Dear All,
I am working on some molecule and I have defined atom types with OPLSaa and
all atom types really exist in oplsaa and well chosen so no approximation
in choosing atom types. During grompp, I found there are dihedral param
missing. e.g.
N CT CT NT
N CT CT N3
Is there any 'good' way of
jalem...@vt.edu wrote:
On 7/25/13 8:25 AM, gromacs query wrote:
Dear All,
I am working on some molecule and I have defined atom types with OPLSaa
and
all atom types really exist in oplsaa and well chosen so no approximation
in choosing atom types. During grompp, I found there are dihedral
Dear Justin,
Parameterization is a hard road that takes a lot of time
I agree and thanks for reply
On Thu, Jul 25, 2013 at 3:47 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/25/13 8:41 AM, gromacs query wrote:
Dear Justin,
Thanks this paper is quite explained and requires much
Dear All,
I have some polymer having peptide bond and want to use OPLSaa. I was
following Justin's example for building polymers
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html
I have few queries:
1) do I need to define improper for peptide in .rtp file to keep it planar?
wrote:
On 7/17/13 10:37 AM, gromacs query wrote:
Dear All,
I have some polymer having peptide bond and want to use OPLSaa. I was
following Justin's example for building polymers
http://lists.gromacs.org/**pipermail/gmx-users/2009-**March/040125.htmlhttp://lists.gromacs.org/pipermail/gmx
wrote:
On 7/17/13 11:39 AM, gromacs query wrote:
Dear Justin,
1) I can understand the improper for stereocenters (chiral) easily but
with
OPLS doesn't use impropers for chiral centers.
bonds I am confused (I have tried to explain below please let me know if I
have defined impropers
wrote:
On 7/17/13 1:33 PM, gromacs query wrote:
Dear Justin,
Thanks for reply and explanation, and..:
you've got an amide flanked by two methylene groups as the repeat unit
All the amino acids in the aminoacids.rtp file specify impropers
centered on the C and N atoms of the peptide bond
and new values. The old values are from modified
oplsaa.ff/ffbonded.itp in which I have already used lowercase atometype
names.
Using gmxdump I can see system B is using modified oplsaa.ff. So does this
mean Gromacs is case insensitive as I get warning even I used lowercase
letters?
regards,
--
gmx
Thanks Mark and Baptiste, yes its case insensitive for atomtype names. I
have changed all names and its working now :-)
regards,
On Thu, Jun 20, 2013 at 2:55 PM, Baptiste Demoulin
bat.demou...@gmail.comwrote:
Hi,
GROMACS is indeed case insensitive when it comes to atomtypes. I had the
same
Dear All,
Is there any way to print parameters used for system (just for the
atomtypes present in system). I have all necessary files (top, tpr, gro and
oplsa.ff)
regards,
Jiom
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* Please search
params from oplsaa for all these. Or do I need to map
atom types for these atom numbers then only I can extract or is there any
inbuilt Gromacs module in this regard
regards,
On Tue, Jun 18, 2013 at 11:32 AM, Mark Abraham mark.j.abra...@gmail.comwrote:
Grep?
On Jun 18, 2013 10:23 AM, gromacs
-
boun...@gromacs.org] Im Auftrag von gromacs query
Gesendet: Dienstag, 18. Juni 2013 10:42
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] to print parameters used from force field
Dear Mark,
Grep?
Sorry but I mean to say I have say .itp file like
listed and the
cross-reference is made. But it is not really intended for human digestion.
You haven't stated your purpose for the information, so it's hard to be
helpful.
Mark
On Tue, Jun 18, 2013 at 11:13 AM, gromacs query gromacsqu...@gmail.com
wrote:
Dear Florian,
I used -pp as you
Dear All,
I have two different membrane systems (membrane with waters only) already
with me. So I dont need to add solvent molecules.
So to start with simulation I need box size (last line in gro file). I used
following command (for both cases):
editconf -f del.pdb -o del.gro -c -bt cubic
, 2013 at 1:37 AM, Justin Lemkul jalem...@vt.edu wrote:
On 6/14/13 4:58 PM, gromacs query wrote:
Dear All,
I have two different membrane systems (membrane with waters only) already
with me. So I dont need to add solvent molecules.
So to start with simulation I need box size (last line
possible way? If I just use
system size dimension (X, Y Z) and do mimization it break my system in
parts!
