On 1/29/13 4:43 AM, SANTU BISWAS wrote:
dear users,
I am performing an energy minimization of
polypeptide(formed by 10-residues of alanine, lysine,leucine,glutamic
acid ) in vacuum box by using
Steepest Descent(initially) and then Conjugate Gradient methods in
...@hotmail.co.ukescreveu:
Thank you for your reply and help.
Regards
Elie
Date: Sat, 15 Sep 2012 13:32:06 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] energy minimisation of carbon nanotubes.
On 9/15/12 12:49 PM, Elie M wrote:
Dear all,
I have a small question
On 9/15/12 12:49 PM, Elie M wrote:
Dear all,
I have a small question regarding energy minimization. I am minimizing a carbon
naotube in vaccuo and my (mdp )input file is: ;
; SWNT (10,0) on its own
; Elie Moujaes, SWNT+polymers project
; Energy minimization input file
;
cpp
Thank you for your reply and help.
Regards
Elie
Date: Sat, 15 Sep 2012 13:32:06 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] energy minimisation of carbon nanotubes.
On 9/15/12 12:49 PM, Elie M wrote:
Dear all,
I have a small question regarding
Ravi Kumar Venkatraman wrote:
*Dear all,
I am trying to minimize the energy of the single molecule
using gromacs. I tried with the following mdp
; VARIOUS PREPROCESSING OPTIONS FOR ENERGY MINIMIZATION OF ISOLATED MOLECULE
include =
define =
;
nikhil damle wrote:
Hi,
I am trying to simulate a dimeric structure and I have already simulated
its monomeric form. I use exactly same parameters which i use for
monomer during dimer minimisation in solvent.
System Details:
# Atoms = 4488 (# Res = 582)
octahedron box with d = 0.9
Solvent
Hi, Natalie,
Obviously, number of coordinates still doesn't match the topology file even
you updated the topol.top *carefully*.
Check the topol.top thoroughly or paste several line of your coordinate and
topology files may be good ideas.
Note that the topology file is lacking information for
Natalie Stephenson wrote:
Hi everyone,
I was hoping you could clear up a problem I'm having when performing
energy minimisation. I'm following the instructions from one of the
tutorials (Justin's Umbrella Sampling) with my own protein, however,
this time when I try to perform the energy
-boun...@gromacs.org] on behalf
of Terry [terrence...@gmail.com]
Sent: 22 September 2010 11:55
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy minimisation problems - coordinate file and
topology file not matching.
Hi, Natalie,
Obviously, number of coordinates still doesn't
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Natalie Stephenson [natalie.stephen...@postgrad.manchester.ac.uk]
Sent: 22 September 2010 13:02
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] Energy minimisation problems
] on
behalf of Natalie Stephenson [natalie.stephen...@postgrad.manchester.ac.uk]
*Sent:* 22 September 2010 13:02
*To:* Discussion list for GROMACS users
*Subject:* RE: [gmx-users] Energy minimisation problems - coordinate
file and topology file not matching.
Thanks for your help Justin Terry
I've been
for GROMACS users
Subject: Re: [gmx-users] Energy minimisation problems - coordinate file and
topology file not matching.
Natalie Stephenson wrote:
Ok ... think I've worked out what's happened ...
There were two 'SOL' groups. So when replacing solvent with ions it has
added double the amount
Hi Nayef,
Can you
- copy-paste the sequence of commands as you have typed them in (not
as you think you typed them in or as they're given in the tutorial)
- provide the output of 'tail 1qlz-water.gro'
Cheers,
Tsjerk
On Mon, Jun 21, 2010 at 9:49 PM, Nayef Daher eltha...@ualberta.ca wrote:
Hi,
for GROMACS users
Subject: Re: [gmx-users] Energy minimisation of solvated protein - Tutorial
Hi Nayef,
Can you
- copy-paste the sequence of commands as you have typed them in (not
as you think you typed them in or as they're given in the tutorial)
- provide the output of 'tail 1qlz-water.gro'
Cheers
Hi Anna,
You should mention the version of Gromacs you're using. One of the
versions did not write the box correctly to pdb files, which I think
happened in your case. If you take as the solvation step
genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro
instead of writing
Kothai Thiruvengadam wrote:
Dear all,
I am using MD simulation of a protein on Silicon nitride surface. The
surface has been created using VMD and tcl script (ref. bionano
tutorial).The protein+surface complex also has been generated using
VMD.Using that PDB file I have done md simulation
On Thursday, August 6, 2009 at 7:59:43 PM Nancy nancy5vi...@gmail.com wrote:
I ran the minimisation, and mdrun gave the following last few lines of output:
==
Step=19990, Dmax= 7.8e-06 nm, Epot= -7.14922e+04 Fmax= 3.19585e+04, atom= 2395
Step=19992, Dmax=
On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy nancy5vi...@gmail.com wrote:
I am trying to run equilibration on my solvated ethylene glycol
(ethanediol) system. I started
with an ethanediol mol2 file from which
topolbuild generated various files. I used editconf
to enlarge to box
of the
The energies simply do not seem to come down any further within several
thousand steps.
