Hi:
I tried to compile GMX source code by VC
6.0.
I found the main function of MD simulation is
in mdrun.c. And then i compiled it as main file.
But some varier type my compiler can not find .
Such as :
LONG;TCHAR;BSTR;
BOOL;DATE;
How can i fix it !
thanks a lot
Hi,
Find them in /include
Yang Ye
主月 :) wrote:
Hi:
I tried to compile GMX source code by VC 6.0.
I found the main function of MD simulation is in mdrun.c. And then i
compiled it as main file.
But some varier type my compiler can not find . Such as :
LONG;
TCHAR;
BSTR;
BOOL;
DATE;
How
Arneh Babakhani wrote:
Can you use this freezegroups function during a minimizaiton? (say if
you wanted to minimize solvent around your protein, while keeping the
protein fixed?)
please try before you buy, sorry before asking questions...
this should work anyway.
David van der Spoel wrote:
Hi:
I tried to compile GMX source code by VC 6.0.
I found the main function of MD simulation is in mdrun.c. And then i
compiled it as main file.
But some varier type my compiler can not find . Such as :
LONG;
TCHAR;
BSTR;
BOOL;
DATE;
Follow the instructions for configure and
Diana Rodriguez Ortiz wrote:
Hi Mr. Spoel,
I am working with a small protein (50 aminoacids) that has a metal atom
near its center. Where can I find the
parameters to be able to run a molecular dynamics of this protein? In this
one, the metal is tied to 4 sulfurs I will
run it with
Thanks a lot Dr. David Spoel :)
I compiled GROMACS again with CFLAGS=-g , after that i ran mdrun_mpi. It is
running fine though with some warning. This time I specified the full path
of mdrun_mpi binary.
But now I am having one strange problem. Sometimes it runs smoothly and
sometimes it
Alok wrote:
Thanks a lot Dr. David Spoel :)
I compiled GROMACS again with CFLAGS=-g , after that i ran mdrun_mpi. It
is running fine though with some warning. This time I specified the full
path of mdrun_mpi binary.
But now I am having one strange problem. Sometimes it runs smoothly and
Thanks again to your help.
I will discuss these issues with my system administrator.
I am really grateful for being a part of this excellent mailing list.
Warm regards,
Alok Jain
- Original Message -
From: David van der Spoel [EMAIL PROTECTED]
To: Discussion list for GROMACS users
Hi users:
I have a little question. I found some L-J parameters for heme iron for the
GROMOS87 FF and I want to use it in the GROMOS ff43a1 . The units as appear
in the paper [biophys. J. 1995 (69) p810] A(kJ nm^ -12 mol ^-1) 4.30115e-5
and B (kJ nm^ -6 mol ^ -1) 8.886909e-3. I need to make
Diana Rodriguez Ortiz wrote:
Hi,
I thank you for your attention. I tried to use the mailing list but
something has changed in that web page and I
did not figure out how to enter my query. The metal is Zn and it is in a
tetrahedral strucuture. It is not completely
shielded from the
Anthony Cruz wrote:
Hi users:
I have a little question. I found some L-J parameters for heme iron for the
GROMOS87 FF and I want to use it in the GROMOS ff43a1 . The units as appear
in the paper [biophys. J. 1995 (69) p810] A(kJ nm^ -12 mol ^-1) 4.30115e-5
and B (kJ nm^ -6 mol ^ -1)
Hello list,
My name is Francisco and I'm configuring a cluster to run gromacs using mpi.
As far as i concern i have to install both gromacs and gromacs-mpi. The
question is: do i have to install it on every cluster machinne?
i have made some tests and it seems that the answer is yes, but i would
Hi, Seems GROMACS implements leap-frog version. What are the stored
quantities, are they the current positions and velocities in the trajectory
file? How do I restart a simulation at the exact point (position and
velocity) of a previous simulaton.
Does GROMACSD have velocity Verlet for an
Robson Pacheco wrote:
Dear Sirs
I am new in molecular simulations, and I am experiencing many problems
in generating topology files (GROMACS) for the systems I intend to
study. I used The Dundee PRODRG Server in order to generate the files
for a GROMACS run, however, the program pdb2gmx
Have you followed the Drug-Enzime complex tutorial found at
http://www2.umdnj.edu/~kerrigje/structbio_II.htm ?
On Fri, 09 Jun 2006 20:40:28 +0200, David van der Spoel [EMAIL PROTECTED]
wrote:
Robson Pacheco wrote:
Dear Sirs
I am new in molecular simulations, and I am experiencing many
Hello, I'm getting the following warning when running grompp:
processing coordinates...
Warning: atom names in ../BuildInitialStructure/NoBadWater.top and
../BuildInitialStructure/NoBadWater.gro don't match (HW2 - OW)
Warning: atom names in ../BuildInitialStructure/NoBadWater.top and
Francisco Tufró wrote:
Hello list,
My name is Francisco and I'm configuring a cluster to run gromacs using mpi.
As far as i concern i have to install both gromacs and gromacs-mpi. The
question is: do i have to install it on every cluster machinne?
i have made some tests and it seems that the
Arneh Babakhani wrote:
*Hello, I'm getting the following warning when running grompp:*
processing coordinates...
Warning: atom names in ../BuildInitialStructure/NoBadWater.top and
../BuildInitialStructure/NoBadWater.gro don't match (HW2 - OW)
Warning: atom names in
No ions, it's a neutral system.
The order of DMPC and Water, in what sense?
In the gro file, the proteins come first, then the DMPC residues, then
the water.
The order is similar in the [system] part of my top file.
Are we allowed to send attachments on this user-list? If so, I'm more
David, thanks for answering.strange. i've installed one version of gromacs on the front end machinne but when it tries to run mprun_mpi it says that cannot find it (obvously because is searching on a node that is not the frontend machinne).
Where can i find a step by step example of working with
Hi Diana
Bredenberg and Nilsson Int journal of Quantum Chem 83, 230-244 2001
This paper describes modeling of Zinc Sulfhydryl bonds in Zinc fingers
The zinc is tetrahedrally coordinated.
Hope it helps.
Alpay
Date: Fri, 09 Jun 2006 15:51:03 +0200
From: David van der Spoel [EMAIL PROTECTED]
Just in case.
The order of atoms in your gro files should match the order in the top
files.Like if we have 1 Protein and then 1 DMPC then again 1 PROTEIN
and 1 DMPC, then top files should read as
Protein 1
DMPC 1
Protein 1
DMPC 1
and so on...
Hope this helps.
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