- Original Message -
From: lloyd riggs
Date: Wednesday, June 23, 2010 15:49
Subject: [gmx-users] Re: chain ids (2)
To: gmx-users@gromacs.org
>
> Dear All,
>
> I am re-posting with some replies to my first message.
>
> > the cell demensions for .gro files are at the bottomn,
>
> yo
- Original Message -
From: 聂雪川
Date: Wednesday, June 23, 2010 18:29
Subject: [gmx-users] Problem of reading the atom'force from trr file using
template.c
To: gmx-users@gromacs.org
---
|
> Dear all,
>I am trying to
Hi all,
I am using the template.c file to make some individual
analyses. Using top.atoms.atomtype[i] I can get the
information of the atom type of atom i. Is it then possible
to use this information to get the mass of this specific
atom?
Thanks a lot
--
gmx-users mailing listgmx-users@groma
Yes, that is an interesting question. I don't know the answer, but is there any
way to get the numerical values of the matrix from Gromacs tools that produce a
matrix in xpm format ? I have problems with g_rms and g_rmsdist is another
candidate.
Andreas
> -Original Message-
> From: gmx
On Wed, Jun 23, 2010 at 10:20:19AM +0100, Kukol, Andreas wrote:
> Yes, that is an interesting question. I don't know the answer, but is there
> any way to get the numerical values of the matrix from Gromacs tools that
> produce a matrix in xpm format ? I have problems with g_rms and g_rmsdist is
Sure. Look through the data structures for arrays of mass.
Mark
- Original Message -
From: Sebastian Waltz
Date: Wednesday, June 23, 2010 19:15
Subject: [gmx-users] get the mass having the atom type
To: gmx-users@gromacs.org
> Hi all,
>
> I am using the template.c file to make some in
Well I would suggest you should do some very careful testing to validate
the combination of CHARMM charges and one dihedral with the rest of the
parameters from OPLS. It is not very common (or generally wise) to mix
and match parameters from different forcefields, see:
http://www.gromacs.org/i
Sebastian Waltz skrev:
Hi all,
I am using the template.c file to make some individual
analyses. Using top.atoms.atomtype[i] I can get the
information of the atom type of atom i. Is it then possible
to use this information to get the mass of this specific
atom?
Thanks a lot
top.atoms.atom[
Dear Mark ;
The ./template dosn't have additional flags as shows below.The "-force" option
dosn't work.
==
=Option Filename Type Description
=
= -s md.tpr
Hi Chuan,
in the template.c file is in the beginning the flag
initialized:
intflags = TRX_READ_X;
If you want to read out the forces you have to change this
to, as:
intflags = TRX_READ_F;
in addition to changing fr.x to fr.f.
Basti
On Wed, 23 Jun 2010 20:00:27 +0800
聂雪川 wr
Dear Andreas and Marc,
Thanks for your reply.
I am not familiar with the gromacs programming code and so I am trying
to build myself the FEL.
I can generate the hisotgram of the number of states from the
projection along principal component 1 and 2 (PC1 and PC2) using
SigmaPlot but here I am stucke
I'm trying to install a local copy of GROMACS on Ohio Super Computer.
I was able to build single and double precision versions (did make
distclean after each), however, got errors while installing parallel
version.
I will appreciate you taking time to help with this installation. Thanks.
This is
Hello All,
I am new in this field, and I want to do simulation study on one of the protein
conatining a metal ion and study its ability to form co-oridnation bond with
other ligand, which is not defined in GROMOS force field which I have tried. If
this choice of force field is correct for such
onetwo wrote:
Hello All,
I am new in this field, and I want to do simulation study on one of the
protein conatining a metal ion and study its ability to form
co-oridnation bond with other ligand, which is not defined in GROMOS
force field which I have tried. If this choice of force field is
Dear Tom:
Thanks for your suggestion. You are absolutely right on doing more
testings. I simply haven't figure out what the appropriate test is
yet. Could you be more specific about "these parameters perform just
as well as"? What kind of test did you do?
Also, is there a reason why you c
Hello Justin,
Thanks for your help. Actually, I meant if I use -d option rather than -box
I would have better control on bond distance between monomer units. By try
and error I found out if I used -d 0.0017 the distance between two adjacent
C (2 monomer ends) is 1.54A. which is the bond length for
I chose the AMBER ATP for OPLS as I wanted to simulate my system with
two different all-atom forcefields and knew that I could use AMBER in
GROMACS with these published parameters (through use of the ffamber
ports). The only other all-atom forcefield in GROMACS at that time was
OPLS and rather
Hi all,
I am trying to use g_sham to generate a free-energy profile based on
the end-to-end distances of a peptide.