I start with a .mol2 file which contains the structure of ethylene glycol
(ethanediol). These are the commands that I use to set up and run the
minimisation:
$ .../topolbuild1_2_1/src/topolbuild -n
Nancy wrote:
snip
I then proceed to enlarge the box and solvate the molecule:
$ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5
$ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_box.gro -p
ethanediol.top -shell 1
So, instead of filling the box, you are simply
On Thursday, August 6, 2009 at 11:58:20 AM, Nancy nancy5vi...@gmail.com wrote:
The energies simply do not seem to come down any further within several
thousand steps.
I
start with a .mol2 file which contains the structure of ethylene glycol
(ethanediol).
These are the commands that I use
I have attempted to perform energy minimisation from scratch again, and
these are the commands that I am using to do so:
$ .../topolbuild1_2_1/src/topolbuild -n ethanediol -dir
.../topolbuild1_2_1/dat/gromacs -ff gmx53a6
which generates the files:
ethanediol.gro
ethanediol.log
On Thursday, August 6, 2009 at 4:08:18 PM, Nancy nancy5vi...@gmail.com wrote:
I have attempted to perform energy minimisation from scratch again, and these
are the
commands that I am using to do so:
$ .../topolbuild1_2_1/src/topolbuild -n ethanediol -dir
.../topolbuild1_2_1/dat/gromacs
I ran the minimisation, and mdrun gave the following last few lines of
output:
==
Step=19990, Dmax= 7.8e-06 nm, Epot= -7.14922e+04 Fmax= 3.19585e+04, atom=
2395
Step=19992, Dmax= 4.7e-06 nm, Epot= -7.14924e+04 Fmax= 8.72456e+03, atom=
2395
Step=19993, Dmax= 5.6e-06
Nancy wrote:
I ran the minimisation, and mdrun gave the following last few lines of
output:
==
Step=19990, Dmax= 7.8e-06 nm, Epot= -7.14922e+04 Fmax= 3.19585e+04, atom=
2395
Step=19992, Dmax= 4.7e-06 nm, Epot= -7.14924e+04 Fmax= 8.72456e+03, atom=
2395
Have you managed to minimise a single molecule?
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When
Nancy wrote:
Hello,
I was trying to run equilibration on my solvated ethylene glycol
system. However, the system seems to be exploding. I believe this is
due to inadequate energy minimisation, however, I am unable to minimise
my system any further. I am using the following .mdp file
I tried decreasing emstep, and also tried increasing the number of steps,
but I still get the following output from mdrun:
==
Steepest Descents did not converge to Fmax 1000 in 5001 steps.
Potential Energy = -6.9329155e+03
Maximum force =
On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy nancy5vi...@gmail.com wrote:
I was trying to run equilibration on my solvated ethylene glycol
system. However, the
system seems to be exploding. I believe this
is due to inadequate energy minimisation,
however, I am unable to
minimise my
Nancy wrote:
I tried decreasing emstep, and also tried increasing the number of
steps, but I still get the following output from mdrun:
==
Steepest Descents did not converge to Fmax 1000 in 5001 steps.
Potential Energy = -6.9329155e+03
Bruce D. Ray wrote:
On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy nancy5vi...@gmail.com wrote:
I was trying to run equilibration on my solvated ethylene glycol
system. However, the
system seems to be exploding. I believe this
is due to inadequate energy minimisation,
however, I am
Nancy wrote:
Hello,
I am trying to run equilibration on my solvated ethylene glycol
(ethanediol) system. I started with an ethanediol mol2 file from which
topolbuild generated various files. I used editconf to enlarge to box
of the ethanediol.gro file:
$ editconf -f ethanediol.gro -o
Maximum force = 9.4016180e+02 on atom 31
As has already been suggested, have you looked at the atoms listed as having
the maximum force to see why?
Addtionally, the structure of the solute is incorrect (all atoms are bonded to
each other).
How are you visualising it? If using VMD, then
and then MD.
Not sure about the energies. Maybe they should be negative ?
