residue. I would like to know how to insert the parameters for zn
coordination. As I am new to Gromacs I would like to have detailed
description.I would like to use OPLS force field.
Thanking you
Dear all
I would like to simulate the molecule which consist of a zn
atom coordinated to four CYS residue. I would like to know how to
insert the parameters for zn coordination. As I am new to Gromacs I
would like to have detailed description.I would like to use OPLS force
field.
Thanking you
E R
Dear all
I would like to simulate the molecule which consist of a zn atom coordinated to
four CYS residue. I would like to know how to insert the parameters for zn
coordination. As I am new to Gromacs I would like to have detailed
description.I would like to use OPLS force field.
Thanking you
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