How to choose optimum box vector in such case?
regards,
On Sat, Jun 15, 2013 at 2:49 AM, Justin Lemkul jalem...@vt.edu wrote:
On 6/14/13 7:37 PM, gromacs query wrote:
Dear Justin
Dear Justin,
Thanks a lot. I used this and it works fine:
editconf -f final.pdb -o final.gro -c -d 0.0
regards,
Jiomm
On Sat, Jun 15, 2013 at 3:09 AM, Justin Lemkul jalem...@vt.edu wrote:
On 6/14/13 8:08 PM, gromacs query wrote:
Dear Justin,
I saw your tutorial (
http
Dear All,
Please any suggestion?
regards,
On Mon, Jun 3, 2013 at 4:53 PM, gromacs query gromacsqu...@gmail.comwrote:
Dear All,
(Sorry for long mail!)
(Thanks Thomas Schlesier for clarifying previous umbrella queries)
I wish to run umbrella samplings using restart file of previous
Dear All,
(Sorry for long mail!)
(Thanks Thomas Schlesier for clarifying previous umbrella queries)
I wish to run umbrella samplings using restart file of previous window.
e.g. initial distance between A (reference) and B (pulled group) is 1 nm
(10 Angs) then I intend to run 10 windows after
Dear Thomas,
In AMBER I remember I did once methane-methane interaction, just
distance based umbrella sampling. But there I did not
provide any direction. So should it not be N N N in Gromacs if I want
to allow them freely move in xyz.
Sorry am wrong that should be Y Y Y in Gromcacs
at the
center of mass of polymer_B).
If you set pull_init1=0 and pull_start=yes, GROMACS adds the distance
between polymer_B and A to pull_init1 (- so pull_init1 is now greater than
0.0). Now the origin of the umbrella potential is at the center of mass of
polymer_A. - A is restrainted to a certian
confused. In AMBER I remember I did once methane-methane interaction,
just distance based umbrella sampling. But there I did not provide any
direction. So should it not be N N N in Gromacs if I want to allow them
freely move in xyz.
thanks,
On Fri, May 31, 2013 at 8:53 PM, Thomas Schlesier schl
Dear All,
I want to do Umbrella sampling between two different polymers (A and B)
interacting with each other with starting configuration separated by some
distance and I am trying to bring them closer.
I have some queries regarding pull inputs: (this is for to run a umbrella
sampling at some
Dear Lloyd,
I have read that but my system is different
regards,
On Thu, May 30, 2013 at 8:28 PM, lloyd riggs lloyd.ri...@gmx.ch wrote:
Dear Jiom,
Look at justines tutorial, there's example pull .mdp.
Stephan Watkins
*Gesendet:* Donnerstag, 30. Mai 2013 um 14:44 Uhr
*Von:* gromacs
Dear All,
I have a system with two solutes (A and B) with water and ions. For
pressure coupling in index file I defined two groups: Solute and Solvent,
where solute consists of A+B and solvent consists of water+ions
Due to some reasons I need to apply position restraints on Solute A only
for few
be
done with Gromacs.
regards,
JIom
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, 2013 at 3:08 PM, gromacs query gromacsqu...@gmail.com
wrote:
Dear All,
I have a huge system and residue number goes beyond 9. So when I
added
waters then residue number goes till 9SOL then again it starts from
0SOL. I tried genconf -renumber option but it does not help
Gromacs do not use residue number or atom number,
OK! Thanks Nuno and Mark
regards,
On Tue, May 14, 2013 at 7:14 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
Try selecting residue 0 with editconf and see for yourself :-)
On May 14, 2013 4:41 PM, gromacs query gromacsqu...@gmail.com
Dear All,
I want to calculate water and ions density around polymer. After MD I see
my polymer goes near the edges of box and rather some part is out of box.
So in order to calculate water and ion density I think polymer should be
near the center of box (please correct me if wrong)
So by doing
Sorry forgot to add:::
by doing this I can see my polymer near the center of box
On Mon, May 6, 2013 at 11:21 AM, gromacs query gromacsqu...@gmail.comwrote:
Dear All,
I want to calculate water and ions density around polymer. After MD I see
my polymer goes near the edges of box and rather
:07 PM, Justin Lemkul jalem...@vt.edu wrote:
On 5/6/13 4:21 AM, gromacs query wrote:
Dear All,
I want to calculate water and ions density around polymer. After MD I see
my polymer goes near the edges of box and rather some part is out of box.
So in order to calculate water and ion density I
,
On Thu, May 2, 2013 at 12:50 AM, Mark Abraham mark.j.abra...@gmail.comwrote:
On Wed, May 1, 2013 at 4:20 PM, gromacs query gromacsqu...@gmail.com
wrote:
Dear All,
I am using Charmm gui built membrane (120 x 2). But during minimization I
was getting error.