The only documentation that I have been able to find is in the GROMACS
v.4 pdf manual, which is a little out-of-date, and the g_sham -h output, which
I assume is
Moeed wrote:
Hello Justin,
Thanks for your help. Actually, I meant if I use -d option rather than
-box I would have better control on bond distance between monomer units.
By try and error I found out if I used -d 0.0017 the distance between
two adjacent C (2 monomer ends) is 1.54A. which i
Warren Gallin wrote:
Hi all,
I am trying to use g_sham to generate a free-energy profile based on
the end-to-end distances of a peptide.
The only documentation that I have been able to find is in the GROMACS
v.4 pdf manual, which is a little out-of-date, and the g_sham -h ou
On Wed, 23 Jun 2010, Andrei Neamtu wrote:
Dear Andreas and Marc,
Thanks for your reply.
I am not familiar with the gromacs programming code and so I am trying
to build myself the FEL.
I can generate the hisotgram of the number of states from the
projection along principal component 1 and 2 (PC1
OK, what if I have only one dimension (end-to-end distance), is there any way
to do that in GROMACS, or is the best way to just write a little app for myself?
Warren Gallin
On 2010-06-23, at 11:29 AM, Justin A. Lemkul wrote:
>
>
> Warren Gallin wrote:
>> Hi all,
>> I am trying to use g_s
Warren Gallin wrote:
OK, what if I have only one dimension (end-to-end distance), is there any way
to do that in GROMACS, or is the best way to just write a little app for myself?
Sounds to me like a problem for PMF, but I seem to recall you had some issues
with that. g_sham requires 2 dim
Justin,
Yes, in order to use the implemented free energy method, the end-to-end
distance has to be treated like a constraint, creating a closed ring of
constraints, which on some rare occasions leads to an instability and the
system blows up.
I think that my best move is to wri
Dear All,
I am trying to run the Position Restrained simulation for the Coarse Grained
DSPC bi-layer. However, I am quite confused that how to generate the
position restraint file for the CG atoms in lipid. Is there a difference
between the position restraint file for the fine grained and coarse g
sunny mishra wrote:
Dear All,
I am trying to run the Position Restrained simulation for the Coarse
Grained DSPC bi-layer. However, I am quite confused that how to generate
the position restraint file for the CG atoms in lipid. Is there a
difference between the position restraint file for th
Hi,
Thanks a lot for the quick reply. I want to position restrain the head group
atoms of CG DSPC but I am not sure about the head group molecules in DSPC.
Can you please tell me how to figure out the head group atoms or molecules.
Also, when you say co-ordinate file then you mean .itp file for t
sunny mishra wrote:
Hi,
Thanks a lot for the quick reply. I want to position restrain the head
group atoms of CG DSPC but I am not sure about the head group molecules
in DSPC. Can you please tell me how to figure out the head group atoms
Presumably there is a structure of DSPC somewhere
Dear Antonio,
thank you.
I think I got the idea. I need to use a cut-off for the probability:
for all the probabilities lower than a certain value I assign to them
that (lower) value so the energy will be constant.
Thanks,
Andrei
On Wed, Jun 23, 2010 at 8:49 PM, wrote:
>
> On Wed, 23 Jun 2010,
Thanks for the response, Chris. And sorry that I was not detailed
enough earlier. I've read through the manual several times, and I'm
familiar with all of the passages that you cited. I am parameterizing
PtdIns4,5P2. OSL is one of the atom types in it (it is a phosphate
ester oxygen).
OSL is i
Are you using the most recent git version? I think the date string indicates
you're using a version that's several months old (I could be wrong). If you
haven't pulled the latest git, please do. There have been several changes
related the the CHARMM implementation and bugs that have been di
Hi
I want to perform water channel simulations, where channel is connected to
bath of bulk water at standard thermodynamic conditions. The objective is to
get the density distribution of water inside the channel , which is in
equilibrium with the bath.
Is there any tutorial specific to gromacs wh
Carsten,
Thanks for your help, I used something like "mpirun -np 3 mdrun -s topol.tpr",
it works but its something like repeating a single job 3 times, simultaneously.
here is the output on the screen :
{
Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.1#
Back Off! I jus
Thanks Justin for the help,
I have Manganese in my protein with other two ligands at the active site.
I am using GROMOS96 43a1 force field.
Mangnese may have topology similar to Magnesium 2+, What I found is that I need
to do changes in ffG43a1.rtp and ffG43a1nb.itp. But how should I calculate
Thanks Justin for the help,
I have Manganese in my protein with other two ligands at the active site.
I am using GROMOS96 43a1 force field.
Mangnese may have topology similar to Magnesium 2+, What I found is that I need
to do changes in ffG43a1.rtp and ffG43a1nb.itp. But how should I calculate
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