Hi, all,
I am still trying to do my simulation with liquid mixtures.
I have a simple question now. When I writing my .top file, how could I
know if I should use epsilon-sigma or c6-c12 parameters for the LJ
potential? It seems that in some examples, c6-c12 parameters are used
and epsilon-sigma
Dear All,
I would like to calculate the dielectric constant of an ice crystal system in a
simulation had about 1 ms.
I used g_dipoles command to do this. The obtained results seemed that they were
only the values of the last frame in the simulation but not the average values,
Dipole moment
On 5/06/2012 4:34 PM, Bao Kai wrote:
Hi, all,
I am still trying to do my simulation with liquid mixtures.
I have a simple question now. When I writing my .top file, how could I
know if I should use epsilon-sigma or c6-c12 parameters for the LJ
potential? It seems that in some examples, c6-c12
Hi, Mark,
The values of c6-c12 parameters are different from the values of
epsilon and sigma, and they can be converted to each other.
My point is which values I should specify in my .top file. Or it does
not matter totally and Gromacs will determine what kinds of values you
are specifying.
On 5/06/2012 5:04 PM, Bao Kai wrote:
Hi, Mark,
The values of c6-c12 parameters are different from the values of
epsilon and sigma, and they can be converted to each other.
My point is which values I should specify in my .top file. Or it does
not matter totally and Gromacs will determine what
Hi all,
I would like to get information about *pi-pi stacking*, *van der
Waals*, *electrostatic
and hydrophobic interactions* for my system (several-peptides in a box
filled with water). Can Gromacs compute these interactions?
As far as I see from mailing-list, to get information on
Hello,
Thank you very much for your reply. I actually carried out very basic
MDs of a peptide in vacuum (no pbc, cut-off for electrostatics and vdw =
infinity, niter = 10^6). The computing results are given in the two
tables below. As they are identical, I am assuming that there is only
On 5/06/2012 6:46 PM, Laurence Leherte wrote:
Hello,
Thank you very much for your reply. I actually carried out very basic
MDs of a peptide in vacuum (no pbc, cut-off for electrostatics and vdw
= infinity, niter = 10^6). The computing results are given in the
two tables below. As they are
I have read the section about Dispersion Correction in the manual 4.5.4 and
there is no reference on how it is implemented. I am most interested on
how this correction affects the surface tension. Can anybody tell me the
reference of the paper and how dispersion corrections influence on surface
On 6/5/12 4:40 AM, Turgay Cakmak wrote:
Hi all,
I would like to get information about *pi-pi stacking*, *van der Waals*,
*electrostatic and hydrophobic interactions* for my system (several-peptides in
a box filled with water). Can Gromacs compute these interactions?
As far as I see from
Thank you for your reply. I will read the manual more carefully.
2012/6/5 Justin A. Lemkul jalem...@vt.edu
On 6/5/12 4:40 AM, Turgay Cakmak wrote:
Hi all,
I would like to get information about *pi-pi stacking*, *van der Waals*,
*electrostatic and hydrophobic interactions* for my system
You mean TMD (Targeted Molecular Dynamics). As far as I know, this is not
implemented in GROMACS (hope anyone corrects me if I am wrong)
2012/6/4 Mike M nmr.mike@gmail.com
Dear Gromacs Users,
I am trying to study the conformational path from state A to state B with
targeted molecular
Take a look at this post:
http://lists.gromacs.org/pipermail/gmx-users/2002-November/003378.html
2012/6/5 Miguel Ángel Mompeán García mig.momp...@gmail.com
You mean TMD (Targeted Molecular Dynamics). As far as I know, this is not
implemented in GROMACS (hope anyone corrects me if I am
Thanks I'll try that
2012/6/5 Peter C. Lai p...@uab.edu
The quick and dirty way is to post-patch Makefile in src/tools.
I think patching the appropriate Makefile.in is sufficient for configure to
pick up and automake into Makefile if all you need to do is append a make
target.
As to your
2012/6/5 Mark Abraham mark.abra...@anu.edu.au
On 5/06/2012 9:11 AM, Peter C. Lai wrote:
The quick and dirty way is to post-patch Makefile in src/tools.
