Hi,
I have installed GROMACS 4.0.5 on our cluster (gcc 4.2.1, Open MPI
1.2.3) whereas only mdrun was install with -enable-mpi flag. When I
try to run it via a script (grompp -f pr_complex.mdp -c
complex_from_EM.gro -p complex.top -n complex.ndx -po
complex_from_PR.mdp -o complex_for_PR.tpr) I get
Itamar Kass wrote:
Hi,
I have installed GROMACS 4.0.5 on our cluster (gcc 4.2.1, Open MPI
1.2.3) whereas only mdrun was install with -enable-mpi flag. When I
try to run it via a script (grompp -f pr_complex.mdp -c
complex_from_EM.gro -p complex.top -n complex.ndx -po
complex_from_PR.mdp -o
Itamar Kass wrote:
Hi,
I have installed GROMACS 4.0.5 on our cluster (gcc 4.2.1, Open MPI
1.2.3) whereas only mdrun was install with -enable-mpi flag. When I
try to run it via a script (grompp -f pr_complex.mdp -c
complex_from_EM.gro -p complex.top -n complex.ndx -po
complex_from_PR.mdp -o
Hi
I want to study protein-dna interaction by gromacs. But I have 2 separate
pdb file for protein and dna(there is no 1 pdb file containing both protein
and dna). Can I do this correctly? Is this work current and usual? please
guide me.
___
gmx-users
leila karami wrote:
Hi
I want to study protein-dna interaction by gromacs. But I have 2 separate
pdb file for protein and dna(there is no 1 pdb file containing both protein
and dna). Can I do this correctly? Is this work current and usual? please
guide me.
You will need to end up with one
qzhao...@yahoo.com.cn
___
好玩贺卡等你发，邮箱贺卡全新上线！
http://card.mail.cn.yahoo.com/___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please
Hi,
when I run PR mdrun, i got the following warning message. the program can
not run further.
Step 481 Warning: Pressure scaling more than 1%.
I would greatly appreciate gromacs users suggestions.
Thanking you,
Yours sincerely,
Thamotharan
___
Thamu wrote:
Hi,
when I run PR mdrun, i got the following warning message. the program
can not run further.
Step 481 Warning: Pressure scaling more than 1%.
Please refer to the wiki entry on this topic:
http://oldwiki.gromacs.org/index.php/Errors#Pressure_scaling_more_than_1.25
What is difference between –ignh and –missing option in pdb2gmx command?
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
leila karami wrote:
What is difference between –ignh and –missing option in pdb2gmx command?
Using -ignh allows pdb2gmx to ignore any hydrogen atoms in the input, usually in
the case of an NMR structure, to properly name and assign those that are
necessary in the output, processed,
there is 1 fatal error in pdb2gmx command about pdb file containing 2
separate pdb file (protein:nmr structure, dna: x-ray structure). error
:[There were 38 missing atoms in molecule, if you want to use this
incomplete topology anyhow, use the option -missing](all of missing atoms
are H atom).
leila karami wrote:
there is 1 fatal error in pdb2gmx command about pdb file containing 2
separate pdb file (protein:nmr structure, dna: x-ray structure). error
:[There were 38 missing atoms in molecule, if you want to use this
incomplete topology anyhow, use the option -missing](all of
I use -ignh option but again there is same error.
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post
hello:
I am now using Gromacs4 to deal with a membrane protein and I am
confused on one NOTE.
When I use the parameters rvdw = 0.9 , rlist = 0.9, rcoulomb =
0.9, fourierspacing = 0.12 at the same time, a NOTE will come out, which is
The optimal PME mesh load for parallel
leila karami wrote:
I use -ignh option but again there is same error.
Which force field are you using? Is there an appropriate .hdb file containing
all the residues that you need to add H to? Can you post the exact error
message (i.e., copy and paste from the terminal)?
-Justin
I am using ffG43a1. in hdb file, there is only amino acids relating to
protein and no nucleic acid relating to dna. I post error message in
previous mail.
___
gmx-users mailing listgmx-users@gromacs.org
leila karami wrote:
I am using ffG43a1. in hdb file, there is only amino acids relating to
protein and no nucleic acid relating to dna. I post error message in
previous mail.
Then the answer is to use a different force field or to create the appropriate
.hdb entries. One typically sees
Hi Gloria,
there is nothing wrong with your parameters, the note just refers to
the direct:reciprocal workload being not optimal from a performance
point of view. With a small cutoff and a fine PME grid you will have
a high workload for the reciprocal space calculations - which is ok
and will
hi all, i am analyzing a trajectory of a membrane protein embedded in DMPC
bilayer. for this i'm using deuterium order analysis where i have created two
different index groups for the acyl chains. now when i am running g_order its
giving an error message like
Program g_order, VERSION 4.0.5
Hi,
yes, the trr is 7GB.
Alex
Berk Hess schrieb:
Hi,
-append yes is incorrect, it should be -append without the yes.
In this case this error has no effect though.
Is your trr file larger than 2 GB?
We have fixed a bug with this in the upcoming 4.0.6 release.
Berk
Date: Fri, 28 Aug
If you need a fix now, it is one line in src/gmxlib/checkpoint.c:
- outputfiles[i].offset = ( ((off_t) offset_high) 32 )
| ( (off_t) offset_low );
+ outputfiles[i].offset = ( ((off_t) offset_high) 32 )
| ( (off_t) offset_low mask );
Berk
Date:
Samik Bhattacharya wrote:
hi all, i am analyzing a trajectory of a membrane protein embedded in
DMPC bilayer. for this i'm using deuterium order analysis where i have
created two different index groups for the acyl chains. now when i am
running g_order its giving an error message like
Hi,
I'm pulling 2 diamond slabs (which enclose two water slabs) in opposite
direction
with pull_rate1=0.01 (nm/ps) in x direction (pbc in 3d).
Now looking at the gro file that is finally output when the sim is
finshied and averaging
the speeds of the two diamonds I get ca. +/-1.78 (I guess
Abhishek Banerjee wrote:
Hi all,
Actually I want simulate some binary liquid mixture like DMF
and methanol and just want to find diffusion coefficient for each of the
components. But the problem is I am not able to create DMF solvent box.
I have created the .itp and .pdb file of
Hi all,
Actually I want simulate some binary liquid mixture like DMF and
methanol and just want to find diffusion coefficient for each of the
components. But the problem is I am not able to create DMF solvent box. I have
created the .itp and .pdb file of DMF from
--- On Mon, 31/8/09, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] error in Deuterium order analysis
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Monday, 31 August, 2009, 7:25 PM
Samik Bhattacharya wrote:
hi all,
Hello,
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www
Hello,
I meet a problem, that is segmentation fault. And this
segmentation fault comes out when I heat my system, the step grompp -f
heat_water.mdp -c...-n ...-p ...-o The original signs are as
follows:
processing topology...
Opening library file
??? wrote:
Hello,
I meet a problem, that is segmentation fault. And this
segmentation fault comes out when I heat my system, the step grompp -f
heat_water.mdp -c...-n ...-p ...-o The original signs are as
follows:
processing topology...
Opening library file
Hello everyone,
I would like to know does the harmonic biasing potential for running
umbrella sampling in gromacs have a 0.5 in front or is the 0.5 term
incorporated into the force constant value that we specify?
On other words is the potential V=0.5*k(x-xo)^2 or V=k(x-xo)^2.
I am using
30 matches
Mail list logo
