Hi,
I extended by 3ns simulation by 2 more ns ... i.e total 5 ns but the .xtc
file shows only the 3ns trajectories and after checking the md.log file ,
its showing that it completed those 2 ns steps also... then how can I get
the trajectory for those 2ns ... I used the following commands for
Dear Dr.Justin
I did it,it works.Thanks.
there are another problem:
I want to add some hydogens to my topology.
I used ADDHYD atomname,But this dosen't work.
PLease let me know how can I include some Hydrogenes in my topology.
Thanks in advance
Mohsen
On Thu, Feb 10, 2011 at 7:56 PM, Justin A.
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Message: 5
Date: Fri, 11 Feb 2011 12:48:31 +0330
From: mohsen ramezanpour ramezanpour.moh...@gmail.com
Subject: Re: [gmx-users] PRODRG
To: jalem
mohsen ramezanpour wrote:
Dear Dr.Justin
I did it,it works.Thanks.
there are another problem:
I want to add some hydogens to my topology.
I used ADDHYD atomname,But this dosen't work.
PLease let me know how can I include some Hydrogenes in my topology.
Use a different force field and don't
On 11/02/2011 8:10 PM, bharat gupta wrote:
Hi,
I extended by 3ns simulation by 2 more ns ... i.e total 5 ns but the
.xtc file shows only the 3ns trajectories and after checking the
md.log file , its showing that it completed those 2 ns steps also...
then how can I get the trajectory for
On 11/02/2011 8:18 PM, mohsen ramezanpour wrote:
Dear Dr.Justin
I did it,it works.Thanks.
there are another problem:
I want to add some hydogens to my topology.
I used ADDHYD atomname,But this dosen't work.
PLease let me know how can I include some Hydrogenes in my topology.
As Justin
On 11/02/2011 9:14 PM, Sanjay Kumar Upadhyay wrote:
Sorry, in previous mail i did not write md protocol in details what i
followed for simulation. after energy minimization steps i did PR for 200
ps and then run the production MD. Even i did vacuum energy minimization
before adding solvent for
Mark Abraham wrote:
On 11/02/2011 9:14 PM, Sanjay Kumar Upadhyay wrote:
Sorry, in previous mail i did not write md protocol in details what i
followed for simulation. after energy minimization steps i did PR for 200
ps and then run the production MD. Even i did vacuum energy minimization
Hi all,
I'm compiling and testing gromacs 4.5.3 in different machines, and I'm
wondering
if it's normal that the ia64 is much slower than the x86_64
I don't know full details of the machines, because I'm not the administrator or
owner, but /proc/cpuinfo says:
ia64 (128 cores): Dual-Core
Dear gmx users,
Does someone know in which file GROMACS store the information on
the protein charge. I've seen that after running pdb2gmx or grompp the
system charge is shown in the screen but we would like to know if this
information is recorded in some file.
With my best
Ya I found that the new trajectory is saved with name traj.trr and traj.xtc
... and I remember I saved the new tpr file as next.tpr..
Now I want to merge the two trajectories and the two .tpr files... I found
trjcat can be used ... I used the following command: -
trjcat -f1 md_0_1.xtc -f2
Tanos Franca wrote:
Dear gmx users,
Does someone know in which file GROMACS store the information on the
protein charge. I've seen that after running pdb2gmx or grompp the
system charge is shown in the screen but we would like to know if this
information is recorded in some file.
bharat gupta wrote:
Ya I found that the new trajectory is saved with name traj.trr and
traj.xtc ... and I remember I saved the new tpr file as next.tpr..
Now I want to merge the two trajectories and the two .tpr files... I
found trjcat can be used ... I used the following command: -
Hello,
I calculate the density of my lquid in the equilibrated time range of the
density-time plots (NPT runs). I use the gro file of these NPT runs for NVT
runs to calculate the self diffusion coefficient at the simulated density.
Concerning this gro file: Is this taken from the end of the
On 12/02/2011 12:02 AM, Thomas Koller wrote:
Hello,
I calculate the density of my lquid in the equilibrated time range of the
density-time plots (NPT runs). I use the gro file of these NPT runs for NVT
runs to calculate the self diffusion coefficient at the simulated density.
