Hi Tiago,
if you swith off PME and suddenly your system scales, then the
problems are likely to result from bad MPI_Alltoall performance. Maybe
this is worth a check. If this is the case, there's a lot more information
about this in the paper Speeding up parallel GROMACS on high-
latency
Zitat von Jagan Mohan [EMAIL PROTECTED]:
Hello,
Just wanted to know if GROMACS 3.3.3 supports multi threading that is can
run four instances of mdrun in the same machine which has 4 cores...
You can run GROMACS in parallel with MPI, which is much more
efficient. Any decent distribution has
Dear all,
I have a mutation free energy calculation from D(asp) to E(glu). The
charge is not changed for the overall mutation. However, following Dr.
David Molbey's suggesion, electrostatic and VDW interaction should be
modified separately, so in the first step we need to turn off the charge
Hi all ,
I am having general doubts regaring GROMACS those are unclear me writing you
1. If a system contain equal number of atoms run these systems in GROMACS and
in AMBER why former one simulates faster than second one?
2.If do minisation while running shows that
Back Off! I just backed
with hydrogen atom of other water molecule in opposite part.
It is a normal behaviour of VMD.
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
tel.: +38-097-8259698
Hi Carsten and Justin,
I am interrupting here as I tried with the option u suggested..
I tried cut-off instead of PME as coulombtype option it is running well for
24 processor, then I tried with 60 processor , following is the result I am
getting
Result1: When tried for 50 ps of run on 24
Just wanted to know if GROMACS 3.3.3 supports multi threading that is can
run four instances of mdrun in the same machine which has 4 cores...
It seems so. If I'm wrong please anybody correct me.
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv
Vitaly Chaban wrote:
Just wanted to know if GROMACS 3.3.3 supports multi threading that is can
run four instances of mdrun in the same machine which has 4 cores...
It seems so. If I'm wrong please anybody correct me.
I just answered this same question yesterday.
--
David van der Spoel,
I am having general doubts regaring GROMACS those are unclear me writing you
1. If a system contain equal number of atoms run these systems in GROMACS
and in AMBER why former one simulates faster
than second one?
Because GROMACS is a great software.
2.If do minisation while running shows
Hi Users,
I have extended the lipid bilayer(popc) from default popc128a.pdb to
200 popc molecules with suffcient water by using genbox.
genbox -cs 128a.pdb -o out.gro -p 128a.top -box 9.2 9.2 6.9, to the
out.gro(contain 200 popc) minimisation ran fine later swtich over to *PR
with
Dear all,
I have read through the journal which David suggested. So,I am wonder how to
generate the graph that show the comparison of the stability of cylindrical and
sperical micell ( as stated as Figure 2 in that paper)
Thanks.
--- On Tue, 9/23/08, David van der Spoel [EMAIL PROTECTED]
Also is there some heme topology in the public domain that I can compare
my parametrisation with ?
at the amber parameter database, all and united atom.
http://www.pharmacy.manchester.ac.uk/bryce/amber
tim
___
gmx-users mailing list
Date: Wed, 24 Sep 2008 10:15:44 -0700
From: Chih-Ying Lin [EMAIL PROTECTED]
Subject: [gmx-users] Forming a micelles
To: [EMAIL PROTECTED]
Cc: gmx-users@gromacs.org
Message-ID:
[EMAIL PROTECTED]
Content-Type: text/plain; charset=ISO-8859-1
Hi
Would you please say more about your system?
How
Dear Lin,
I have suggestions:
Micelles should (theoretically) form above the CMC. So if you want a micelle,
the concentration should be CMC
I suggest that you find the CMC experimentally, then convert the concentration
to nm^3 (let say: mv/1000nm^3)
The number of molecules should be able to
Hi There,
I am trying to scale my system(system with 45000 atoms which is one protein
molecule in water box) to run on more number of processor
I have asked a number of related queries, but now I am getting warning
pasted below...
Fatal error:
Too many LINCS warnings (11587) - aborting to avoid
On Fri, 26 Sep 2008 13:18:24 +0530
sudheer babu [EMAIL PROTECTED] wrote:
Hi Users,
I have extended the lipid bilayer(popc) from default popc128a.pdb to
200 popc molecules with suffcient water by using genbox.
genbox -cs 128a.pdb -o out.gro -p 128a.top -box 9.2 9.2 6.9, to the
I am having general doubts regaring GROMACS those are unclear me writing you
1. If a system contain equal number of atoms run these systems in GROMACS
and in AMBER why former one simulates faster
than second one?
Because GROMACS is a great software.
Thanks for the reply, what may
Because GROMACS is a great software.
Thanks for the reply, what may be the reason GROMACS became great?
