dear friends
i want to simulate a water medium in which 5 types of different ions flow in
it. how can i do that with gromacs?
thanks
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Please tell me how gromacs calculates degree of overlap between
conformational spaces of the two proteins is it from RMSIP (Root mean square
inner products)? if yes then give me the reference in gromacs tutorial 4.0
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Pawan
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Dear gmx-usres,
In our university we have a cluster containing 20 nodes each with 4 processors,
which I want to use that for the simulation project.
As a test I submitted a run that I have tested it before in the Imperial
College (London).
Here the structure of the cluster is so that I should
Dear All
I downloaded dsspcmbi.tar.gz, and compiled using command
./DsspCompileGCC as given in Readme.txt file. when I try to run
do_dssp command in gromacs I get error
Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)
I checked for DSSP executible in
Hi,
On May 18, 2010, at 9:35 AM, delara aghaie wrote:
Dear gmx-usres,
In our university we have a cluster containing 20 nodes each with 4
processors, which I want to use that for the simulation project.
As a test I submitted a run that I have tested it before in the Imperial
College
Dear Justin,
thank you for your answer. Actually I did the changes that you suggest, but
the problem seems to be the fact that I called lig my molecule. In fact,
the error message told that The moleculetype lig is redefined. When I
changed its name, it seemed to work. Is there some problem in
Hi You Zou,
Complementing Justin's message, I would invite you to take a look at
acpype.googlecode.com. It's my attempt to address problems like yours.
There's also links to some options besides ACPYPE.
Bear in mind that you should know what you're doing. I would suggest you to
read the Wiki's
Hi ALL,
I want to calculate the distance between a number of atom pairs using
g_dist. For this I want to submit the job through a submission script so
that g_dist calculates the distances for all the pairs one after the other.
But I need to select the two groups from an index file. How can I give
To the second question:
PRODRG makes usually a very small box (sometimes smaller then the
molecule, if i remember correctly), so if you want to use periodic
boundary conditions you must make the box large enough, so that there
are no problems with cut-offs.
The easiest way to make the
Hi,
I wanna keep crystallographic water with tip4p model for md simulation but
when I use pdb2gmx even if I set -water tip4p it protonates oxygens to spc
water model instead.
Is there any way to replace spc water molecules with tip4p water molecules
in the same orientation?
Btw what happen if I'll
Hi ALL,
I want to calculate the distance between a number of atom pairs using
g_dist. For this I want to submit the job through a submission script so
that g_dist calculates the distances for all the pairs one after the other.
But I need to select the two groups from an index file. How can I give
Anirban Ghosh wrote:
Hi ALL,
I want to calculate the distance between a number of atom pairs using
g_dist. For this I want to submit the job through a submission script so
that g_dist calculates the distances for all the pairs one after the
other. But I need to select the two groups from
tahereh tekieh wrote:
dear friends
i want to simulate a water medium in which 5 types of different ions
flow in it. how can i do that with gromacs?
thanks
Assuming they are monoatomic, you can use genion after you have added water. If
they are polyatomic, use genbox -ci -nmol (before
Anna Marabotti wrote:
Dear Justin,
thank you for your answer. Actually I did the changes that you suggest, but
the problem seems to be the fact that I called lig my molecule. In fact,
the error message told that The moleculetype lig is redefined. When I
changed its name, it seemed to work. Is
shahid nayeem wrote:
Dear All
I downloaded dsspcmbi.tar.gz, and compiled using command
./DsspCompileGCC as given in Readme.txt file. when I try to run
do_dssp command in gromacs I get error
Well, what happened?
Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv
Thanks a lot Justin.
On Tue, May 18, 2010 at 4:36 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Hi ALL,
I want to calculate the distance between a number of atom pairs using
g_dist. For this I want to submit the job through a submission script so
that g_dist
The PLUMED Developers are proud to announce that the NEW version
of PLUMED, version number 1.2.0, is available from
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PLUMED is a plugin for free-energy calculations in molecular systems
that can be interfaced with some of the most popular molecular dynamics codes
Hi
After posting this mail I did some google search and after changing the
executible name to dssp I moved it in /usr/local/bin/ After this when I did
do_dssp it starts running asks to select a group I choose main chain 5, then
it generates some intermediate file and gives error as segmentation
shahid nayeem wrote:
Hi
After posting this mail I did some google search and after changing the
executible name to dssp I moved it in /usr/local/bin/ After this when I
did do_dssp it starts running asks to select a group I choose main chain
5, then it generates some intermediate file and
Shahid,
Before trying for do_dssp a gromacs utility calling dssp program , try first
dssp program itself by passing simple input like pdb and I hope by that way
you can resolve your problem
B.Nataraj
-Original Message-
From: gmx-users-boun...@gromacs.org
Archana S Achalere wrote:
Thank you Dr. Justin for the reply.
Here are the details of my simulation.
I am simulating lipid bilayer (DPPC + water) where I give equal and
opposite force (along bilayer normal) on lipid and water molecules
I am using 128 DPPC and 3655 water. The .pdb file is
Hi gromacs users
1) after doing simulated annealing simulation, who can I understand that
obtained structure is in global minimum and not in local minimum?
2) who can I understand that parameters used in mdp file (annealing_npoints,
annealing_time, annealing_temp) are true?
Any help will highly
Hi
When I run dssp alone with a .pdb file it works well. But when I run with
Gromacs as do_dssp it gives segmentation fault and does not do any
calculation except giving some intermediate files as follows.
Opening library file /usr/local/gromacs/share/gromacs/top/ss.map
Reading frame 0
shahid nayeem wrote:
Hi
When I run dssp alone with a .pdb file it works well. But when I run
with Gromacs as do_dssp it gives segmentation fault and does not do any
calculation except giving some intermediate files as follows.