I think patching the appropriate Makefile.in is sufficient for configure
to
pick up and automake into Makefile if all you need to do is
5 jun 2012 kl. 14.23 skrev Shay Teaching:
2012/6/5 Mark Abraham mark.abra...@anu.edu.au
On 5/06/2012 9:11 AM, Peter C. Lai wrote:
The quick and dirty way is to post-patch Makefile in src/tools.
I think patching the appropriate Makefile.in is sufficient for configure to
pick up and
Hi, all,
It is very easy for me to get the following message.
WARNING: nmol = 1, this may not be what you want.
Temperature dependent fluctuation properties at T = 317.98.
I am wondering if somebody can tell me what does it mean or if it is a
problem to improve?
Thank you very much.
Best
I am interested in pulling out the trajectories (x,y,z coordinates) of water
molecules within a certain distance of my solute molecule. I have tried
using g_select, but that will only give me the atom numbers and not the
trajectories. I can create an index file using this command but
On 6/5/12 9:02 AM, rankinb wrote:
I am interested in pulling out the trajectories (x,y,z coordinates) of water
molecules within a certain distance of my solute molecule. I have tried
using g_select, but that will only give me the atom numbers and not the
trajectories. I can create an index
2012/6/5 Erik Marklund er...@xray.bmc.uu.se
5 jun 2012 kl. 14.23 skrev Shay Teaching:
2012/6/5 Mark Abraham mark.abra...@anu.edu.au
On 5/06/2012 9:11 AM, Peter C. Lai wrote:
The quick and dirty way is to post-patch Makefile in src/tools.
I think patching the appropriate Makefile.in is
On 5/06/2012 10:51 PM, Bao Kai wrote:
Hi, all,
It is very easy for me to get the following message.
WARNING: nmol = 1, this may not be what you want.
Temperature dependent fluctuation properties at T = 317.98.
I am wondering if somebody can tell me what does it mean or if it is a
problem to
5 jun 2012 kl. 15.05 skrev Justin A. Lemkul:
On 6/5/12 9:02 AM, rankinb wrote:
I am interested in pulling out the trajectories (x,y,z coordinates) of water
molecules within a certain distance of my solute molecule. I have tried
using g_select, but that will only give me the atom numbers
HI All,
I run the tip5p water model, i found the computed properties are not good, e.g.
energy.
Can anyone know the problem? i need to get the surface potential, it can get -1
V
regards
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Hi, Mark,
Following please find the information.
pure_water]$ g_energy_d -f step11.edr
:-) G R O M A C S (-:
GROwing Monsters And Cloning Shrimps
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen
Dear Rankinib,
You can do it with a 5 line bash script as well, cat everything times x,y,z and
just cut and past them into a spread sheet, and save it with tabs or spaces.
Stephan Watkins
Original-Nachricht
Datum: Tue, 05 Jun 2012 09:05:09 -0400
Von: Justin A. Lemkul
Original-Nachricht
Datum: Tue, 05 Jun 2012 09:05:09 -0400
Von: Justin A. Lemkul jalem...@vt.edu
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Trajectories
On 6/5/12 9:02 AM, rankinb wrote:
I am interested in pulling out the
Hi,
I think Erik meant to say that the program is trjorder (not g_order) for
the ordering of molecules by distance.
Cheers
Tom
On 05/06/12 14:41, Erik Marklund wrote:
5 jun 2012 kl. 15.05 skrev Justin A. Lemkul:
On 6/5/12 9:02 AM, rankinb wrote:
I am interested in pulling out the
Thank you all for your replies.
Stephan -- can you explain a little more about your 5 line bash script idea?
