Hi All,
I had a few MD runs with double precision in gromacs, Can I use single
precision version of gromacs to play with those files e.g making movie files
and extracting h_bond information.
I am afraid if it will affect my results.
Please suggest
With thanks,
Vivek
__
Hi Justin,
Thanks for your reply. I am using the gmx Gromacs Forcefield. As you said
the topology file does contain the bonds and I need not have made the
modificatins to specbond.dat. But using the original specbond.dat does not
prevent the protonation of CYS. I renamed CYS as CYS2 in the input p
Nice trick with %n on sscanf. I went with the manual replacement but I
do appreciate learning new things, thanks Berk,
Chris.
###
Hi,
That is an annoying bug.
I fixed it for 4.0.3.
If you want it fixed now, the diff is below.
Berk
RCS file: /home/gmx/cvs/gmx/src/kernel/gmxcpp.c,v
retrievi
sarbani chattopadhyay wrote:
Hi,
I am new to Replica exchange molecular dynamics.
I obtained the optimal temperature distribution based on the lowest
and highest
tempearture and exchange probability from the REMD caclulator ,
available through the
gromacs homepage.
There were 17 temper
If there is fraying at the edges only, you can impose distance
restraints on some of the hydrogen bonds at the ends. You need to
modify md.mdp to turn on distance restraints and have a new file
called disres.itp that mentions the distances to be restrained.
Hope this helps,
Mrinalini
On Wed, Nov
He, Yang wrote:
Hi all users,
when I am using the gromacs to simulate the course grain model for DNA, it
seems that the software doesn't recognize my force field file. I have included
all the bond and non-bond parameters in the bon.itp and nb.itp file.
During my simulation , I found that th
Hi,
That is an annoying bug.
I fixed it for 4.0.3.
If you want it fixed now, the diff is below.
Berk
RCS file: /home/gmx/cvs/gmx/src/kernel/gmxcpp.c,v
retrieving revision 1.9
diff -r1.9 gmxcpp.c
121,122c121,122
< sscanf(define,"%s",name);
< ptr = define + strlen(name);
---
> sscanf(defi
When two spaces are included the #define KEYWORD is incompletely removed
from the file.
In case my conclusion about the exact nature of the error is incorrect,
here is more information.
I have a ffcharmbon.itp file that contains:
[ dihedraltypes ]
#define improper_NC2_X_X_C_ 180.0 83.68
Hi everyone,
As I wrote yesterday, I'm having problems running stable simulations with
vsites and constraints in all bonds in different time-steps using
gmx-4.0.2. As long as the dna strand does not cross pbc, the simulations
run fine (the longest I did was 5ns). The dna topology was generated wit
I think that it is worth having a central repository that lists modifications
to forcefield files during development -- especially
changes as opposed to simple additions. It's not always a huge deal, but it would be nice if this information was easily available.
Revision history might be one pla
Dear all:
I am trying to show the dodecahedron box only in vmd since my simulation box
is dodecahedron. If I include water, I can see the box is dodecahedron. But
I want to get rid off all of water, then my box will not appear there. How
can I keep the dodecahedron box boundaries and solute only?
Hi all users,
when I am using the gromacs to simulate the course grain model for DNA, it
seems that the software doesn't recognize my force field file. I have included
all the bond and non-bond parameters in the bon.itp and nb.itp file.
During my simulation , I found that the base pair for C-G
On Tue, 25 Nov 2008 20:39:37 +0530
"Suman Chakrabarty" <[EMAIL PROTECTED]> wrote:
Dear all,
is there an easy way to extract only the water molecules in the
hydration layer/shell around the protein/polymer chain? I need them
both for visualization of the trajectory and some analysis.
trjorder w
Dear all,
is there an easy way to extract only the water molecules in the
hydration layer/shell around the protein/polymer chain? I need them
both for visualization of the trajectory and some analysis.
I can do this by writing my own program alright, but I wanted to know
if there is any in-built
Jenny Hsu wrote:
Dear Justin:
I try to include lipid.itp into ffgmxnb.itp
and I also tried to add the different sections [ atomtypes ], [ pairtypes ],
etc... of the lipid.itp files to ffgmx* files
All you should have to do is copy all the sections of lipid.itp into
ffgmxnb.itp, with the e
[EMAIL PROTECTED] wrote:
Hello,
Sorry, I realised the HEME HEC naming was not the problem. But still the
pdb2gmx causes loss of all bonds of FE in HEME. The cystine also gets
protonated and doesnot form a bond with HEME. I tried to preserve the
bonds by editing the specbond.dat file. I do not k
Dear Justin:
I try to include lipid.itp into ffgmxnb.itp
and I also tried to add the different sections [ atomtypes ], [ pairtypes ],
etc... of the lipid.itp files to ffgmx* files
but when i run grompp, i got another fetal error
"Atomtype 'C' not found"
Jenny
2008/11/25 Justin A. Lemkul <[EMAIL
Hello,
Sorry, I realised the HEME HEC naming was not the problem. But still the
pdb2gmx causes loss of all bonds of FE in HEME. The cystine also gets
protonated and doesnot form a bond with HEME. I tried to preserve the
bonds by editing the specbond.dat file. I do not know if it can be used
for int
Jenny Hsu wrote:
Hi all
when i run grompp
but it gives "Atomtype LC3 not found"
Could anyone explain me briefly?