Potential Energy
Dear All,
I am using Charmm gui built membrane (120 x 2). But during minimization I
was getting error.
Potential Energy = 4.6809051e+19
Maximum force =inf on atom 4281
Norm of force =inf
(inf means? means infinite/NAN)
I removed the full lipid residue having
Dear All,
I have a pdb file in which has only heavy atoms (means all atoms except
hydrogen) and a corresponding itp file with all atoms (including
hydrogens). The heavy atoms in pdb file are in sequence order as in itp
file.
e.g.
itp pdb (no Hydrogens)
*
C1 C1
H1
Thanks a lot Dr. Justin
On Wed, Mar 6, 2013 at 2:52 PM, Justin Lemkul jalem...@vt.edu wrote:
On 3/6/13 7:35 AM, gromacs query wrote:
Dear All,
How md engine in GROMACS (mdrun) detects which energy function to be used
as it varies for different force fields (FF). Does it detects
Dear Erik,
I am new to Gromacs and used AMBER before, and I am exploring various
options in GROMACS too. Surely I will look in to g_select. Also as I was
using sed, one should include an extra space (using vi) in gro file just
before residue number and then can use sed to remove like this: sed -e
numbers.
1) Is there some way to feed the residue numbers to make_ndx? Or I need to
make index file format my self by some scritpting Or is there is rather
easier way of doing in gromacs.
2) Also is there any direct command which helps to remove a residue number
directly from a gro file without using
be automated.
Furthermore, the gro format is also simple, so you can filter out the
unwanted residues there instead of using an index file.
Erik
On Mar 1, 2013, at 1:42 PM, gromacs query wrote:
Dear All,
I know the residue numbers of SOL molecules (which are more than
thousands)
which I want
on the criteria based on X Y Z
coordinates (some space fixed and outlier waters are to be removed)
regards,
On Fri, Mar 1, 2013 at 3:09 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote:
On Mar 1, 2013, at 1:58 PM, gromacs query wrote:
Dear Erik,
so you
Dear All,
I have installed gromacs-4.5.5 on CENTOS 64 bit. I have tried following
options and I was successful to install by all of following methods but
every time I am getting this error when I use any command e.g. mdrun,
g_analyze
error while loading shared libraries: libfftw3f.so.3: cannot
Dear Justin,
Just to add: I can echo all variables (
http://www.gromacs.org/Documentation/Terminology/Environment_Variables)
except GMXLIB so my bashrc is like this: which is still not helping
export GMXLIB=/usr/local/gromacs/share/gromacs/top
export LD_LIBRARY_PATH=/usr/local/bin
#export PATH
Dear Justin,
thanks its working, sorry it was my mistake I used wrongly /usr/local/bin,
so export LD_LIBRARY_PATH=/usr/local/lib is working fine now.
regards,
On Sun, Nov 4, 2012 at 11:02 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/4/12 12:23 PM, gromacs query wrote:
Dear Justin
Hi,guys
I obtained surface tension of water and salt solution. But the value RMSD was
always very big although the value of 65 is reasonable. Is it all right about
the RMSD??
Energy Average Err.Est. RMSD Tot-Drift
Hi,guys
I obtained surface tension of water and salt solution. But the value RMSD was
always very big although the value of 65 is reasonable. Is it all right about
the RMSD??
Energy Average Err.Est. RMSD Tot-Drift
Hi, guys
Water molecule starting at atom 10578 can not be settled.
Check for bad contacts and/or reduce the timestep.
When i run 6x6x1.3nm water box. i used several methods to do EM. So i can do
several EM. But which .gro should i select as my input .gro for my running？
Because when i use
Hi Everyone,
Program ngmx, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/tpxio.c, line: 1708
Fatal error:
reading tpx file (md1.tpr) version 73 with version 58 program
I installed 4.0.7 before, and now i installed 4.5.3. How can i use ngmx now?
The second question is running C2H5OH
Hi guys,
I created my .tpr through my own desktop (without parallel) using gromacs 4.0.7.
can i run .tpr parallelly using Gromacs 4.5.3(has parallel) in cluster
computer??
I want creat all my .tpr files in my own computer, and then run on HPC (High
performance computer).
Thanks
HI Friends,
I get the following note,
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.
I want to keep the T at 300K, so does it matter to select any thermostat method?
