Dear Sirs:
I wang to know simulate coarse-graied system using gromacs, but I don not
know how to use atom2cg.awk to convert CG model!
Thank you very much!
___
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Hi, Yanmei
On Fri, May 8, 2009 at 2:20 AM, Yanmei Song yson...@asu.edu wrote:
NOTE 2 [file aminoacids.dat, line 1]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-off
Dear all,
I am trying to simulate a water-liquid crystal system. My initial is box is
creating by merging two well equilibrated boxes of water and LC. After a steep
simulation of about 1,000,000 steps I try to do an md simulation but I get the
error
Water molecule starting at atom 9103 can
Can someone confirm that GMX 4.x is already released with updated
OPLS/AA files as once mentioned in
http://www.gromacs.org/component/option,com_docman/task,doc_details/gid,7/Itemid,26/
?
Many thanks in advance.
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of
Hi,
I have come to the conclusion that the v-rescale thermostat is only correct
in the limit of large numbers of degrees of freedom, which is equivalent to a
small scaling limit.
The conservation of the conserved energy quantity improves as the system gets
bigger.
But I noticed that in 4.0
Dear colleagues,
I'm looking for clarifications on what exactly I need to do in order to get
a correct scaling of 1-4 interactions for OPLS-AA in a topology made by
x2top. Specifically, will the command
x2top -f in.gro -o out.top
result in a topology that, when fed into grompp, will give a .tpr
Hi,
Thanks for your confirmation of this problem. One thing is not clear to
me from your answer. Has v-rescale fundamental problems with a Harmonic
oscillator or is it a problem with the GROMACS implementation?
Kind regards,
Servaas
Message: 3
Date: Fri, 8 May 2009 10:12:45 +0200
From:
Hi,
That is a fundamental problem of most global thermostats,
just like Nose-Hoover. Nose-Hoover chains solve this.
The only thermostats that guarantee proper ensembles for any system
are local ones such as Langevin dynamics.
Berk
From: servaas.michielss...@student.kuleuven.be
To:
Antonia V. wrote:
Dear all,
I am trying to simulate a water-liquid crystal system. My initial is box
is creating by merging two well equilibrated boxes of water and LC.
After a steep simulation of about 1,000,000 steps I try to do an md
simulation but I get the error
Water molecule starting
Hi,
I just put one box on top of the other in order to make my new system.
I use no constraints for the system, and I can't figure out the problem. It
seems that the water molecules of the new system are getting crazy...
Antonia
/attachments/20090508/8b339ca0/attachment-0001.html
--
Message: 2
Date: Fri, 08 May 2009 11:17:33 +0200
From: servaas servaas.michielss...@student.kuleuven.be
Subject: [gmx-users] Re: v-rescale - harmonic oscillator
To: gmx-users@gromacs.org
Message-ID
Date: Fri, 8 May 2009 19:38:41 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] (no subject)
Antonia V. wrote:
Dear all,
I am trying to simulate a water-liquid crystal system. My initial is box
is creating by merging two well equilibrated
Antonia V. wrote:
Hi,
I just put one box on top of the other in order to make my new system.
I use no constraints for the system, and I can't figure out the problem.
It seems that the water molecules of the new system are getting crazy...
Unfortunately, on top is also not a helpful
Unfortunately, it' s the only way I can do it, since I want two completely
separated phases.
With the tools provided by GROMACS I get a mixture, is there a way to get a box
with two separated phases?
Antonia
_
Show them the way!
Antonia V. wrote:
Please use a descriptive subject line and reply quoting the previous
message. It's not your reader's job to work out your context if you're
the one asking for free help!
Unfortunately, it' s the only way I can do it, since I want two
completely separated phases.
I have
xi zhao wrote:
Dear Sirs:
I wang to know simulate coarse-graied system using gromacs, but I don
not know how to use atom2cg.awk to convert CG model!
Thank you very much!
./atom2cg_v2.1_tryout.awk my.pdb out.pdb
Note that the script available online needs to be modified to include a
Hi there,
So I decided to give a try with x2top.
x2top -f aaa.gro -o aaa.top
However, the program starts and seems to never finishing holding as:
[snip]
There are 23 name to type translations
Generating bonds from distances...
atom 0
And 'atom 0' stays there while I clearly see my cpu running
Is this version 4.0.4? I get the same thing under the newest version. I think
x2top fluctuates in terms of its level of usability, since it is in an ongoing
state of development. Older versions (i.e., 3.3.3) should work, at least in
terms of generating a basic topology.
-Justin
Alan
Justin A. Lemkul wrote:
Is this version 4.0.4? I get the same thing under the newest version.
I think x2top fluctuates in terms of its level of usability, since it is
in an ongoing state of development. Older versions (i.e., 3.3.3) should
work, at least in terms of generating a basic
Dear Justin:
Thanks for your message.
When I open the gro file using VMD it shows:
atom:1950
bonds 1907
residue:43
I was thinking the problem may not come from the artifact of visualization.
Since if the gro file is fine it should be like:
atom:1950
bonds 1944
residue:6
because I have 6
Thanks, Justin. Then does it mean I cannot use the program to do simulation
at this point? any suggestion on it?
Johnny
Date: Fri, 08 May 2009 12:31:31 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Test-set
To: Discussion list for GROMACS users gmx-users@gromacs.org
Payman Pirzadeh wrote:
Thanks Diego,
But, the latest I found on downloads of gromcs webpage was 4.0.3! Is
4.0.4 somewhere else?
The homepage and wiki both have the links to 4.0.4, or you can simply change the
ftp link to point to gromacs-4.0.4 instead of 4.0.3.
-Justin
Payman
VMD guesses bonds based on distances, so it is not necessarily very smart.
I have no idea why increasing the box causes the molecules to be displayed
correctly, other than that VMD cannot deal with the periodicity correctly, as I
implied before. Causing all of the molecules to be within the
Thanks Justin.
I thought by default everything should be in downloads.
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: May 8, 2009 12:23 PM
To: Discussion list for GROMACS users
Subject: Re:
Dear Justin:
Sorry to bother so many times. After EM everything looks fine. However the
mdrun died with the error:
---
Program mdrun_d, VERSION 4.0.4
Source code file: gmx_fft_mkl.c, line: 825
Fatal error:
Error executing Intel MKL FFT.
Dear gromacs users,
I am trying to calculate the PMF along the end-to-end distance for a short
polymer (hexa-ethylene glycol), using the pull code in gromacs-4.0.4. I run
grompp with: grompp_s -v -n OH_ends.ndx -f sd.mdp -c 0.425nm.pdb -p 6EG.top,
where sd.mdp is:
title
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