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 processo
> 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 6
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, Ph.D
> 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 sh
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 fc-100
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
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gmx-users mailing listgmx-users@gro
>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 yo
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 ob
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 lo
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
out.gr
> > 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, w
>>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
-
>
>
>
> > 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 swti
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 (11
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 simulat
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
> out.gro(
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 -c
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(co
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
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 experimentatio
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 50
> 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 pr
>
> 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 o
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
afr
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 t
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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