On 4/23/12 9:47 PM, Juliana Angeiras wrote:
Hello,
I'm trying to build a box with nbutanol using the residue below for nbutanol
(But), added in ffoplsaa.rtp
; Butanol
[ But ]
[ atoms ]
;
C1 opls_135 -0.18 1
H11 opls_140 0.06 1
H12 opls_140 0.06 1
H13 opls_140 0.06 1
C2 opls_136 -0.12 2
H21 opls
Hello,
I'm trying to build a box with nbutanol using the residue below for nbutanol
(But), added in ffoplsaa.rtp
; Butanol
[ But ]
[ atoms ]
;
C1 opls_135 -0.18 1
H11 opls_140 0.06 1
H12 opls_140 0.06
On Fri, Apr 20, 2012 at 14:49, Olivia Waring wrote:
> My invocation of mdrun, using 8 processors and the following mdp file:
> ...
> There are: 1184 Atoms
> ...
> DD step 4 load imb.: force 181.0%
>
> Not all bonded interactions have been properly assigned to the domain
> decomposition cells
Hi
On 4/23/12 5:54 PM, Andrew DeYoung wrote:
Hi,
If you have time, I have a somewhat embarrassing question to ask. It is
embarrassing because I feel like I should be able to understand or search
for the answer, but I have not had success. So I apologize if this is a
silly question (and it proba
On 4/23/12 5:38 PM, Rashek Kazi wrote:
Dear all,
I am trying to conduct some simple ligand binding studies for a protein system
solvated in water. After inputting the command:
mdrun -v -deffnm em -nt 1
I get the log shown below, nothing completes after this 0 step. Any help would
be apprecia
Hi,
If you have time, I have a somewhat embarrassing question to ask. It is
embarrassing because I feel like I should be able to understand or search
for the answer, but I have not had success. So I apologize if this is a
silly question (and it probably is).
On the mailing list, I have read th
Dear all,
I am trying to conduct some simple ligand binding studies for a protein
system solvated in water. After inputting the command:
mdrun -v -deffnm em -nt 1
I get the log shown below, nothing completes after this 0 step. Any help
would be appreciated.
Back Off! I just backed up em.log to
On Mon, Apr 23, 2012 at 6:45 PM, Justin A. Lemkul wrote:
>
>
> On 4/23/12 1:38 PM, Steven Neumann wrote:
>
>> Dear Gromacs Users,
>>
>> My job failed on the cluster and I would like to run in from the
>> checkpoint time
>> created:
>>
>> mdrun -s umbrella0.tpr -cpi umbrella0.cpt -deffnm umbrella0
On 4/23/12 1:38 PM, Steven Neumann wrote:
Dear Gromacs Users,
My job failed on the cluster and I would like to run in from the checkpoint time
created:
mdrun -s umbrella0.tpr -cpi umbrella0.cpt -deffnm umbrella0 -pf
pullf-umbrella0.xvg -px pullx-umbrella0.xvg
Will existing files pullf-umbrel
On 4/23/12 1:27 PM, Lara Bunte wrote:
Hi
In this case my problem is not solvable with gromacs?
All I have is the my_molecule.pdb which is a small molecule in a water box and
my generated index.ndx file, size.xvg file and output.xtc file.
Supply your .pdb file to the -s flag. Sorry for my
Dear Gromacs Users,
My job failed on the cluster and I would like to run in from the checkpoint
time created:
mdrun -s umbrella0.tpr -cpi umbrella0.cpt -deffnm umbrella0 -pf
pullf-umbrella0.xvg -px pullx-umbrella0.xvg
Will existing files pullf-umbrella0.xvg and pullx-umbrella0.xvg be updated
as
Hi
In this case my problem is not solvable with gromacs?
All I have is the my_molecule.pdb which is a small molecule in a water box and
my generated index.ndx file, size.xvg file and output.xtc file.