Concerning this
Thomas Koller wrote:
Hello,
I calculate the density of my lquid in the equilibrated time range of the
density-time plots (NPT runs). I use the gro file of these NPT runs for NVT
runs to calculate the self diffusion coefficient at the simulated density.
Concerning this gro file: Is this taken
On 11/02/2011 11:33 PM, Ignacio Fernández Galván wrote:
Hi all,
I'm compiling and testing gromacs 4.5.3 in different machines, and I'm wondering
if it's normal that the ia64 is much slower than the x86_64
I don't know full details of the machines, because I'm not the administrator or
owner,
I am a user of gromacs. I am quite confused when I came across the
relation of rlist and rvdw / rcoulomb in vdw and coulomb calculation.
In cut-off, it says rvdw / rcoulomb should be greater than rlist, while
in switch/shift, it says rvdw should be smaller than rlist...
I guess in cut-off, it's
Mark Abraham skrev 2011-02-11 14.17:
I am a user of gromacs. I am quite confused when I came across the
relation of rlist and rvdw / rcoulomb in vdw and coulomb calculation.
In cut-off, it says rvdw / rcoulomb should be greater than rlist, while
in switch/shift, it says rvdw should be smaller
Original Message
From: Mark Abraham mark.abra...@anu.edu.au
We can't say with the information given. For best performance, the number of
threads cannot exceed the number of physical cores available to one processor.
To go higher, you need to compile and use GROMACS with MPI, not
Hi Ignacio,
On Feb 11, 2011, at 1:33 PM, Ignacio Fernández Galván wrote:
Hi all,
I'm compiling and testing gromacs 4.5.3 in different machines, and I'm
wondering
if it's normal that the ia64 is much slower than the x86_64
I don't know full details of the machines, because I'm not
hi all
I would like to extract my protein structure with the first
hydration shell around the active site which contains an ion from counfout.gro.
Is there any program script able to do this?
Cordially DRICI nedjoua
--
gmx-users mailing list
najwa drici wrote:
hi all
I would like to extract my protein structure with the first hydration
shell around the active site which contains an ion from counfout.gro.
Is there any program script able to do this?
Not in one step, no. You could:
1. Use make_ndx to create an index group
Hello gromacs users, I have asked this question before but perhaps I was not
clear enough. I noticed that in Gromacs verisons 4.5.3 and 3.3.4 when the
initial structure has some side chains located very close to each other then
after energy minimisation they become distorted (for example, Phe
abdullah ahmed wrote:
Hello gromacs users,
I have asked this question before but perhaps I was not clear enough. I
noticed that in Gromacs verisons 4.5.3 and 3.3.4 when the initial structure
has some side chains located very close to each other then after energy
minimisation they become
Hi,
I've used g_confrms from gromacs-4.5.1 to compare two structures with the
following command line -
g_confrms -f1 1OMB.pdb -f2 md.gro -o fit.pdb
fit.pdb is supposed to be the output file which would show the 2 structures
superimposed on each other. But when I visualised it with vmd. I
sorry, forgot to attached the file...
From: Kwee Hong jestan1...@yahoo.com
To: gmx-users gmx-users@gromacs.org
Sent: Friday, February 11, 2011 23:38:55
Subject: only one model is displayed
Hi,
I've used g_confrms from gromacs-4.5.1 to compare two structures
There are two models. VMD loads them as sequential frames such that they can be
animated. You'll see frame 0 and 1 in the VMD main window.
-Justin
Kwee Hong wrote:
sorry, forgot to attached the file...
*From:* Kwee
Hi Tsjerk,
Thanks for the help. I got it.
But do you have any idea how to solve this in vmd?
Regards,
Joyce
From: Tsjerk Wassenaar tsje...@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Saturday, January 22, 2011 15:53:22
Subject:
On 12/02/2011 2:55 AM, Kwee Hong wrote:
Hi Tsjerk,
Thanks for the help. I got it.
But do you have any idea how to solve this in vmd?
Use trjconv -sep on the .pdb file to split it.
