subarna thakur wrote:
Hello
We dont have the parameters for Fe4S4 cluster in any of the the gomacs force
fields but if we able to make the .itp file for the cluster manually with the
help of Quantum mechanical calculations, can we place the .itp file of fe4s4 in
the include section of the pro
Hello
We dont have the parameters for Fe4S4 cluster in any of the the gomacs force
fields but if we able to make the .itp file for the cluster manually with the
help of Quantum mechanical calculations, can we place the .itp file of fe4s4 in
the include section of the protein .top file later as
Luis Paulo wrote:
Please
I need to fix all atoms of a proetin and I need to calculte the initital
enregy without to exceute septs of dynsmics.
How can i do this ?
Please start a fresh email when posting, lest search engines be confused
by the contents of some other discussion.
You can do
Lee Soin wrote:
So there is no place to specify electrostatic interactions for pair
interactions?
No. The charges are specified in the [ atoms ] directive. Read the
example in chapter 5.
Mark
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Sounds to me like you have a 52 atom lipid and have a posre.itp file
with more than 52 atoms (or referencing atom numbers greater than 52).
What one usually does is has a somelipid.itp file that, upon some .mdp
define, includes a someposre.itp file that looks like this:
[ position_restraint
--- On Mon, 27/7/09, Morteza Khabiri wrote:
From: Morteza Khabiri
Subject: [gmx-users] POSITION-RESTRAIN
To: gmx-users@gromacs.org
Date: Monday, 27 July, 2009, 7:35 PM
Dear gmxusers.
I want to restrain the lipids in my system which contains protein,lipid
and water. I make the restraint itp f
What hydrogen did you use? Without substantially more cut and paste on
your end I am in the dark and can't help very much.
On the side, I'll mention that your sigma, and especially your
epsilon, looks very low here. I'm no gold expert though, and I am just
pointing that out even though that
Darrell;
If memory serves, there was a paper in the late '80s of a simulation of
monolayer NH3/graphite by William Steele. It reproduced the lattice dimensions
of our experiments, but seemed to over-estimate the corrugation in the binding
energy relative to our diffraction experiments.
Hope t
Darrell Koskinen wrote:
Hi Justin,
With regard to your comment about using other force fields for my
simulation of graphene surrounded by ammonia gas, are referring to the
force fields for both graphene and ammonia or only to the force field
for graphene?
The "force field" should be one
All,
Is there any chance of getting an "official" patch released for 3.3.3
that fixes the mdrun bug I have pointed out in the past, or perhaps an
official, super-minor point release? I can provide the patch -- I'd
just like it posted somewhere official.
The reason for this is that I'm try
Hi Justin,
With regard to your comment about using other force fields for my
simulation of graphene surrounded by ammonia gas, are referring to the
force fields for both graphene and ammonia or only to the force field
for graphene?
I reviewed my selection of the force field parameters for gra
Here are some more details:
My cg minimized structure has a distance of 0.3 Angstroms between Ag
and another atom of another molecule.
Changing all my Ag to hydrogens and running a cg still gives a
distance of 0.3 Angstroms.
I could also add that each Ag belongs to its own charge group, so they
s
what's your minimum atomic distance achieved between Ag and your other molecule (g_mindist)?
If it's < 0.09 nm then you definitely do have some error in your setup. For
proof of that, generate a new system that is identical to yours
but this time use only standard OPLS atom-types and see the pr
Hi Chris,
I've done a gmxdump and there aren't any zeros for any of the LJ values.
No capital letter problems either.
Chris Rowan
Mon, 27 Jul 2009 12:30:54 -0700
Sounds like your topology/forcefield is incorrect or incomplete.
Does your log file from mdrun or the stderr/stdout from grompp/md
Sounds like your topology/forcefield is incorrect or incomplete.
Does your log file from mdrun or the stderr/stdout from grompp/mdrun indicate
that you don't have any LJ parameters for
some atom types? Try a gmxdump on your .tpr file and inspect the LJ parameters
by hand. Are there any zero's w
Gromacs uses nm as the unit of distance. Did you account for that? If so, please add some .mdp file
snippits and any other relevant files so that we can see directly what you are doing.
Chris.
--- original message ---
Hello users,
I am trying to reproduce a calculation that I carried out in D
Hello,
I am recently experimenting with a 5 fs timestep using virtual hydrogens
and LINCS. I am getting sporadic LINCS warnings, although the system
appears stable and does not blow up during the 100ns in which I get such
warnings. If I reduce the timestep to 4 fs from 5 fs (and increase
nstl
Hello,
I'm using ffoplsaa with a new atom type (Ag) that I've included in the .atp
file, LJ parameters I've specified in the nb file. My system topology I've
written by hand in an itp file. The problem is that after any kind of run
the molecule penetrates the metal surface! This shouldn't be ha
Hello users,
I am trying to reproduce a calculation that I carried out in DL_POLY.
It is to calculate the transport diffusion coefficient for CH4 in a
frozen mesoporous silica.
In DL_POLY I used an external force of 0.1 kJ mol-1 A-1. (0.1 KJ per
mole per angstrom). This equates to 10 dl_p
o effect.ac anyone pls tell me how to install Grace in Fedora of Redhat?
