Hi,
Thankyou for the prompt response. I am using the methanol box provided along
with gromacs software
This is the itp file I am using ...
usr/local/gromacs/share/gromacs/top$ more methanol.itp
#ifndef _FF_GROMOS96
[ atomtypes ]
; type masschargeptype c6c12
OM
Pedro Alberto Valiente Flores wrote:
Hi:
I am trying to compile gromacs 4.03_mpi in ubuntu hardy.
I use this comand-line:
./configure --enable-mpi --prefix=$HOME/software/gmx403 MPICC=
$HOME/software/openmpi/bin/mpicc CPPFLAGS="-I
$HOME/software/openmpi/include -I$HOME/software/fftw/include/"
avinash kumar wrote:
Dear all.
I wish to calculate the surface tension of an interface between two
fluids. Looking at the last year user forum discussions one way
was to use the option "
Use the option "#Surf*SurfTens" in g_energy."
My question is that whether it will be added in the comma
Dear all.
I wish to calculate the surface tension of an interface between two fluids.
Looking at the last year user forum discussions one way
was to use the option "
Use the option "#Surf*SurfTens" in g_energy."
My question is that whether it will be added in the command prompt or where
?
--
A
Hi:
I am trying to compile gromacs 4.03_mpi in ubuntu hardy.
I use this comand-line:
./configure --enable-mpi --prefix=$HOME/software/gmx403 MPICC=
$HOME/software/openmpi/bin/mpicc CPPFLAGS="-I
$HOME/software/openmpi/include -I$HOME/software/fftw/include/"
LDFLAGS="-L$HOME/software/openmpi/lib -L$
Dear All,
I wish to calculate the components of pressure (pressure tensor) of a group,
ie x,y and z components . Is there any any function in GROMACS which will do
it for a group as a function of height. Or do I have to write my own code
for postprocessing. Thank you.
--
Avinash Kumar.
_
Hi,
I just tested it and it runs fine for me with 4.0.3.
Which version are you using?
If it is 4.0.3, please file a bugzilla and attach the tpr file.
Berk
From: lulany...@msn.com
To: gmx-users@gromacs.org
Date: Thu, 29 Jan 2009 15:07:27 -0500
Subject: [gmx-users] "nstlist=-1" dosen't work for
Hi,
Sorry for not being clear on this issue.
I am currently following and preparing lectures and exercises for a workshop
and do not have time to sit back and go deeply into this issue.
What my conclusion is from looking at the code:
With TIP4P water and free-energy any non-perturbed atoms
that
Thanks.
Summary:
1) *.gro from pdb2gmx has no chain id information
2) pdb2gmx has an option to output pdb file
3) If you want to make groups based on chain id :
pdb2gmx -ignh -ff ${forcefield} -f input.pdb -o a.pdb
make_ndx -f a.pdb -o a.ndx > a.output.make_ndx
4) mdrun has an o
Sarah Witzke wrote:
Dear gromacs users,
I'm doing simulations of small molecules in lipid bilayers. Doing the
simulations with a DMPC bilayer works fine for all 4.x versions of gromacs. But
when I try to do an energy minimization of a POPC bilayer, grompp gives the
following error:
/people/d
avinash kumar wrote:
Hello all,
I am working on liquid vapour interfaces. How do I determine which atom
is in vapour state and which one in liquid. What thermodynamics property
will tell me that? Thank you.
You can try using g_clustsize.
From the pure liquid you can compute enthalpy of vap
Hello all,
I am working on liquid vapour interfaces. How do I determine which atom is
in vapour state and which one in liquid. What thermodynamics property will
tell me that? Thank you.
--
Avinash Kumar.
___
gmx-users mailing listgmx-users@gromacs
Hi,
Again I have a problem regarding the "nstlist=-1" option and this time it's
related to parallel runs.
With the help from Berk, I can run my system with nstlist=-1 option and 1 cpu
without any problem. However, each time when I run it using more than one cpu
under MPI, the run crashes immedi
Xiang Mao wrote:
Dear All:
How are you.
Sorry to bother you. I am trying do use gromacs to do MD on a
protein-ligand complex. I am following Dr. Kerrigan's tutorial on
simulation of protein-ligand complex. Here I have a question about the
topology of ligand generated by prodrg. And
Dear All:
How are you.
Sorry to bother you. I am trying do use gromacs to do MD on a protein-
ligand complex. I am following Dr. Kerrigan's tutorial on simulation of
protein-ligand complex. Here I have a question about the topology of
ligandgenerated by
prodrg. And when I run pdb2gmx on my
Since I also use the pull code on these systems (while not using the
free energy code), I tested that system and verified that, for my
system, the tip4p-based Coulomb (SR) discrepancy does not appear to
result when the pull code is used in gromacs 4.0.3.
With pull code and using energygrps
Liu Shiyong wrote:
*.gro has no chain id information.
I can not make energy group(based on chain id) from *.gro file generated
by pdb2gmx
See the mail I just sent.
3. Don't strip H, just to add them back again :)
I have the structure minimized.pdb after EM.
minimized.pdb is
Liu Shiyong wrote:
I tried to make energy groups from the "output" (*.gro) from pdb2gmx.
>
Found 0 atoms with chain identifier B
Group is empty
>
Found 0 atoms with chain identifier A
Group is empty
That means no chain id information in *.gro, but I have to define the
energy groups a
I just realized that my previous post was incorrect on its final test.
