Hi
I am having a trouble during inflategro scaling my
system.gro
perl inflategro system.gro 4 POPE 14 system_inflated.gro 5 area.dat
Reading.
Scaling lipids
There are 0 lipids...
Illegal division by zero at inflategro line 300.
regards:
shikha
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Dear Users, I am unable to get pass the first step of ./configure . This
step works, but when typing "make" it says:
no targets specified and no makefile found.
Should it be like this, or is it compulsory to use cmake?
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Dear Gromacs Enthusiasts.
I am experiencing problems with mdrun_mpi (4.5.3) on a Nehalem cluster.
Problem:
This runs fine:
mpiexec -np 72 /../mdrun_mpi -pd -s full031K_mdrun_ions.tpr
This produces a segmentation fault:
mpiexec -np 128 /../mdrun_mpi -pd -s full031K_mdrun_ions.tpr
So the only dif
Try POP instead of POPE :)
From: gmx-users-boun...@gromacs.org on behalf of shikha agarwal
Sent: Thu 12/23/2010 4:21 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Illegal division by zero at inflategro
Hi
I am having a trouble during inflategro sc
On 23/12/2010 6:58 PM, gromacs wrote:
I think the batch system will be more efficient. The interactive mode
is not good, because we have to wait for the job.
So is there any program or do we have to write some small program to
creat a batch jobs?
You normally need to write a script. The admini
On 23/12/2010 10:01 PM, Wojtyczka, André wrote:
Dear Gromacs Enthusiasts.
I am experiencing problems with mdrun_mpi (4.5.3) on a Nehalem cluster.
Problem:
This runs fine:
mpiexec -np 72 /../mdrun_mpi -pd -s full031K_mdrun_ions.tpr
This produces a segmentation fault:
mpiexec -np 128 /../mdrun_m
On 23/12/2010 6:02 PM, gromacs564 wrote:
Hi ,
I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam
web(they are glycam06 force field,included in AMBER) ,but cannot converted
this amber files to gromacs files format.
Can anyone help me to convert this (amber
I would like to suggest to you read [1]
Furthermore, you can read INSTALL.cmake file which explains some steps to
compile Gromacs through cmake command.
[1] http://www.gromacs.org/Developer_Zone/Cmake
--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - U
Dear All,
This year, the 25th Molecular Modelling Workshop
(http://www.chemie.uni-erlangen.de/ccc/conference/mmws11/)
will take place on April, 4th to 6th. For the ninth time, the workshop will be
hosted by the University of Erlangen-Nuremberg.
The research group of Professor Tim Clark at the
Quoting shikha agarwal :
> Hello Justin,
>
> Thank you for your reply.
>
> I modifed ffG53a6bn_lipid.itp
This is not ffG53a6nb_lipid.itp, this is simply a modified lipid.itp to which it
looks like you've added a line for OW (which contains the wrong mass). The
instructions in the tutorial d
Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private help service. I have CC'ed this message to the list and I would ask
that all further correspondence be sent to the list. See comments below.
Quoting AJANI HARESH :
> Respected Sir,
>
>
> I am HARESH AJANI
>On 23/12/2010 10:01 PM, Wojtyczka, André wrote:
>> Dear Gromacs Enthusiasts.
>>
>> I am experiencing problems with mdrun_mpi (4.5.3) on a Nehalem cluster.
>>
>> Problem:
>> This runs fine:
>> mpiexec -np 72 /../mdrun_mpi -pd -s full031K_mdrun_ions.tpr
>>
>> This produces a segmentation fault:
>> m
Hello all !!
I have a 30 ns trajectory in two parts (0-20 & 20-30). I am using Gromacs
4.0.7. I concatenated using trjcat (*echo 2 | trjconv -s md10-30.tpr -f
0-30.trr -o pbc_whole.trr -n index_grdf.ndx -nice 0*).
Then I converted the concatenated trajectory into pbc trajectory using
trjconv (*ec
Have a look at acpype.googlecode.com
Alan
2010/12/23 gromacs564
>
> Hi ,
>
> I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam
> web(they are glycam06 force field,included in AMBER) , but cannot converted
> this amber files to gromacs files format.
>
>
> Can
Does anybody know if it is possible to optimize the box size during an
energy minimization in Gromacs?
Can I make pressure coupling if it's possible?
Is there a workaround if there is no direct way?
Thanks!
Ting
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Dear users,
I made the a topology, but when I grompp for EM I get this weird message:
Fatal error:
Syntax error - File forcefield.itp, line 12
Last line read:
'Buckingham 1 no 1.0 1.0'
Found a second defaults directive.
I attached the topology here with t
On 24/12/2010 7:01 AM, Sergio Manzetti wrote:
Dear users,
I made the a topology, but when I grompp for EM I get this weird message:
Fatal error:
Syntax error - File forcefield.itp, line 12
Last line read:
'Buckingham 1 no 1.0 1.0'
Found a second defaults
Hi,
Not sure exactly what you plan to simulate but here are a couple of
potential pitfalls:
Does acpype call amb2gmx.pl or is it new code that converts? If it is a
amb2gmx.pl call I'd check the torsions on the NAc group if you have one.
They didn't get translated when I used it.
When using amber
On 24/12/2010 3:28 AM, Wojtyczka, André wrote:
On 23/12/2010 10:01 PM, Wojtyczka, André wrote:
Dear Gromacs Enthusiasts.
I am experiencing problems with mdrun_mpi (4.5.3) on a Nehalem cluster.
