Dear All,
I require a CG database of POPC for coarse grained simulation. Can anyone give
some suggestions for where to find it or how to make it by myself?
PS: the structure file of POPC was from the Biocomputing, Department of
Biological Sciences, University of Calgary.
Thank you in advance.
Jiangfeng Du, PhD Student
Cardiovascular Research Institute Maastricht
Department of Biochemistry
P.O. Box 616
Mobile: +31-681741859
FAX: +31-43-3884159
6200 MD Maastricht
The Netherlands
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Sent: Wednesday, May 11, 2011 5:16 PM
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Subject: gmx-users Digest, Vol 85, Issue 88
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Today's Topics:
1. Re: REMD: after replica exchange breakdown (SebastianWaltz)
2. Re: Surface area calculation (XAvier Periole)
3. Re: Surface area calculation (Erik Marklund)
4. reg pushing rate (vidhya sankar)
5. Re: reg pushing rate (Justin A. Lemkul)
6. about g_hbond (lina)
7. Re: about g_hbond (Justin A. Lemkul)
8. Re: about g_hbond (lina)
----------------------------------------------------------------------
Message: 1
Date: Wed, 11 May 2011 14:59:22 +0200
From: SebastianWaltz <[email protected]>
Subject: Re: [gmx-users] REMD: after replica exchange breakdown
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1
On 05/11/2011 05:20 AM, Mark Abraham wrote:
> On 05/11/2011 02:32 AM, SebastianWaltz wrote:
>> Dear GROMACS User,
>>
>> I'm running a REMD MD of 32 replicas. It worked for the first few
>> replica exchanges. After 30ps again two replicas were exchanged and I
>> received the Error:
>> x particles communicated to PME node y are more than a cell length out
>> of the domain decomposition cell of their charge group
>
> The only rationale I can see is that a velocity was scaled after
> exchange that was now large enough to lead to the normal sort of
> exploding system. Was the exploding replica going up in temperature?
> How did you equilibrate the systems?
I did a NPT equilibration for each replica which leads obviously to
different volumes and looks like to cause some problems. If I use the
same volume for each replica it works fine.
>
>> I am using NVT assembles for each replica with a exchanging interval of
>> 5ps. For each replica I use 4 processors. Constraint are only the bonds
>> to hydrogens (constraints = hbonds). Using PME for electro static.
>
> Information like GROMACS version, simulation system dimensions and
> contents would be useful. What replica temperature distribution exists?
I am using version 4.0.7. My system consists of a small peptide soluted
in ~1500 rigid CHCl3 molecules. System equilibrated with NPT and NVT
production run seems to work only if I increase the number of replicas
(32->64) meaning that I also decrease the difference of the volumes. The
temperature is exponentially distributed from 200 to 450K.
>
>> When running each replica for its own everything is working fine,
>> nothing is blowing up like one would expect after getting the above
>> Error.
>
> Good trouble-shooting :) You'd have been told to try this otherwise...
>
> Mark
>
Thanks a lot
Sebastian
------------------------------
Message: 2
Date: Wed, 11 May 2011 15:04:25 +0200
From: XAvier Periole <[email protected]>
Subject: Re: [gmx-users] Surface area calculation
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
reference:
Eisenhaber F, Lijnzaad P, Argos P, Sander C, & Scharf M (1995) J.
Comput. Chem. 16, 273-284.
On May 11, 2011, at 2:34 PM, Laura Leay wrote:
> Can anyone explain in detail the method that gromacs uses to calculate
> surface area? Which surface area is it calculating (e.g., connolley,
> accessible)?
>
> I am under the impression that the final result is given in nm^2. Is
> this correct?
>
>
> Carrying out the surface area calculation in gromacs using the OPLS
> all
> atom force field I obtain a value of 4.43 nm^2 for methane (carbon =
> opls_138, sigma = 0.35 and hydrogen = opls_140, sigma = 0.25) (CT-HC
> ideal bond length = 0.109, e=284512). The command was
>
> g_sas -f conf.gro -s topol.tpr -oa -or -tv -probe 0.2 -ndots 200 -
> nopbc
>
> and the result was taken from resarea.xvg
>
>
> I have written a program to calculate the geometric accessible surface
> area using the van der waals radius of the atoms and a probe of a
> given
> size. The surface is defined from the centre of the probe. Using the
> above values for sigma I obtain a value for methane of 1.15 nm^2
> with a
> probe diameter of 0.2 nm.
>
> Obviously the two do not match and I am not sure why.
>
> The individual atom areas for my molecule are:
> C 0.22
> H 0.24
> H 0.23
> H 0.22
> H 0.24
>
> Attached are the files used in the gromacs calculation along with the
> output and my own program. If any one has any suggestions please let
> me
> know.
> <
> area
> .xvg
> >
> <
> atomarea
> .xvg
> >
> <
> conf
> .gro
> >
> <grompp.mdp><methane.itp><resarea.xvg><topol.top><PIsurfaceOPLS.f90>--
> gmx-users mailing list [email protected]
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search
> before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [email protected].
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------------------------------
Message: 3
Date: Wed, 11 May 2011 15:48:36 +0200
From: Erik Marklund <[email protected]>
Subject: Re: [gmx-users] Surface area calculation
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Laura Leay skrev 2011-05-11 14.34:
> Can anyone explain in detail the method that gromacs uses to calculate
> surface area? Which surface area is it calculating (e.g., connolley,
> accessible)?
>
> I am under the impression that the final result is given in nm^2. Is
> this correct?