The correct conclusion is:
I have done some tests that, for a single system, empirically indicate
that the coulomb(SR) discrepancy occurs only with use of the free
energy code and only when tip4p is in the same energygrps as
Hi,
If I want to define non bonded interactions in my top. I already have
the sigma and epsi values. What I wanted to do is to to use
combination rule 2, then how should I write the pairs part?
ai aj fuc0, c1, ...
1 6 1 ; CAA CBH
2 7
I have done some tests that, for a single system, empirically indicate
that the coulomb(SR) discrepancy occurs only with use of the free
energy code and only when tip4p is in the same energygrps as any part
of the molecule which is perturbed, even if the common atoms are not
perturbed thems
On Wed, Jan 28, 2009 at 6:32 PM, Justin A. Lemkul wrote:
>
>
> Liu Shiyong wrote:
>
>> Hi,
>>
>> Thank for your helpful reply.
>>
>> I understand your feeling. If you have time, please see the following.
>>
>> mdrun has an option to output the final structure(-c). I just knew it
>> after read
Hi,
On Wed, Jan 28, 2009 at 6:31 PM, Mark Abraham wrote:
> Liu Shiyong wrote:
>
>> Hi,
>>
>
>
>> *Step 2:*
>> Starting structure: clean2.pdb
>>
>> I am trying to calculate the energy according to energy groups
>>
>>
>> pdb2gmx -ff G53a6 -f clean2.pdb -p clean2_0.6.top -i
>> clean2_0.6.posre.
Yes, I could use clarification here as well.
I had previously suspected a specific bug relating to the free energy
code and water models (TIP4P-Ew) and contacted the list about this a
few weeks ago. At that time Berk told me that there was no
water-specific free energy code, which I take to mean t
Berk, David, and other developers,
I believe that all the relevant information has already been posted,
but since I use TIP4P ubiquitously, I would like to get some
clarification regarding simulations that may be affected. I currently
understand that:
1. Utilization of TIP4P in the absenc
All,
I just wanted to pass along the below e-mail, previously sent to the
mailing list, and highlight the potential implications.
If I understand properly, there was a bug in all Gromacs versions
beginning prior to 3.3 (probably not 3.1.4) and through 4.0.3 that
affected the TIP4P and TIP
In the manual, have a look at Table 5.4; you are missing lots of parameters
within the topology (masses, force constants for bonds and angles...)
-Justin
Oliver Masur wrote:
Hi,
i'm still trying to use the genbox command to put h2po4 (aka DHP) in the
box.
i've got a gro file for h2po4:*
*DH
Hi,
i'm still trying to use the genbox command to put h2po4 (aka DHP) in the
box.
i've got a gro file for h2po4:*
*DHP
7
1DHP O1 1 2.725 1.500 1.066 -0.0608 0.4317 -0.3840
1DHP O2 2 0.438 0.887 1.066 -0.1943 -0.6301 -0.3887
1DHP O3 3 0.438 2.113 1
sharada wrote:
Hello,
I am doing a simulation of melittin molecule in methanol box for 3 ns.
I am finding that it is unfolding very rapidly and is behaving more like
in water.
Melittin behaviour in water, methanol and also in lipids is well
documented and known since quite some time. I am
Hello,
I am doing a simulation of melittin molecule in methanol box for 3 ns. I am
finding that it is unfolding very rapidly and is behaving more like in water.
Melittin behaviour in water, methanol and also in lipids is well documented and
known since quite some time. I am using the methanol21
Marius Retegan wrote:
Hello
I have a question regarding the different implementation of x2top
program in Gromacs versions 3.3.1 and 3.3.3 (I didn't test version 4).
While trying to generate a very rough topology for a sugar molecule,
when I use x2top version 3.3.3 I get the following error:
From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Re: free energy with TIP4P bug fixed
Date: Thu, 29 Jan 2009 13:48:20 +0100
Hi,
You can apply the cvs diff.
But even simpler, as I said, is just putting your solute and solvent in
separate charge** groups.
** I
Dear gromacs users,
I'm doing simulations of small molecules in lipid bilayers. Doing the
simulations with a DMPC bilayer works fine for all 4.x versions of gromacs. But
when I try to do an energy minimization of a POPC bilayer, grompp gives the
following error:
/people/disk2/sarah/gromacs-4.0
Hi,
You can apply the cvs diff.
But even simpler, as I said, is just putting your solute and solvent in
separate charge groups.
This should circumvent the issue.
Berk
From: dmob...@gmail.com
To: g...@hotmail.com
Date: Thu, 29 Jan 2009 06:35:24 -0600
CC: gmx-users@gromacs.org
Subject: [gmx-user
Hello
I have a question regarding the different implementation of x2top program in
Gromacs versions 3.3.1 and 3.3.3 (I didn't test version 4). While trying to
generate a very rough topology for a sugar molecule, when I use x2top
version 3.3.3 I get the following error:
Berk,
Any chance of getting a fix for 3.3.x versions also? I have several
papers which probably are affected by this problem and I will need to
repeat the calculations with a fixed version and produce errata. I
would prefer to do this with 3.3.x since (a) not all of the data is
with TIP4P
Hi,
The Coulomb energy difference that Chris Neale observed recently
was caused by a bug in the neighborlist assignment with the combination
of free energy and tip4p water optimization.
This bug would cause a few tip4p-tip4p charge interactions to be missing.
I think it has been present in all Gr
dgayat...@ibab.ac.in wrote:
Respected Sir,
Please help me to run the position restraining step of
gromacs by setting the concerned angles,distance &
dihedrals.
Try some of the material here
http://wiki.gromacs.org/index.php/Category:Tutorials
mark
__
Respected Sir,
Please help me to run the position restraining step of
gromacs by setting the concerned angles,distance &
dihedrals.
___
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