Opening library file
I have a little concept problem regarding principal component analysis. So
my question is about ED sampling are as follows:
1. I have read from the manual that g_covar calculates and diagonalize the
(mass-weighted) covariance matrix. So what is the meaning of mass-weighted
in covariance matrix?
I think the force I have applied on the two systems balance each other.
If I calculate total force on each group:
DPPC = 734 amu, water = 18 amu
734*128 = 93952 (This thing you calculated as 90282)
18*3655 = 65790
93952*0.07 = 6576.64
65790*0.1 = 6579
If I reduce values of acceleration
Archana S Achalere wrote:
I think the force I have applied on the two systems balance each other.
If I calculate total force on each group:
DPPC = 734 amu, water = 18 amu
734*128 = 93952 (This thing you calculated as 90282)
Ah yes, typo. Sorry :)
18*3655 = 65790
93952*0.07 =
Hi,
could you guide me how one can create .ndx file format. I thought it would
be accessible in library directory like rtp ..files.
Thanks,
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Please search the archive at
Moeed skrev:
Hi,
could you guide me how one can create .ndx file format. I thought it
would be accessible in library directory like rtp ..files.
Thanks,
Use make_ndx to create a ndx file. The format is pretty straightforward
and the files themselves quite readable. Not enoyable, mind you,
When you re-generate hydrogens, you are introducing some extra disorder
to the system. What I did is to write a script to rename the hydrogens.
For example, there are residues that have the hydrogen numbering
starting from 2 (eg. hydrogens on CB of lysine had hydrogens starting
from HB2). In the
- Original Message -
From: pawan raghav pwnr...@gmail.com
Date: Tuesday, May 18, 2010 17:34
Subject: [gmx-users] RMSIP (Root mean square inner products)?
To: gmx-users@gromacs.org
Please tell me how gromacs calculates degree of overlap between
conformational spaces of the two
- Original Message -
From: Павел Кудрявцев pavk...@gmail.com
Date: Tuesday, May 18, 2010 20:55
Subject: [gmx-users] crystallographic water to tip4p model
To: gmx-users@gromacs.org
Hi,
I wanna keep crystallographic water with tip4p model for md simulation but
when I use pdb2gmx even
- Original Message -
From: shahab shariati shahab.shari...@gmail.com
Date: Tuesday, May 18, 2010 23:36
Subject: [gmx-users] simulated annealing (SA)
To: gmx-users@gromacs.org
Hi gromacs users
1) after doing simulated annealing simulation, who can I understand that
obtained
Dear Friends
I tried
to obtain the XY density maps of the heme using g_densmap tool.
The
molecule was centered in the box
The
system was rotated to maintain the XY plane on the molecular plane.
In the
reference gro file, the molecule was also centered and the plane XY was on the
Hello,
I am trying to create an index file to get interaction energies between
hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in my system.
To do this how should I define my index groups. Should I include all 125
molecuels in index file? now I have only the first 20 atoms (first
- Original Message -
From: Moeed lecie...@googlemail.com
Date: Wednesday, May 19, 2010 4:41
Subject: [gmx-users] how to define an index file
To: gmx-users@gromacs.org
Hello,
I am trying to create an index file to get interaction energies between
hexane (C6H14, 20atoms) molecules.
Please use a descriptive subject line to help everybody.
I suspect your use editconf is your problem. -princ may not preserve your box
the way you've assumed. Try -princ -c, or editconf -princ then editconf -c.
It's also pointless and error-prone to compile MPI versions of the GROMACS
tools.
Hi all,
I try to use the energy exclusion keyword in the MDP file:
energygrp_excl = CNT CNT
and got the warning -
WARNING 2 [file aminoacids.dat, line 1]:
Can not exclude the lattice Coulomb energy between energy groups
What can be the source of this issue?
BTW, there are only LJ
Vitaly Chaban wrote:
Hi all,
I try to use the energy exclusion keyword in the MDP file:
energygrp_excl = CNT CNT
and got the warning -
WARNING 2 [file aminoacids.dat, line 1]:
Can not exclude the lattice Coulomb energy between energy groups
What can be the source of this
I am trying to create an index file to get interaction energies between
hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in my
system.
To do this how should I define my index groups. Should I include all 125
molecuels in index file? now I have only the first 20 atoms (first
Vitaly Chaban wrote:
I am trying to create an index file to get interaction energies between
hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in my
system.
To do this how should I define my index groups. Should I include all 125
molecuels in index file? now I
Hello gmx-users users :)
I am modifying the 'g_msd' utility to be able to calculate viscosities
using the corresponding Einstein relationship according to equation
3.14 in Helfand E., Physical Review, 119, 1, 1960. The equation is
similar to the mean-square displacement equation for
On Tue, May 18, 2010 at 2:00 PM, Gaurav Goel gauravgoel...@gmail.comwrote:
Hello gmx-users users :)
I am modifying the 'g_msd' utility to be able to calculate viscosities
using the corresponding Einstein relationship according to equation
3.14 in Helfand E., Physical Review, 119, 1, 1960.
Hello,
I am trying to create an index file to get interaction energies between
hexane (C6H14, 20atoms) molecules (interaction energy between two hexane
molecules) I have 125 hexane molecules in my system. Please help me figure
out what the problem is.
make_ndx -f Hexane-Stack125.gro -o index.ndx
Moeed wrote:
Hello,
I am trying to create an index file to get interaction energies between
hexane (C6H14, 20atoms) molecules (interaction energy between two hexane
molecules) I have 125 hexane molecules in my system. Please help me
figure out what the problem is.
make_ndx -f
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