Blaise Mathias-Costa wrote:
Hello All,
The program was stopped twice with the following error:
Constraint error in algorithm Lincs at step 54646
t = 109.292 ps: Water molecule starting at atom 13293 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
Mark Abraham wrote:
Hello,
In the same context that my question of yesterday (see the post at the
end of this message), I'm interested in calculating the force of the
interaction between lipids and solvent. More precisely, I want to
calculate the norm of the force vector related to all non-bon
Hi, GROMACS users:
I'm trying to calculate the lifetime distribution between pairs of vectors.
The problem can be simplified as: there are many vectors in any one frame of
a MD trajectory, and when one vector is within a cutoff distance with
another vector, and their angle is larger than a cutoff a
Hello All,The program was stopped twice with the following error: Constraint error in algorithm Lincs at step 54646t = 109.292 ps: Water molecule starting at atom 13293 can not be settled.Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinatesGrid:
> Hello,
>
> In the same context that my question of yesterday (see the post at the
> end of this message), I'm interested in calculating the force of the
> interaction between lipids and solvent. More precisely, I want to
> calculate the norm of the force vector related to all non-bonded
> inter
> Dear Gromacs users,
>
> Could you please help me to find any examples of 2 component simple
> reactions with
> all the preliminary calculations and further data files for simulations on
> Gromacs.
http://catb.org/~esr/faqs/smart-questions.html#homework
Why would we want to do your work for fr
hi Lanyuan,
Thanks for your replay. I have tried the current(3.3.1) and 3.3 version g_wham.
They both dont work. What do you mean by original?
With best regards,
Abu Naser
School Of Life Sciences
Heriot-Watt University
Edinburgh EH14 4AS
Email: [EMAIL PROTECTED]
Phone: +44(0)1314518265
F
Hi,
I don't remember whether the bug has been fixed for 3.3.*. Can any gromacs guy
clarify that?
Abu, have you tried the original g_wham first? If it really dosen't work,
please shoot me an email.
Then I can send you the correct file.
Lanyuan Lu
> Date: Fr
Hello,
In the same context that my question of yesterday (see the post at the
end of this message), I'm interested in calculating the force of the
interaction between lipids and solvent. More precisely, I want to
calculate the norm of the force vector related to all non-bonded
interactions (
On 9/14/2007 5:35 PM, [EMAIL PROTECTED] wrote:
Selon Yang Ye <[EMAIL PROTECTED]>:
Deshuffling shall be made before 2), 3) and 4).
Furthermore, be aware that if you use the 'sort' option, you'll also need to
desort ...
IIRC, there is a g_desort program that does all in one (it was publ
Dear Gromacs users,
Could you please help me to find any examples of 2 component simple reactions
with
all the preliminary calculations and further data files for simulations on
Gromacs.
Thank you in advance
Alex
-
Take the Internet to Go
Naser, Md Abu wrote:
Hi All,
I have been getting segmenation fault with current(3.3.1) version of
g_sorient.
Dose anybody know why?
please submit a bugzilla.
With best regards,
Abu Naser
School Of Life Sciences
Heriot-Watt University
Edinburgh EH14 4AS
Email: [EMAIL PROTECTED]
Phone: +4
Rigden, LucianeVMello wrote:
Dear all,
I am trying to generate a postscript file using xpm2ps.
I had a look in the archive, where they suggest the use of gimp to
visualise ss.xpm.
However, for some reason the colour I got with gimp is not the same in
ps. And the display with gimp is not colour
Dear all,
I am trying to generate a postscript file using xpm2ps.
I had a look in the archive, where they suggest the use of gimp to visualise
ss.xpm.
However, for some reason the colour I got with gimp is not the same in ps. And
the display with gimp is not colour coded. I can tell by comparing
Hi All,
I have been getting segmenation fault with current(3.3.1) version of g_sorient.
Dose anybody know why?
With best regards,
Abu Naser
School Of Life Sciences
Heriot-Watt University
Edinburgh EH14 4AS
Email: [EMAIL PROTECTED]
Phone: +44(0)1314518265
Fax : +44(0) 131 451 3009
___
Hi,
Is there any way I can get corrected version of g_wham? I know form the
discussion archive
that David Bostick has a copy of the corrected g_wham.
With regards,
Abu Naser
School Of Life Sciences
Heriot-Watt University
Edinburgh EH14 4AS
Email: [EMAIL PROTECTED]
Phone: +44(0)1314518265
Just a quick look at the ffG45a3.rtp shows that there is an entry for ADE,
however the ADE entry is for Adenine.
For help with your problem check out:
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
Tom
--On Friday, September 14, 2007 14:13:55
Hi,
I have facing some problem when converting .pdb file to .gro and .top .
I have a .pdb of alpha d-mannose (1-6) alpha d-mannose. I was using the
pdb2gmx command and 45a3 forcefield .
Showing the fatal error:
Atom O in residue ADE 1 not found in rtp entry with 25 atoms
Selon Yang Ye <[EMAIL PROTECTED]>:
> Deshuffling shall be made before 2), 3) and 4).
Furthermore, be aware that if you use the 'sort' option, you'll also need to
desort ...
IIRC, there is a g_desort program that does all in one (it was published on the
list some time ago), and should be avaialbe
Deshuffling shall be made before 2), 3) and 4).
On 9/14/2007 11:36 AM, Frankie Montenegro wrote:
Hi guys,
A stupid question: I got myself confused with this
shuffling/deshuffling thing, which I
shouldn't have been doing with protein in the first place. So this
are my steps, done
on the same 4
From: toma0052 <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: [gmx-users] Applying a Uniform Shear
Date: Thu, 13 Sep 2007 12:00:12 CDT
Hello,
I am looking for a way in Gromacs that I could apply a uniform shear.
I
have
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