Greetings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Lara Bunte
On 4/23/12 1:13 PM, Lara Bunte wrote:
Hi
If I use
trjconv -n index.ndx -f my_molecule.pdb -o output.pdb
I got this error again
Can not open file:
topol.tpr
Whats now the problem?
Apparently you need a .tpr file supplied to the -s flag to do such a
transformation. I'm not sure why it's
Hi
If I use
trjconv -n index.ndx -f my_molecule.pdb -o output.pdb
I got this error again
Can not open file:
topol.tpr
Whats now the problem?
Greetings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Discussion list for GROMACS users
CC:
Gesendet: 18:39 Montag, 23.
On 4/23/12 8:54 AM, Marcelo Lopez wrote:
I get no answer so I insist... ¿Do my questions gets in to the email list?
Your messages are arriving on the list. The documentation for tablep.xvg
contents is certainly lacking, and unfortunately so too are the threads in the
archive on the same t
On 4/23/12 10:20 AM, rama david wrote:
Hi Gromacs Friends,
Sorry me for asking stupid question
I am using gromacs 4.5.4
To calculate Hydrogen bonds,
I use the command
g_hbond -f nojump_fit.xtc -s input_md.tpr
-num hbnum_nojump.xvg -dist hbdist.xvg -ang hbang.xvg -hbm bmap.
On 4/23/12 11:36 AM, Bala subramanian wrote:
Friends,
I have created the top (attached) file for a tripeptide using pdb2gmx tool of
gromacs. However in the top file, i dnt see the pdb2gmx writing the ff
parameters.
I guess that the ff parameters are read directly from the ff.itp given in the
On 4/23/12 11:01 AM, Lara Bunte wrote:
Hi
What do you mean with
Specify a .pdb file as the output of your original command.
I wrote in
trjconv -s -f output.xtc -o output.pdb
in the last part output.pdb. What should I specify more?
When I was referring to your "original command," I
On 4/23/12 10:59 AM, Shilpi Chaurasia wrote:
Hi Gromacs users,
I am using pull code to separate two units of a protein dimer. I have run the
pulling simulation for 650 ps and got pullx.xvg and pullf.xvg files, where the
data is printed at every 0.01 ps (according to pull_nstxout & pull_nstfo
But the best would be to grompp (NPT) windows (lets say every 10-20 frames) of
your configuration and at the end of grompp you will see the actual distance
the gromacs will consider.
Jan
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on beh
Friends,
I have created the top (attached) file for a tripeptide using pdb2gmx tool
of gromacs. However in the top file, i dnt see the pdb2gmx writing the ff
parameters.
I guess that the ff parameters are read directly from the ff.itp given in
the given as #include "amber03.ff/forcefield.itp". Is
Use trjconv -skip first for your trajcetory so you can rewrite it every
frame/time step you want. Then proceed to g_dist.
Jan
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Shilpi Chaurasia [shilpi.chaura...@unimi.it]
Sent: Mon
?Hi Gromacs users,
I am using pull code to separate two units of a protein dimer. I have run the
pulling simulation for 650 ps and got pullx.xvg and pullf.xvg files, where the data
is printed at every 0.01 ps (according to pull_nstxout& pull_nstfout, both are
10 in this case) as given below
Hi
What do you mean with
>Specify a .pdb file as the output of your original command.
I wrote in
trjconv -s -f output.xtc -o output.pdb
in the last part output.pdb. What should I specify more?
Thanks
Greetings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Discussi
Hi Ignacio,
actually .cpt contains velocities and, to extract a .gro containing them,
you can try to use editconf.
Francesco
Il giorno 23 aprile 2012 16:45, Ignacio Fernández Galván
ha scritto:
> --- On Mon, 23/4/12, Alex Marshall wrote:
>
> > I'm pretty sure .cpt files don't store velocity in
Hi Gromacs users,
I am using pull code to separate two units of a protein dimer. I have run the
pulling simulation for 650 ps and got pullx.xvg and pullf.xvg files, where the
data is printed at every 0.01 ps (according to pull_nstxout & pull_nstfout,
both are 10 in this case) as given below
--- On Mon, 23/4/12, Alex Marshall wrote:
> I'm pretty sure .cpt files don't store velocity information. Try using a
> trr file instead.