Mark
Regards,
Joyce
*From:* Tsjerk
On 12/02/2011 1:51 AM, Justin A. Lemkul wrote:
najwa drici wrote:
hi all
I would like to extract my protein structure with the first hydration
shell around the active site which contains an ion from counfout.gro.
Is there any program script able to do this?
Not in one step, no. You
Hi Folks,
I have added a custom DNA residue to the amber99sb ff, and everything works
perfectly, (thanks to Justin!).
The residue is incorporated perfectly into the sequence, with no abnormal
events during simulations. I have updated all the files to include the new
residue.
I have since
On 12/02/2011 12:44 AM, Ignacio Fernández Galván wrote:
Original Message
From: Mark Abrahammark.abra...@anu.edu.au
We can't say with the information given. For best performance, the number of
threads cannot exceed the number of physical cores available to one processor.
To go higher,
On 12/02/2011 3:14 AM, william Stebbeds wrote:
Hi Folks,
I have added a custom DNA residue to the amber99sb ff, and everything
works perfectly, (thanks to Justin!).
The residue is incorporated perfectly into the sequence, with no
abnormal events during simulations. I have updated all the
Thanks for the quick reply,
I have already done that, and GROMACS, in all other cases, knows it is DNA, as
it automatically forms the bonds with other residues.
it is only when it makes its index files that it doesnt know that my residue is
DNA.
Cheers
Will
Date: Sat, 12 Feb 2011
Hi Mark,
I tried but with this error:
Fatal error:
Number of atoms in pdb frame 0 is 331 instead of 491
Joyce
From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Saturday, February 12, 2011 0:01:39
Thanks for the quick reply,
I have already done that, and GROMACS, in all other cases, knows it is
DNA, as it automatically forms the bonds with other residues.
it is only when it makes its index files that it doesnt know that my
residue is DNA.
Did you make the change in
Indeed I did
DGO DNA
Cheers
Will
Date: Fri, 11 Feb 2011 17:57:32 +0100
Subject: RE: [gmx-users] Add custom residue to DNA index group
From: dsar...@gwdg.de
To: gmx-users@gromacs.org
Thanks for the quick reply,
I have already done that, and GROMACS, in all other cases, knows it
william Stebbeds wrote:
Indeed I did
DGO DNA
Did you make the change system-wide, or in a local directory? If the latter,
you have to issue all your commands in that same directory or else the default
residuetypes.dat (in GMXLIB) will be read.
Can you post the make_ndx output (i.e.
I made the changes to ../gromacs/top/residuetypes.dat
the Make_ndx output:
0 System : 34023 atoms
1 DNA : 650 atoms
2 DGO :66 atoms
3 K :43 atoms
4 CL :21 atoms
5 Other :
Hi all,
Does anyone know how to make a positional restraint file for the terminal atoms in a protein/rna/dna chain via genrestr? I know I can get the backbone, C-alpha, etc.
Doing this by hand will be time consuming, and if there was an automated way of
william Stebbeds wrote:
I made the changes to ../gromacs/top/residuetypes.dat
the Make_ndx output:
0 System : 34023 atoms
1 DNA : 650 atoms
2 DGO :66 atoms
3 K :43 atoms
4 CL :21 atoms
5
TJ Mustard wrote:
Hi all,
Does anyone know how to make a positional restraint file for the
terminal atoms in a protein/rna/dna chain via genrestr? I know I can get
the backbone, C-alpha, etc.
Doing this by hand will be time consuming, and if there was an automated
way of doing this
Ok, will do.
Thanks very much
Will
Date: Fri, 11 Feb 2011 13:29:53 -0500
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Add custom residue to DNA index group
william Stebbeds wrote:
I made the changes to ../gromacs/top/residuetypes.dat
the Make_ndx
Justin,
Yes but how can I automatically select the terminal residues alpha carbons, without having to individually select residues?
Read the manual and some internet pages and found that you can easily select the alpha carbons on select residues by
TJ Mustard wrote:
Justin,
Yes but how can I automatically select the terminal residue's alpha
carbons, without having to individually select residues?