Problem:
This runs fine:
mpiexec -np 72 /../mdrun_mpi -pd -s full031K_mdrun_ions.tpr
This produces a
On 24/12/2010 5:17 AM, MyLinkka wrote:
Does anybody know if it is possible to optimize the box size
during an energy minimization in Gromacs?
Optimize for what criterion?
Can I make pressure coupling if it's possible?
Sure, that's in the manual and covered in tutorials.
Mark
On 24/12/2010 4:58 AM, Chandan Choudhury wrote:
Hello all !!
I have a 30 ns trajectory in two parts (0-20 & 20-30). I am using
Gromacs 4.0.7. I concatenated using trjcat (*echo 2 | trjconv -s
md10-30.tpr -f 0-30.trr -o pbc_whole.trr -n index_grdf.ndx -nice 0*).
That looks like subset creati
On 24/12/2010 8:34 AM, Mark Abraham wrote:
On 24/12/2010 3:28 AM, Wojtyczka, André wrote:
On 23/12/2010 10:01 PM, Wojtyczka, André wrote:
Dear Gromacs Enthusiasts.
I am experiencing problems with mdrun_mpi (4.5.3) on a Nehalem
cluster.
Problem:
This runs fine:
mpiexec -np 72 /../mdrun_mpi -
On 23/12/2010 9:12 PM, Sergio Manzetti wrote:
Dear Users, I am unable to get pass the first step of ./configure .
This step works, but when typing "make" it says:
no targets specified and no makefile found.
That suggests configure did not work.
Should it be like this, or is it compulso
Hi,
1. How can I learn the box shape and size of a completed simulation?
2. I want to keep going the previous completed energy minimization by
increasing nsteps. How can I do this?
Best wishes
Mustafa
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On Thu, Dec 23, 2010 at 2:41 PM, mustafa bilsel wrote:
> Hi,
>
> 1. How can I learn the box shape and size of a completed simulation?
>
check the end of the resulting gro file .
> 2. I want to keep going the previous completed energy minimization by
> increasing nsteps. How can I do this?
>
i
Hey -
I need to see"rrg.itp" and "drg.itp" to undesrtand the situation.
=
* Dr. Vitaly V. Chaban | skype: vvchaban *
* Department of Chemistry | email: v.cha...@rochester.edu
Hi,
I have a problem with dssp programme.
I have the programme in /home/m/DSSP. When I write
export DSSP=/usr/local/bin
and then I check /usr/local/bin I couldn't see dssp.
How can I handle this problem. I have caheceked gromacs website
export DSSP=/path/to/dssp
setenv DSSP /path/to/dssp
command
On Fri, Dec 24, 2010 at 8:12 AM, Amit Choubey wrote:
>
>
> On Thu, Dec 23, 2010 at 2:41 PM, mustafa bilsel wrote:
>
>> Hi,
>>
>> 1. How can I learn the box shape and size of a completed simulation?
>>
>
> check the end of the resulting gro file .
>
>
>> 2. I want to keep going the previous comple
On Fri, Dec 24, 2010 at 11:38 AM, mustafa bilsel wrote:
> Hi,
> I have a problem with dssp programme.
> I have the programme in /home/m/DSSP. When I write
> export DSSP=/usr/local/bin
> and then I check /usr/local/bin I couldn't see dssp.
> How can I handle this problem. I have caheceked gromacs
Hi,
I have a problem with dssp programme.
I have the programme in /home/m/DSSP. When I write
export DSSP=/usr/local/bin
and then I check /usr/local/bin I couldn't see dssp.
How can I handle this problem. I have caheceked gromacs website
export DSSP=/path/to/dssp
setenv DSSP /path/to/dssp
command
On Fri, Dec 24, 2010 at 5:36 AM, Mark Abraham wrote:
> On 24/12/2010 5:17 AM, MyLinkka wrote:
>
> Does anybody know if it is possible to optimize the box size during an
> energy minimization in Gromacs?
>
>
> Optimize for what criterion?
>
>
> Can I make pressure coupling if it's possible?
>
>
D
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Fri, Dec 24, 2010 at 3:13 AM, Mark Abraham wrote:
> On 24/12/2010 4:58 AM, Chandan Choudhury wrote:
>
> Hello all !!
>
> I have a 30 ns trajectory in two parts (0-20 & 20-30). I am using Gromacs
> 4.0.7. I concatenated using trjcat (*echo 2 | trjco
Hi thanks, but if I use make it says make no Makefile found...
On Thu, Dec 23, 2010 at 10:46 PM, Mark Abraham wrote:
> On 23/12/2010 9:12 PM, Sergio Manzetti wrote:
>
>>
>>
>>
>>
>> Dear Users, I am unable to get pass the first step of ./configure . This
>> step works, but when typing "make" it
hi ,
Mr. justin
thanx a lot for ur help!
now i m able to generate system_inflated.gro.
but while i m performing Run energy minimization accorning to tutorial
getting this error
grompp -f minim.mdp -c pope.gro -p topol_pope.top -o em1.tpr
mdrun -v -s em1 -o em1 -c after_em -g emlog
Fatal erro
On Fri, Dec 24, 2010 at 3:45 PM, Sergio Manzetti <
sergio.manze...@vestforsk.no> wrote:
> Hi thanks, but if I use make it says make no Makefile found...
>
> Yes, Makefile should be generated by configure. You should check the last
few lines that configure output to your screen and the configure lo
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