Hi,
To support an upcoming promotional video being prepared by the CRESTA
project (http://cresta-project.eu) which provides some of the funding
support for GROMACS development, it would be nice to have some
real-life examples of work being done with GROMACS as the visual
element while a voice-over
On 4/16/13 9:07 AM, Group Gro wrote:
Dear GROMACS users,
Hi.
I want to study different protein-drug complexes and I follow the procedure
mentioned in the
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/.
I copied and pasted the positions of each drug to the end
Dear GROMACS users,
Hi.
I want to study different protein-drug complexes and I follow the procedure
mentioned in the
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/.
I copied and pasted the positions of each drug to the end of conf.gro and did
other steps. Is thi
se topics are discussed routinely.
-Justin
Thanks alot.
ali kazemi
department of biochemistry
islamic azad university shahrekord branch
*From:* Justin Lemkul
*To:* Group Gro ; Discussion list for GROMACS users
*Sent:
On 2/25/13 6:09 AM, Group Gro wrote:
Dear Gromacs Users.
I apologize for asking a question that has come up several times by numerous users in the
previous e-mails, but I have read the answers and suggestions to those posts and I am not
still able to solve the problem based on them. It i
Dear Gromacs Users.
I apologize for asking a question that has come up several times by numerous
users in the previous e-mails, but I have read the answers and suggestions to
those posts and I am not still able to solve the problem based on them. It is
completely possible that I am just not
Przemek Bartha wrote:
Dear gmx users,
my goal is to aquire a PMF courve of two amino-acids (ASP and LYS) of
which one is pulled from the other. I followed Justin's tutorial on
umbrella sampling.
Here are the results.
profile.xvg:
http://przemekbartha.pl/upload/profile.png
histo.xvg:
http://p
Dear gmx users,
my goal is to aquire a PMF courve of two amino-acids (ASP and LYS) of which one
is pulled from the other. I followed Justin's tutorial on umbrella sampling.
Here are the results.
profile.xvg:
http://przemekbartha.pl/upload/profile.png
histo.xvg:
http://przemekbartha.pl/upload/histo
ITHAYARAJA wrote:
Dear Sir,
Greetings!
I found the following error while preforming pdb2gmx command,
Fatal error:
Incomplete ring in HIS-3
You have an incomplete starting structure. In order for pdb2gmx to work, you
need an intact coordinate file. If your input is a .pdb file, it may
Dear Sir,
Greetings!
I found the following error while preforming pdb2gmx command,
Fatal error:
Incomplete ring in HIS-3
I request you to do your best as possible as earlier.
Thanks in advance...
--
**
Ithayaraja M,
Research Scholar,
Department of Bionformatics,
Bharathiar University,
- Original Message -
From: leila separdar
Date: Sunday, November 21, 2010 19:15
Subject: Re: [gmx-users] request
To: Discussion list for GROMACS users
>
> hi
> do I need any .pdb file for making .gro and .top file?
>
> I make .pdb file with hyperchem software
hi
do I need any .pdb file for making .gro and .top file?
I make .pdb file with hyperchem software and then I used pdb2gmx command in
order to make .gro and .top files. but I think my way is wrong. is it true?
is there anybody that done this simulation?
leila
On Sun, Nov 21, 2010 at 11:24 A
Hi,
Define an itp file which has the non-bonded info. Then define a mdp (md
parameter file) and also make a structure file (gro). Also you need a
topology file (top) which corresponds to the structure file.
You will have to do some background work. Manual should be your friend.
amit
On Sat, Nov
I am beginner with gromacs. I would like to simulate the behavior of glassy
materials starting with simple Lennard Jones liquid.
please advise me as to how to begin.
a relevent flowchart or tutorial would be of immerse help
thank you very much indeed.
--
gmx-users mailing listgmx-users@gromacs
I (Brock Palen) host an HPC podcast with Jeff Squyres of Open-MPI fame.
We would like to have a gromacs dev or two on the show as a guest.
The show is friendly (find the show at www.rce-cast.com for
examples). Lasts about an hour, and very low key.
If you are interested please contact me,
Dear user
Can anyone please send me the below mentioned journal paper
"Performance of the general amber force field in modeling aqueous POPC membrane
bilayers" thw link is
http://www3.interscience.wiley.com/journal/114209721/abstract. Mu institute
does not have access.
I will be very thankf
[EMAIL PROTECTED] wrote:
Is it possible for the moderators to change some setting that
would automatically word-wrap all posts on the mailing list
archive?
This would be a good thing. It is also normally possible to set your own
word wrap in an email client.
Mark
Is it possible for the moderators to change some setting that
would automatically word-wrap all posts on the mailing list
archive?
Many of my posts end up spanning more than the horizontal
space on one screen when viewed from the mailing list
archive. I try to remember to add hard returns on each
I am interested in obtaining forces on particular atoms at each
integration step. It seems wasteful to use "nstfout = 1" when I only
want the forces on a couple atoms out of tens of thousands.
My point of interest is this: If I am doing umbrella sampling over a
spatial coordinate or using d
This is not a question.
Previously I posted under this title when I was having difficulty
reproducing alanine dipeptide 2D PMFs for Phi/Psi.
Update: Literature results have been reproduced. My entire problem was
based on having a cis peptide bond for the C-terminal peptide bond in
ALA. Af
Hi,
I am trying to start a simulation involving
self-assembly of protein on Au (111) surface where 111
designates the miller indices of the plane.