Read the manual and some internet pages and found that you can easily
select the alpha carbons on select residues by specifying them
Justin,
Ok, if I find a way I will post it back here. And thank you for the recommendations.
Thank you,
TJ Mustard
On February 11, 2011 at 11:05 AM Justin A. Lemkul jalem...@vt.edu wrote:
TJ Mustard wrote:
Hi,
On Fri, Feb 11, 2011 at 21:05, Justin A. Lemkul jalem...@vt.edu wrote:
I don't know of any Gromacs tool (other than pdb2gmx) that is smart enough
to determine terminal residues on its own. If you have multiple copies of
the same molecule, then you know how many atoms are in each, so you
Teemu Murtola wrote:
Hi,
On Fri, Feb 11, 2011 at 21:05, Justin A. Lemkul jalem...@vt.edu wrote:
I don't know of any Gromacs tool (other than pdb2gmx) that is smart enough
to determine terminal residues on its own. If you have multiple copies of
the same molecule, then you know how many
Dear gmx users,
I am using gromacs (version 4.0.7)
to setup a 2-butoxyethanol-water simulation.
I created topology and coordinate file (.pdb) for BE using AUTOMATED TOPOLOGY
BUILDER server.
It created a topology file (for united atom) compatible with GROMOS ffG53a6
forcefield.
I want to
On 12/02/2011 3:45 AM, Kwee Hong wrote:
Hi Mark,
I tried but with this error:
Fatal error:
Number of atoms in pdb frame 0 is 331 instead of 491
OK. I don't know why two frames with different numbers of atoms are
written. Maybe g_confrms -one is useful. Or you can chop apart the PDB
by hand
Rini Gupta wrote:
Dear gmx users,
I am using gromacs (version 4.0.7)
to setup a 2-butoxyethanol-water simulation.
I created topology and coordinate file (.pdb) for BE using AUTOMATED
TOPOLOGY BUILDER server.
It created a topology file (for united atom) compatible with GROMOS
ffG53a6
On 12/02/2011 7:18 AM, Teemu Murtola wrote:
Still, the only critique I've heard so far (from several
people, it seems) is a vague the documentation sucks, which doesn't
really help in improving things, or even figuring out where people
face problems. g_select does provide some on-line help (by
On 12/02/2011 7:51 AM, Rini Gupta wrote:
Dear gmx users,
I am using gromacs (version 4.0.7)
to setup a 2-butoxyethanol-water simulation.
I created topology and coordinate file (.pdb) for BE using AUTOMATED
TOPOLOGY BUILDER server.
It created a topology file (for united atom) compatible with
Justin,
Regarding my question I forgot to tell you that after expanding the
system 4X, we have performed 26 shrinking steps at the 0.95 rate.
The system we are working with is one in which we have embedded two
proteins into the bilayer, one of them is a toxin and the other a
putative
On 12/02/2011 12:22 PM, Justin A. Lemkul wrote:
Do the -ci and -cs steps separately and see if that gives you the
proper output. I have found that the two are incompatible, but in
theory, I don't know why one couldn't do everything in one step.
It can depend on the assumptions about the
Dr. Ramón Garduño-Juárez wrote:
Justin,
Regarding my question I forgot to tell you that after expanding the
system 4X, we have performed 26 shrinking steps at the 0.95 rate.
The system we are working with is one in which we have embedded two
proteins into the bilayer, one of them is a
Hello Mark,
Thanks for the reply.
I tried to first make a box using editconf
editconf_d_mpi -f conf.gro -o be.gro -bt cubic -box 2.7 2.7 2.7
Box is successfully created and then I use
genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 19 -o out.gro
still, I am getting only one
On 12/02/2011 12:51 PM, Rini Gupta wrote:
Hello Mark,
Thanks for the reply.
I tried to first make a box using editconf
editconf_d_mpi -f conf.gro -o be.gro -bt cubic -box 2.7 2.7 2.7
Box is successfully created and then I use
genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 19 -o
Hi,
I am getting following output after using editconf to create a box
followed by
genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 2 -o out.gro
This time i tried to insert just 2 molecules still the command is not
working.
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