Please see the tutorial as for algorithms for non-bonded interactions
in gromacs.
2.If do minisation while running shows that
Back Off! I just backed up step53.pdb what may be the
-
Hi Users,
I have extended the lipid bilayer(popc) from default popc128a.pdb to
200 popc molecules with suffcient water by using genbox.
genbox -cs 128a.pdb -o out.gro -p 128a.top -box 9.2 9.2 6.9, to the
out.gro(contain 200 popc) minimisation ran fine later swtich over to
vivek sharma wrote:
Hi There,
I am trying to scale my system(system with 45000 atoms which is one
protein molecule in water box) to run on more number of processor
I have asked a number of related queries, but now I am getting warning
pasted below...
Fatal error:
Too many LINCS warnings
Dear Lin,
Actually I chose the concentration randomly and viewed the
pictures. I used united atom force field. Surfactant is Behenyl trimethyl
ammonium chloride and co surfactant is stearyl alcohol. I did carry out
simulations for 4 different concentrations. I did not carry out
sudheer babu wrote:
-
Hi Users,
I have extended the lipid bilayer(popc) from default
popc128a.pdb to
200 popc molecules with suffcient water by using genbox.
genbox -cs 128a.pdb -o out.gro -p 128a.top -box 9.2 9.2 6.9,
to the
On Fri, 26 Sep 2008 07:30:13 -0400
Justin A. Lemkul [EMAIL PROTECTED] wrote:
sudheer babu wrote:
-
Hi Users,
I have extended the lipid bilayer(popc) from default
popc128a.pdb to
200 popc molecules with suffcient water by using genbox.
genbox -cs
Hi all
We are sorry to bother you on perhaps a simple question, but elusive to us.
We want to run a MD simulation of three units of chitosan (B(1-4)GlcN).
We are using Gromacs ffG53A6 force field and we can not find in the
corresponding library the charges corresponding to the NH2 group in
Hi Users,
I have extended the lipid bilayer(popc) from default
popc128a.pdb to
200 popc molecules with suffcient water by using genbox.
genbox -cs 128a.pdb -o out.gro -p 128a.top -box 9.2 9.2 6.9,
to the
out.gro(contain 200 popc)
On Fri, 26 Sep 2008 18:11:15 +0530
sudheer babu [EMAIL PROTECTED] wrote:
Hi Users,
I have extended the lipid bilayer(popc) from default
popc128a.pdb to
200 popc molecules with suffcient water by using genbox.
genbox -cs 128a.pdb -o out.gro -p 128a.top
Hi Justin,
thanks for your replyI am using the GROMACS-3.3.3 version compiled with
hpmpi.
my system is having 45999 no. of atoms out of which protein is having 2627
no. of atoms.
so according to you it should go upto 45999/2621= 18 cpus approxthat is
what I am getting with my
vivek sharma wrote:
Hi Carsten and Justin,
I am interrupting here as I tried with the option u suggested..
I tried cut-off instead of PME as coulombtype option it is running well
for 24 processor, then I tried with 60 processor , following is the
result I am getting
Result1: When tried for
One other way to KNOW the surfactants formed micelle is by measuring the
surface tension (use g_energy). But g_energy gives surface*surface tension
value, so you'll need to work on that. (HINT: Surface tension value drop
drastically at CMC)
the surface tension drop is due mainly to the
Thank you very much to Xavier for your valuable suggestion
Hi Users,
I have extended the lipid bilayer(popc) from default
popc128a.pdb to
200 popc molecules with suffcient water by using genbox.
genbox -cs 128a.pdb -o out.gro -p 128a.top -box 9.2
Hi gmx-users,
My system has a 7*7*22 box and 3dc geometry for PME is applid (large vacuum
space is in the z direction. I found a crash caused by particles
communicated to PME node. Note that this problem had a fix already (
http://www.gromacs.org/component/option,com_wrapper/Itemid,90/), I was
Dear all,
I have a mutation free energy calculation from D(asp) to E(glu). The charge
is not changed for the overall mutation. However, following Dr. David
Mobley's suggetion, electrostatic and VDW interaction should be modified
separately, so in the first step we need to turn off the charge from
Hi,
We've corrected some minor things, and one major: there was a pointer
not always being updated in the PME loop (new optimization stuff we
introduced very late, so CVS versions have been fine until 20080918)
which could lead to force errors.
So, please point your browsers/ftp-clients
Hello.
Is any work being done to have GROMACS compute on GPUs?
I'm interested in performing research in this area.
Best regards,
Tiago Marques
___
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Hi
Is there TIP4P-Ew in the Gromacs 3.3.3 available?
In the top file, there is only tip4p.top and tip4p.gro.
Are they the same as TIP4P-Ew model?
Thank you
Lin
___
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