There's lots of information about this type of error in the list archives.
Take, for example:
http://www.gromacs.org/pipermail/gmx-users/2004-August/011867.html
-Justin
Q. Y. HUAN wrote:
Dear all,
After trjcat, I wish to view the combined trajactory using ngmx. The problem
is, how can i get the tpr combined file in oder to view the trajectory using
ngmx?
No such "combined" .tpr file is necessary; it wouldn't make any sense. What's
in a .tpr? Initial c
Hello,
The file in the local directory is the one that is considered. I am sorry
for the previous mail.
Regards,
Sarada
Graduate student,
NCBS, Bangalore.
Hello,
> I am working in a cluster environment and so, all files there including
> specbond.dat file are write protected. Can someone indicate
>
> Thanks in advance,
> Sarbani
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___
Hello,
I am working in a cluster environment and so, all files there including
specbond.dat file are write protected. Can someone indicate how I can
specify that the program must consider the modified file (specbond.dat) in
my local working directory rather than the one in the main directory?
Than
Hi all
when i run grompp
but it gives "Atomtype LC3 not found"
Could anyone explain me briefly?
Jenny Hsu
--
Jenny Hsu, Biotechnology Dept.,
Ming Chuan University, Taiwan, R.O.C
___
gmx-users mailing list
Hello,
I am working with the simulation of cytochromeP450. In the output of the
pdb2gmx command, the iron atom in the HEME loses all the bonds, including
the sulphide bond with cystine. Also, the command changed the residue name
from HEME to HEC. During the execution of the pdb2gmx, I get this warn
Hi,
You only need to give ngmx 1) combined xtc files 2) single tpr file in
order to visualize the trajectory.
YY
>
> Dear all,
>
> After trjcat, I wish to view the combined trajactory using ngmx. The problem
> is, how can i get the tpr combined file in oder to view the trajectory using
> ngmx
Dear all,
After trjcat, I wish to view the combined trajactory using ngmx. The problem
is, how can i get the tpr combined file in oder to view the trajectory using
ngmx?
thanks for the help
QIU YI HUAN
DEPARTMENT OF CHEMISTRY,
FACULTY OF SCIENCE,
UNIVERSITY PUTRA MALAYSIA,
MALAYSIA.
_
On Mon, 24 Nov 2008 22:28:36 -0500
"Justin A. Lemkul" <[EMAIL PROTECTED]> wrote:
BIN ZHANG wrote:
Hi,:
Is it possible to solvate the system using coarse grained water
molecule?
I tried command: genbox -cp cg_protein.pdb -cs cgwat.pdb -o
cg_protein_water.pdb, but get Segmentation f
Hi QIU YI HUAN,
Was it a warning or did it exit without producing output? Please be
more complete in your postings. Maybe a good idea to include the
output of the program?
In case of an error use gmxcheck first on each of the trajectories. It
seems that one of them is giving an error. Then, if yo
Hi,
I am new to Replica exchange molecular dynamics.
I obtained the optimal temperature distribution based on the lowest and
highest
tempearture and exchange probability from the REMD caclulator , available
through the
gromacs homepage.
There were 17 temperaure values as output. I pr
--- Missatge original
Assumpte:
De: [EMAIL PROTECTED]
Data: Tue, Novembre 25, 2008 9:52 am
A:"Discussion list for GROMACS users"
[EMAIL PROTECTED]
--
Justin A. Lemkul wrote:
>
>
> [EMAIL PROTECTED] wrote:
>>
>> Hi everyone,
>>
>> I'm having problems running an md simulation (with gmx-4.0.2) using vsites
>> and a time step of 4fs. I did generate the tpr with pdb2gmx. The problem
>> seems to occur when the molecule crosses pbc, since the first
Dear all ,
I did a simulation for 2 ns then i extanded the simulation using tpbconv for
another 2 ns. After that, I tried to combine the two trajectory files by using
trjcat by using the following command:
trjcat -f md1.xtc extend1.xtc -o combine.xtc
but it showed a warning that it couldn't rea
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