The only part I am not sure about is pulling out the water molecules within a
certain distance. Are you suggesting to write a script that calculates atom
distance and saves only
Hi,
I would like to use g_select_d to generate an index file containing the
atoms of BF4 residues whose centers of mass are in the range z12.24 nm. I
have tried the following:
g_select -f traj.xtc -s topol.tpr -select 'resname BF4 and res_com and
z12.24' -on output.ndx
But the selection
You can also use something like VMD where you load the trajectory then
select your atoms, then increment the frames and extract the xyz coordinates
of each of your atoms in the selection. You can do that in 5 lines of TCL
script (just don't update the select within selection after each frame or
On 6/5/12 2:55 PM, Andrew DeYoung wrote:
Hi,
I would like to use g_select_d to generate an index file containing the
atoms of BF4 residues whose centers of mass are in the range z12.24 nm. I
have tried the following:
g_select -f traj.xtc -s topol.tpr -select 'resname BF4 and res_com and
On 6/5/12 6:03 PM, Yun Shi wrote:
Hello all,
Assuming that I made my own .itp file for amber99sb-compatible DMSO parameters
(based on Thomas Fox and Peter A. Kollman. J. Phys. Chem. B., 1998, 102,
8070-8079) and included that in the .top file, how can I add DMSO to my system?
Should I also
Dear GMX users,
I have some trajectories of Ala-Ala dipepetides with COOH terminals
(Cap-Ala-Ala-COOH), However, I saw the chirality of the Ala-COOH doesn't
maintained as L form during the simulation, there are D-forms, is it
because there are some lacks of parameters of this part or Gromacs
I am trying to simulate a system with a phosphorylated threonine residue
using Gromacs 4.5.5. I took the parameters for the TPO residue from the
gromos43a1p force field and added them to the gromos43a1 force field,
following the steps as provided on the Gromacs website. I then successfully
On 6/5/12 7:36 PM, Alex Cumberworth wrote:
I am trying to simulate a system with a phosphorylated threonine residue using
Gromacs 4.5.5. I took the parameters for the TPO residue from the gromos43a1p
force field and added them to the gromos43a1 force field, following the steps as
provided on
Hi!
I want to perform a simulation with TIP4P water model. I want to know this
simulation how much slower than TIP3P water model or spc216 model approximately?
number of solvent molecules in my system are about 2500.
--
gmx-users mailing listgmx-users@gromacs.org
I apologize to anyone who wasted their time reading my original post: I
found that integrator had been misspelt in the em.mdp file, causing it to
default to integrator = md. After fixing the mistake, no more errors
resulted.
Alex
On Tue, Jun 5, 2012 at 4:46 PM, Justin A. Lemkul jalem...@vt.edu
On 6/06/2012 8:31 AM, mu xiaojia wrote:
Dear GMX users,
I have some trajectories of Ala-Ala dipepetides with COOH terminals
(Cap-Ala-Ala-COOH), However, I saw the chirality of the Ala-COOH
doesn't maintained as L form during the simulation, there are D-forms,
is it because there are some
On 6/06/2012 10:33 AM, Amir Abbasi wrote:
Hi!
I want to perform a simulation with TIP4P water model. I want to know
this simulation how much slower than TIP3P water model or spc216 model
approximately?
number of solvent molecules in my system are about 2500.
Do a 5 minute test on each and
Dear Justin,
Thank you very much for the reply
Sogol
From: Justin A. Lemkul jalem...@vt.edu
To: Kowsar Bagherzadeh kw_bagherza...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Sent: Monday, May 28, 2012 6:06 PM
Subject: Re: [gmx-users]
Dear all gromacs users,
While i am running pdb2gmx commond i am
getting following error.
Fatal error:
incomplete ring in HIS231
Kindly tell me how to overcome this error and how to
On 6/06/2012 12:26 AM, Bao Kai wrote:
Hi, Mark,
Following please find the information.
pure_water]$ g_energy_d -f step11.edr
:-) G R O M A C S (-:
GROwing Monsters And Cloning Shrimps
:-) VERSION 4.5.5
On 5/06/2012 11:47 PM, MD wrote:
HI All,
I run the tip5p water model, i found the computed properties are not
good, e.g. energy.
Probably you haven't run it well enough or long enough.
Can anyone know the problem? i need to get the surface potential, it
can get -1 V
Not unless they are
Dear all gromacs users,
I have 1VZV.pdb file, in that file HIS231
has incomplete ring as N atom is missing.Can i add N atom to the .pdb file
if possible how can i add that atom to .pdb file.
Suryanarayana Seera,
PhD student,
India.
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