I know how to construct a FCC lattice and the
coordinates of a system using Fortran code. But I have
no clue of how to get the coordinates of (111)
Chris,
>Right. I remember looking into this at one point, and I don't think
>the manual is correct; it looks to me like dihres.c handles
>periodicity properly. In particular, there is the followign comment in
>dihres.c:
It's good to see that this is actually a comment in the source code, I didn
Vojtech.:
I have done similar calculation. Look at the supporting
info for http://dx.doi.org/10.1021/jp068587c. If you find
anything useful for you feel free to contact me.
Thanks Vojtech. I am going to try to repeat your Figure 2. If I can do that then I can confirm that there is some problem
Chris,
I have included my .top file. The relevant section is in [ dihedral_restraints ]
This file is a template that I use like this:
sed 's/PHI/${phi_value}/' template.top | sed 's/PSI/${psi_value}/' >
phi${phi_value}_psi${psi_value}.top
Just out of curiousity, which GROMACS version are you
I'll have to assume you know what you're doing with using impropers to
calculate PMFs. I've done this using the dihedral restraints code.
Have you double-checked that? That's the first place I would look.
Many thanks for your thoughtful reply.
I have included my .top file. The relevant section
Chris,
I'll have to assume you know what you're doing with using impropers to
calculate PMFs. I've done this using the dihedral restraints code.
Have you double-checked that? That's the first place I would look.
Otherwise, I don't have a great test system for you.
David
On 4/25/07, Chris Neal
Does anybody have a good test system for reproducing the PMF about a
dihedral? I believe that my procedure is correct, and I have
successfully reproduced a 1d dihedral PMF for a 4 atom chain system
simulated in the absence of nonbonded interactions.
However, my results using an oplsaa interpre
David Konerding wrote:
Hi
I was happy to see the 'Speeding up Parallel GROMACS' paper. I'd like
to try
the GROMACS patch for better all-to-all, as well as the all-to-all test
program referred
to on the paper. I can't find it on the GROMACS site.
Hi David,
you can download both at
www.grom
Hi
I was happy to see the 'Speeding up Parallel GROMACS' paper. I'd like to
try
the GROMACS patch for better all-to-all, as well as the all-to-all test
program referred
to on the paper. I can't find it on the GROMACS site.
We've got a Cisco 6500 and when I run tcpdump during MPI runs I see a h
hadi behzadi wrote:
Program grompp, VERSION 3.3
Source code file: topio.c, line: 385
Fatal error:
Invalid order for directive moleculetype, file ""1.top"", line 17
The line 17 is [ moleculetype ].
As it says, this directive is out of order. You have to #include some
forcefield files first, whi
>Fatal error:
>Invalid order for directive moleculetype, file ""1.top"", line 17
>The line 17 is [ moleculetype ].
>I request you all to give suggestion for this.
Go to www.gromacs.org, click on the link that says search, which will
take you to http://www.gromacs.org/external/search.html
In the
Hi all users
I constructed topology and gro (1.gro and 1.top) file for propane (
CH3CH2CH3) molecule from PRODRG server as follow:
1.go
PRODRG COORDS
3
1DRG CAB 1 -0.128 0.172 0.000
1DRG CAA 2 -0.128 0.019 0.000
1DRG CAC 3 0.01
-users@gromacs.orgDate: Mon, 22 May 2006 12:22:29 -0700 (PDT)
Subject: [gmx-users] request
hello
I have a topology file for propanol as is in below , how we can
obtain topology file for 100 molecule of propanol
thanks
;
;
; This file was generated by PRODRG
version 05120
hadi behzadi wrote:
hello
I have a topology file for propanol as is in below , how we can obtain
topology file for 100 molecule of propanol
thanks
chapter 5
are you sure you want this force field by the way?
in the systems section write
drg 100
;
;
; This file was gen
hello I have a topology file for propanol as is in below , how we can obtain topology file for 100 molecule of propanol thanks ; ; ; This file was generated by PRODRG version 051202.0518; PRODRG written/copyrighted by Daan van Aalten; ; Questions/comm
Mikko Hellgren wrote:
>
> Hi all Gromacs users and developers, I wonder if anybody has pdb files
> for NAD+ (NADH in Gromacs), NADH (NADP) and Retinol (RTOL) with the same
> labels as in Gromacs topologies. This would save me a lot of time in my
> work since the atom names in my PDB for the ligan
Mobley <[EMAIL PROTECTED]>
Date: Tuesday, March 28, 2006 5:30 pm
Subject: Re: [gmx-users] Request for PDB with the same label as in
Gromocs topologies.
To: [EMAIL PROTECTED], Discussion list for GROMACS users
> Mikko,
>
> If I understand correctly what you're asking (that is, what at
Mikko,
If I understand correctly what you're asking (that is, what atom types
in GROMACS correspond to what names in the PDB) this is really
nontrivial and there isn't one answer. In particular, each force field
has its own set of atom types. There are, for example, many different
types of carbon
Hi all Gromacs users and developers, I wonder if anybody has pdb files
for NAD+ (NADH in Gromacs), NADH (NADP) and Retinol (RTOL) with the same
labels as in Gromacs topologies. This would save me a lot of time in my
work since the atom names in my PDB for the ligands are different from
Gromacs atom
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