Andreas
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Jussi Lehtola
Sent: 14 May 2008 04:28
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] Energy
First try the EM/MD of 1 molecule in vacuum ('ethanol-gas') and check, if it
looks reasonable.
You could also have a look at the definition of ETHH in the GROMOS96
forcefield, e.g. in ffG43a2.rtp. Although this is a united atom topology it
might give you clues, if something is wrong.
Andreas
On Tue, 2008-05-13 at 14:34 +0100, Kukol, Andreas wrote:
First try the EM/MD of 1 molecule in vacuum ('ethanol-gas') and check, if it
looks reasonable.
You could also have a look at the definition of ETHH in the GROMOS96
forcefield, e.g. in ffG43a2.rtp. Although this is a united atom
On Tue, 2008-05-13 at 20:32 +0300, Jussi Lehtola wrote:
On Tue, 2008-05-13 at 14:34 +0100, Kukol, Andreas wrote:
First try the EM/MD of 1 molecule in vacuum ('ethanol-gas') and check, if
it looks reasonable.
Thanks, using the vacuum method I seem to get better results.
It seems I spoke
silvester.thu
2008-05-14
发件人： Jussi Lehtola
发送时间： 2008-05-14 11:28:31
收件人： Discussion list for GROMACS users
抄送：
主题： RE: [gmx-users] Energy minimisation problem
On Tue, 2008-05-13 at 20:32 +0300, Jussi Lehtola wrote:
On Tue, 2008-05-13 at 14:34 +0100, Kukol, Andreas wrote
Hi Jestin,
As I said, the last line in the .gro file codes for the box. So, you have a
singular box! You probably did something wrong with editconf. Did you give
it box dimensions at all (-box/-d). Have a look at the help: editconf -h
Besides that, do have a look at the procedure you used to
the last lines gives 0.000 0.000 0. in my file and in the examples
it is not.
I assume it is the dimension of the box, isn' it?
That is correct. So that full explains what you see occuring.
I built up the gro file using editconf -f *.pdb file.
You need to specify the size of the box with
Jestin,
Please don't use all capitals. As Mark has pointed out several times, that's
considered shouting. You're probably frustrated that things don't work
according to your expectations, but the frustration comes from you not
knowing what your doing. Don't blame us for that, go read a manual.
Quoting JMandumpal [EMAIL PROTECTED]:
Dear Justin,
I made some changes in my .mdp file, but the result is same.
My box size, as mentioned in the previous mail, is 20.1 A. The cut off I used
is 8 angstrom.
I attach the input file here.
**
cpp
As noted by someone, please post the last couple of lines of the .gro
file you provide to grompp.
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61
Dear users,
What I see the difference between the .gro file given at the examples in the
tutor directory and my own .gro file is that
the last lines gives 0.000 0.000 0. in my file and in the examples it is
not.
I assume it is the dimension of the box, isn' it?
I built up the gro file
Dear Gromacs users,
Thanks for the messages.
Tsjerk,
I was not aware that capital letters denote unpolite. I just used them to
highlight the problem so others can easily pick out. Thanks for the suggestions
as well.
I modified the file:
Quoting JMandumpal [EMAIL PROTECTED]:
Dear Gromacs users
When I run Energy minimisation using the command,
grompp -f em.mdp -p topol.top -c out.gro -o pr.tpr, I received the following
error message.
**
processing coordinates...
Dear Justin,
Thanks for the response.
This is my input file (em.mdp) which contains parameters for doing energy
minimisation.
cpp= /lib/cpp
define = -DPOSRES -DFLEX_
constraints= none
morse = no
integrator = steep
nsteps = 2000
; Energy
Dear Justin,
It seems, the given link which was directed to a post where I got contents of
ENERGY MINIMISATION FILE .mdp in my previous mail is not the right one, so I
paste its content here.
***
Geraudis Mustelier gera at
Quoting Justin A. Lemkul [EMAIL PROTECTED]:
Quoting JMandumpal [EMAIL PROTECTED]:
Dear Justin,
Thanks for the response.
This is my input file (em.mdp) which contains parameters for doing energy
minimisation.
cpp= /lib/cpp
define = -DPOSRES -DFLEX_
supti mukherjee wrote:
Dear all,
I was minimising a protein structure. I added polar hydrogens to the
protein by some program and then proceeded for the energy minimisation.
I chose Conjugate Gradient of 1000 steps with emtol as 100. The mdrun
came out with the following error.
During
nur avneet wrote:
dear all
hi,
When we do energy minimisation in vaccum...what ensemble should we use...
what do you mean by that? em does not create proper therrmodynamic
ensembles. what is pressure or temperature during an em? and constant
energy you surely don't want either.
however,
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