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
gromacs_4.5.5_doub
creveu:
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:
> >
>
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:
> >
&g
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
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 =/usr/bin/cpp
define
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 =
;
*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 =
; RUN CONTROL PARAMETERS
integrator
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,
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 (spce water model) dens
t 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 h
[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 - coordinate
file and topology file not matching.
Thanks for
7; groups.
Thanks for the help!
xxx
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-
.@gromacs.org [gmx-users-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, num
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 mi
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 *28*
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 minimisation it throws out this
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.gr
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 wrote:
> Hi,
>
> I have the same
Hi,
I have the same problem as listed below back in February. I am using
the latest gromacs version (4.0.7) and tried the solution below by
entering
genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro
instead of making the output as pdb file. Yet the same result occurs
w
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 output
Hi,
I've been trying to go through the 'Introduction to Molecular Dynamics
Simulations and Analysis' tutorial written by Tsjerk Wassenaar, one of
the tutorials listed on the GROMACS website.
I've got to the stage where I am performing energy minimisation on my
solvated protein but when I
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 in
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 in gromacs. One itp file
for silicon
On Thursday, August 6, 2009 at 7:59:43 PM 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=
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 t
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
Step=19993,
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
On Thursday, August 6, 2009 at 4:08:18 PM, Nancy 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 -ff gmx53a6
>
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
ethanediolMOL.mol2
On Thursday, August 6, 2009 at 11:58:20 AM, Nancy 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 to set up and run
tion
with emtol = 10.0 ?
--
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
*From:* Nancy mailto:nancy5vi...@gmail.com>>
=
>
> {remainder snipped}
>
> The energies do seem large. What happens if you do energy minimization
> with emtol = 10.0 ?
>
>
> --
> Bruce D. Ray, Ph.D.
> Associate Scientist, and Operations Director
> NMR Center
> IUPUI
> Physics Dept.
> 40
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
>
>From: Nancy
>To: Discussion list for GROMACS users
>Sent: Wednesday, August 5, 2009 10:28:47 PM
>Subject: [gmx-users] Energy Minimisation
> 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, th
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
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 ethanediol_box.gro -b
Bruce D. Ray wrote:
On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy 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
Maximu
hat's just based on examples I've seen where
others have used that value.
--
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
>
>From: Nancy
>To: Discussion list for GROMACS users
&g
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 = 2.1
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 "m
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 "minim.mdp" for
minimsa
Hi gmx-users,
I am having small doubt on energy minimisation that is
I have started protein system, when I do EM its showing that
Step size too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 800
Double precision normally gives you higher a
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:
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 wr
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
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
.
Andreas
> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> On Behalf Of Jussi Lehtola
> Sent: 13 May 2008 11:36
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Energy minimisation problem
>
> Hi,
>
>
>
> I have constructed
Hi,
I have constructed topologies for methanol, ethanol, propanol and
butanol using x2top with the atomic coordinates from NIST Chemistry
WebBook. I have modified the topologies by putting the CH3s, CH2s and
OHs in their separate charge groups.
Now I have run into problems when trying to minimi
>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 wit
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 obta
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 u
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:
***
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
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.
> **
>
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= /lib/cpp
define = -DPOSRES-DF
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.
If
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
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 ict.c
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 minimizi
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 coordi
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...
double-checking input for internal consistency
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 neig
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 neighborsearching, we assign each
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, h
dear all
When we do energy minimisation in vaccum...what ensemble should we use...
nur
-
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