> thanking you all
> Shamik
>
>
>
> See the Web's breaking stories, chosen by people like you. Check
> out Yahoo! Buzz. http://in.buzz.yahoo.com/
> -- next part --
> A
So there is no place to specify electrostatic interactions for pair
interactions?
2009/7/27 Mark Abraham
> Lee Soin wrote:
>
>> I see in the .top file generated by pdb2gmx:
>> [ pairs ]
>> ; aiaj functc0c1c2c3
>>
>> The [ pairs ] directive a
Lee Soin wrote:
I see in the .top file generated by pdb2gmx:
[ pairs ]
; aiaj functc0c1c2c3
The [ pairs ] directive accepts these four parameters c0, c1, c2 and c3. Do
c2 and c3 parametrize electrostatic interactions? And what do they stand fo
jimkress_58 wrote:
If you are using a vanilla RedHat system, the yum method will work.
However, if you are using a prepackaged clustering environment (like ROCKS)
you may break it.
All you nee to know to install grace is the location of the headers and
libraries for Lesstiff. You then supply th
Morteza Khabiri wrote:
Dear gmxusers.
I want to restrain the lipids in my system which contains protein,lipid
and water. I make the restraint itp file by genpr then I added it in
toplogy file.
After doing grompp to make tpr file I get the following message:
Fatal error:
[ file "posre_entirelipi
Dear gmxusers.
I want to restrain the lipids in my system which contains protein,lipid
and water. I make the restraint itp file by genpr then I added it in
toplogy file.
After doing grompp to make tpr file I get the following message:
Fatal error:
[ file "posre_entirelipid1.itp", line 56 ]:
If you are using a vanilla RedHat system, the yum method will work.
However, if you are using a prepackaged clustering environment (like ROCKS)
you may break it.
All you nee to know to install grace is the location of the headers and
libraries for Lesstiff. You then supply them to grace as a part
I see in the .top file generated by pdb2gmx:
[ pairs ]
; aiaj functc0c1c2c3
The [ pairs ] directive accepts these four parameters c0, c1, c2 and c3. Do
c2 and c3 parametrize electrostatic interactions? And what do they stand for
respectively? Th
On Mon, 2009-07-27 at 16:48 +0530, Samik Bhattacharya wrote:
> hi alli'm facing alot of trouble in installing grace in my redhat
> machine. its always complaining about Motiff API.. ive installed
> Lesstiff but even afetr that grace is not getting installedi can't
> make out how to install it?
hi alli'm facing alot of trouble in installing grace in my redhat machine. its
always complaining about Motiff API. ive installed Lesstiff but even afetr that
grace is not getting installed...i can't make out how to install it? is there
any problem in the path? should i've to set path before gr
Enemark Soeren wrote:
-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel
Sent: Monday, July 27, 2009 5:12 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] diffusion, g_msd and trestart
Enemark S
-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel
Sent: Monday, July 27, 2009 5:12 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] diffusion, g_msd and trestart
Enemark Soeren wrote:
> Dear all
subarna thakur wrote:
Hello
The protein I am considering is a homodimer with two chains with a Fe4S4 cluster situated at the interface of two chains with connections with both the chains by cystein residues.I have generated the .itp file of the Fe4S4 cluster and .top of the protein with pdb2gmx c
-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel
Sent: Monday, July 27, 2009 5:12 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] diffusion, g_msd and trestart
Enemark Soeren wrote:
> Dear all
> Date: Mon, 27 Jul 2009 11:12:16 +0200
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] diffusion, g_msd and trestart
>
> Enemark Soeren wrote:
> > Dear all,
> >
> > I am trying to calculate diffusion coefficients for a system of (30)
> > glycine molecules
David van der Spoel wrote:
> Emanuel Peter wrote:
>> Dear Gromacs-users,
>>
>> At the moment I have a question which regards the different
>> electrostatic algorithms mentioned in the Gromacs-manual.
>>
>> I did some simulations and I tried three different electrostatic
>> algorithms: Cut-off, Shif
Enemark Soeren wrote:
Dear all,
I am trying to calculate diffusion coefficients for a system of (30)
glycine molecules in a box with (1000) water.
After running:
g_msd –f md.xtc –s md.tpr –mol –n molindex.ndx
I get a list of diffusion coefficients – one for each glycine molecule.
I
Dear all,
I am trying to calculate diffusion coefficients for a system of (30)
glycine molecules in a box with (1000) water.
After running:
g_msd -f md.xtc -s md.tpr -mol -n molindex.ndx
I get a list of diffusion coefficients - one for each glycine molecule.
I then calculate the average a
Hello
The protein I am considering is a homodimer with two chains with a Fe4S4
cluster situated at the interface of two chains with connections with both the
chains by cystein residues.I have generated the .itp file of the Fe4S4 cluster
and .top of the protein with pdb2gmx command.The .top file
Emanuel Peter wrote:
Dear Gromacs-users,
At the moment I have a question which regards the different
electrostatic algorithms mentioned in the Gromacs-manual.
I did some simulations and I tried three different electrostatic
algorithms: Cut-off, Shift and PME.
It is clear to me what Shift and P
Dear Gromacs-users,
At the moment I have a question which regards the different
electrostatic algorithms mentioned in the Gromacs-manual.
I did some simulations and I tried three different electrostatic
algorithms: Cut-off, Shift and PME.
It is clear to me what Shift and PME means principally, b
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