Another note when i use PME:
load of the PME mesh part: 0.97
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4d3ecaa8.60...@vt.edu
Content-Type: text/plain; charset=UTF-8; format=flowed
gromacs wrote:
HI Friends,
I get the following note,
The Berendsen thermostat does not generate the correct
bonds ROH (sreelakshmi ramesh)
6. How to get sufactant.gro, sufactant.top, (gromacs)
7. Re: How to get sufactant.gro, sufactant.top, (Mark Abraham)
--
Message: 1
Date: 4 Jan 2011 01:23:06 +0100
From: wibke.sudh
Hi expert,
I'd like to add sufactant to water. That means i should first get the
sufactant.gro, and sufactant.top.
Someone said that we cannot get sufactant.gro and sufactant.top through grompp
() sufactant.pdb. Because grompp .pdb could mainly use for macro-biology big
moleculars, which
I think thebatch system will be more efficient. Theinteractive 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?
Thanks
Forwarding messages
From: gromacs ptf1...@163.com
Date
model to Gromacs? do i need to modify the .mdp
paremeter?
Tiefeng--
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Please don't post (un)subscribe
Hi,
I want to simulate 3x3x0.8 water film (bulk water) first creat the water,
genbox -cs -o film.gro -box 3 3 0.8
then, i EM the bulk water;
Using steep, but
t = 0.011 ps: Water molecule starting at atom 298 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb
Message: 3
Date: Thu, 16 Dec 2010 11:50:51 -0500
From: Vitaly Chaban vvcha...@gmail.com
Subject: [gmx-users] Re: water genbox 3x3x0.8 EM not successful T not
high
To: gmx-users@gromacs.org
Cc: gromacs ptf1...@163.com
Message-ID:
aanlktikykv=-oev10bxgys5n_nmqxbonwbhxkybuh
is not at proper situation or
position. Anyway, i will have a try first.
If i have problem or success, i will give an answer to all.
At 2010-12-17 09:51:57，Vitaly Chaban vvcha...@gmail.com wrote:
Hey, gromacs -
Nice to hear from you here... It is a bad idea to simulate something
with any cartesian dimension
Forwarding messages From: gromacs ptf1...@163.com Date:
2010-12-17 12:48:55To: vvcha...@gmail.com Cc: gmx-users@gromacs.org Subject:
Re:Re: water genbox 3x3x0.8 EM not successful T not high OK. I will use your
method. But i am afraid there will be something wrong. Because
film, then the only solution is to follow my
former suggestion.
In no case should you use 3x3x0.8 NPT MD box! If somebody suggested
you to do such thing, then this person simply does not understand
classical MD simulations.
--
Dr.Vitaly V. Chaban
On Thu, Dec 16, 2010 at 11:48 PM, gromacs ptf1
Hi ,
I have installed PSFTP and PuTTY. I have seen the Gromacs-4.0.7 in ./opt in
wivenhoe (cluster), and i know how to upload my file to my folder using PSFTP.
However i donot know how to run it in HPC; when i using Gromacs-4.0.7 in my
desktop, if the Gromacs is installed properly
Hi, experts,
I'd like to calculate the surface tension at water-air interface using Gromacs.
which ensemble should i choose?
when i run simulation, .mdp how can i select p-coupling?
whether should i use p-coupling?
I can creat a air-water-air structure (.gro)
Thanks?--
gmx-users mailing
Hi users:
I run pure water MD. I need to run different water models. How can i get
spce.gro, which means how can i get .gro of spce water?
How can i get .gro of TIP4P?
If i select TIP4P water model, which force field should i select? you know, i
need .top, and .top should include force
Hi,
I am getting this error number of times when I am trying to run Md with a 9
residue peptide in water box using spc216.gro
It says
Number of grid cells is zero. Probably the system and box collapsed.
earlier after grompp it gives me warning that the protein atom number is
less than 10% of
Hi,
Can someone please provide me the link? I couldnt find the link in gromacs
webpage related to these.also in wiki, this is not clearly described.
On Fri, Sep 5, 2008 at 2:47 AM, Xavier Periole [EMAIL PROTECTED] wrote:
On Thu, 4 Sep 2008 23:22:35 -0500
NAMD GROMACS [EMAIL PROTECTED] wrote
dihedrals)
3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
7: [DEPRECATED] Gromacs force field (see manual)
8: [DEPRECATED
Dear Users of Gromacs,This is Alex. I am a new user of Gromacs. As you know to do my simulation with Gromacs, I need to have a PDB file. Let me know a powerful software to construct my PDB file in Mac OS X? I know the Materials Studio is a very good software. But unfortunately it does not work
Dear all,
I am trying to run a simulation of the interaction between two HEME in water.
I have done it without problem, but when I use the calculated charge of HEME
atoms from ab initio calculation I have problem.
The enery minimaization was run without problem with the results:
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