>
>
> Carrying out the surface area calculation in gromacs using the OPLS all
> atom force field I obtain a value of 4.43 nm^2 for methane (carbon =
> opls_138, sigma = 0.35 and hydrogen = opls_140, sigma = 0.25) (CT-HC
> ideal bond length = 0.109, e=284512). The command was
>
> g_sas -f conf.gro -s topol.tpr -oa -or -tv -probe 0.2 -ndots 200 -nopbc
>
> and the result was taken from resarea.xvg
>
>
> I have written a program to calculate the geometric accessible surface
> area using the van der waals radius of the atoms and a probe of a given
> size. The surface is defined from the centre of the probe. Using the
> above values for sigma I obtain a value for methane of 1.15 nm^2 with a
> probe diameter of 0.2 nm.
One difference is that g_sas -probe 0.2 uses a probe with a 0.2 nm
*radius*, while your code use a 0.2 nm diameter. That doesn't on its own
explain the difference you report, but you probably want to use the same
probe when comparing.
Erik
> Obviously the two do not match and I am not sure why.
>
> The individual atom areas for my molecule are:
> C 0.22
> H 0.24
> H 0.23
> H 0.22
> H 0.24
>
> Attached are the files used in the gromacs calculation along with the
> output and my own program. If any one has any suggestions please let me
> know.
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[email protected] http://folding.bmc.uu.se/
------------------------------
Message: 4
Date: Wed, 11 May 2011 20:15:20 +0530 (IST)
From: vidhya sankar <[email protected]>
Subject: [gmx-users] reg pushing rate
To: [email protected]
Message-ID: <[email protected]>
Content-Type: text/plain; charset="iso-8859-1"
Dear justin thank you for your mail
???????????????
to push a mobile group towards reference group? I set the pull_rate in negative
value (-0.1) as u said My question is
?when i change the pull rate to less negative value (-0.01) will push rate
increases or decreases?
?because my doubt is about sign .it means if set pull rate to high negative
value will push rate decrases or increase sign confuse me? i am expcting?
valuable reply
Thanks in Advance
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------------------------------
Message: 5
Date: Wed, 11 May 2011 10:47:59 -0400
From: "Justin A. Lemkul" <[email protected]>
Subject: Re: [gmx-users] reg pushing rate
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
vidhya sankar wrote:
> Dear justin thank you for your mail
>
> to push a mobile group towards reference group I set the pull_rate in
> negative value (-0.1) as u said My question is
> when i change the pull rate to less negative value (-0.01) will push
> rate increases or decreases?
> because my doubt is about sign .it means if set pull rate to high
> negative value will push rate decrases or increase sign confuse me i am
You can answer this question yourself with a simple test. As stated in the
manual, pull_rate is the rate of change in the position of the pulled group.
-Justin
> expcting valuable reply
> Thanks in Advance
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 6
Date: Wed, 11 May 2011 23:06:15 +0800
From: lina <[email protected]>
Subject: [gmx-users] about g_hbond
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1
Hi,
For group A, b, C.
It's no doubt can get hb forming number between A-b, b-C. b-(A or C).
But I don't know how to get the number of residues of b forming both
with A and B at the same time. namely b-A&C, not with AC group.
Thanks,
--
Best Regards,
lina
--
Best Regards,
lina
------------------------------
Message: 7
Date: Wed, 11 May 2011 11:10:57 -0400
From: "Justin A. Lemkul" <[email protected]>
Subject: Re: [gmx-users] about g_hbond
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
lina wrote:
> Hi,
>
> For group A, b, C.
>
> It's no doubt can get hb forming number between A-b, b-C. b-(A or C).
>
> But I don't know how to get the number of residues of b forming both
> with A and B at the same time. namely b-A&C, not with AC group.
>
There's no direct way to do it, but from the output files of g_hbond it can be
done. You'd need the .xpm files of A-C and B-C hydrogen bonds, and write some
script that parses the .xpm files, and whenever there is an entry of A-C in the
same frame as B-C, then you have a hydrogen bond mediated between the two.
There's lots of discussion in the list archive about water-mediated hydrogen
bonds that is likely applicable here.
Note that if you're using g_hbond in version 4.5, there is an important bug that
was fixed just yesterday:
http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html
-Justin
> Thanks,
> --
> Best Regards,
>
> lina
>
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 8
Date: Wed, 11 May 2011 23:15:23 +0800
From: lina <[email protected]>
Subject: Re: [gmx-users] about g_hbond
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1
On Wed, May 11, 2011 at 11:10 PM, Justin A. Lemkul <[email protected]> wrote:
>
>
> lina wrote:
>>
>> Hi,
>>
>> For group A, b, C.
>>
>> It's no doubt can get hb forming number between A-b, b-C. b-(A or C).
>>
>> But I don't know how to get the number of residues of b forming both
>> with A and B at the same time. namely b-A&C, not with AC group.
>>
>
> There's no direct way to do it, but from the output files of g_hbond it can
> be done. ?You'd need the .xpm files of A-C and B-C hydrogen bonds, and write
> some script that parses the .xpm files, and whenever there is an entry of
> A-C in the same frame as B-C, then you have a hydrogen bond mediated between
> the two. There's lots of discussion in the list archive about water-mediated
> hydrogen bonds that is likely applicable here.
Thanks, I will try.
>
> Note that if you're using g_hbond in version 4.5, there is an important bug
> that was fixed just yesterday:
>
> http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html
I noticed yesterday and recompiled the gromacs already. Thanks for reminding.
>
> -Justin
>
>> Thanks,
>> --
>> Best Regards,
>>
>> lina
>>
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list ? [email protected]
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to [email protected].
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
Best Regards,
lina
------------------------------
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