Well, I'm pretty sure .cpt files do store velocities:
1. What good would be checkpoint files without velocities?
2. It works with version 4.5.3
3. "gmxcheck -
Hi Gromacs Friends,
Sorry me for asking stupid question
I am using gromacs 4.5.4
To calculate Hydrogen bonds,
I use the command
g_hbond -f nojump_fit.xtc -s input_md.tpr
-num hbnum_nojump.xvg -dist hbdist.xvg -ang hbang.xvg -hbm bmap.xpm
-n my_index.ndx
I got the plot that show
I get no answer so I insist... ¿Do my questions gets in to the email list?
Hi all: I'm trying to run a coarse grained system with 3 different
kind of particles, lets call them "A", "B" and "C", and the
interactions between them are set by means of 3 tabulated potentials
(not LJ, totally customized
I'm pretty sure .cpt files don't store velocity information. Try using a
trr file instead.
On Mon, Apr 23, 2012 at 4:40 AM, Ignacio Fernández Galván
wrote:
> Hi all,
>
> I'm trying to get a .gro file with velocities. This command line works in
> 4.5.3:
>
> $ trjconv -f file.cpt -s file.tpr -o fil
I get no answer so I insist... ¿Do my questions gets in to the email list?
Hi all again: I'm trying to run a coarse grained system with 3 different
kind of particles, lets call them "A", "B" and "C", and the
interactions between them are set by means of 3 tabulated potentials
(not LJ, totally cus
Not sure but you could compare with unbiased histogram constructed
independently.
On Apr 23, 2012, at 11:55 AM, Gavin Melaugh wrote:
Hi all
Are the histograms from histo.xvg (output of g_wham) the biased or
unbiased distributions?
Cheers
Gavin
--
gmx-users mailing listgmx-users@groma
On 4/23/12 7:12 AM, Shima Arasteh wrote:
I made it as the format of .top and .itp files, but still get the same error.
If you have a topology (either .top or .itp), there is no need to run pdb2gmx.
-Justin
*F
I made it as the format of .top and .itp files, but still get the same error.
From: Shima Arasteh
To: Discussion list for GROMACS users
Sent: Monday, April 23, 2012 3:05 PM
Subject: [gmx-users] .top file for POPC membrane
Dear all gmx users,
I performed t
On 4/23/12 3:46 AM, Lara Bunte wrote:
Hi
that worked. I used
trjconv -n index.ndx -f my_molecule.pdb -o output
After this I got an trajectory file output.xtc
Now I have to get really a coordinate file, i.e. pdb file. I used the command
trjconv -s -f output.xtc -o output.pdb
to convert
Dear all gmx users,
I performed the pdb2gmx to get the .top file, but I faced this error: " Residue
'POP' not found in residue topology database ". So I decided to make a top file.
How can I make the .top file for popc.itp?
Anybody can guide me please?
Thanks in advance,
Shima
--
gmx-users ma
Hi all
Are the histograms from histo.xvg (output of g_wham) the biased or
unbiased distributions?
Cheers
Gavin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search
Hi all,
I'm trying to get a .gro file with velocities. This command line works in 4.5.3:
$ trjconv -f file.cpt -s file.tpr -o file.gro -pbc mol -center -boxcenter zero
-ur compact -ndec 6
But in 4.5.5 the output .gro file is written without the velocities, even
though the -vel option is listed
Hi
that worked. I used
trjconv -n index.ndx -f my_molecule.pdb -o output
After this I got an trajectory file output.xtc
Now I have to get really a coordinate file, i.e. pdb file. I used the command
trjconv -s -f output.xtc -o output.pdb
to convert it to pdb, as I read it in this tutorial
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