Hi Jim
i tried what you suggested and that is
1. yes the popc.gro file had all POPC residues truncated to POP, so i
went ahead and changed the entries of popc.itp to pop, and i also did
the same for topol.top file where inthe end you have to mention the
number ofmolecules.
but still the problem remains and it say again "LC3" atomtypes not found.
so me still stuck. plz help. thanks.
arindam ganguly
On 5/24/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
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Today's Topics:
1. CHARMM force field in GROMACS (Mark Abraham)
2. Re: Simulating crystalls (karamyog singh)
3. Position restrain (Alessandro Mattozzi)
4. Re: Position restrain (Xavier Periole)
5. Stange results of bonds fep (Oleg Stroganov)
6. POPC simulation (Arindam Ganguly)
7. Re: Simulating crystalls (Yang Ye)
8. Re: POPC simulation (Jim Fonseca)
----------------------------------------------------------------------
Message: 1
Date: Wed, 24 May 2006 23:22:14 +1000
From: Mark Abraham <[EMAIL PROTECTED]>
Subject: [gmx-users] CHARMM force field in GROMACS
To: Gromacs Users <[email protected]>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi,
I am making available under GPL two perl scripts, one of which converts
a CHARMM27 .prm file into the necessary .itp files for pdb2gmx to use to
produce .top files, and another that massages that .top file into
something that will produce a .tpr file that will get CHARMM energy &
force evaluations. I have submitted it for inclusion on the GROMACS web
page and hopefully it will appear there shortly.
In the meantime, because I know there is interest in these scripts, if
you want an email copy of the distribution that I hope will go up on the
GROMACS web page, please email me off-list.
Regards,
Mark Abraham
------------------------------
Message: 2
Date: Wed, 24 May 2006 17:06:52 +0200
From: "karamyog singh" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Simulating crystalls
To: "Discussion list for GROMACS users" <[email protected]>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
I am trying to simulate a crystal too. I have a box size of .65 nm and there
are 8 bcc crystals in the system. Lattice parameter = 0.287 nm.
I get a segmentation fault after mdrun -v. Is an atom with co-ordinates
0.574 0.000 0.000 equivalent to 0.287 0.000 0.000 in such a system? What I
am trying to ask is, does GROMACS consider these as 2 different atoms placed
at the respective positions or do the 2 atoms overlap?
What could be the reason for the segmentation fault? Is it because the atoms
are too close to each other?
-
Karamyog.
On 5/23/06, Mark Abraham <[EMAIL PROTECTED]> wrote:
>
> David van der Spoel wrote:
> > Gale, Ella wrote:
> >
> >>
> >> Thanks for the advice, but my force-field has no charges and hence no
> >> coulomb potential, so I want the atoms to interact with itself via the
> >> Van der Waals functions. I'm using 3.2.1 at the moment and there is no
> >> option to use any of the Ewald summation techniques. Is this something
> >> that has been added in the most recent version?
> >
> > Ewald variant are only for Coulomb so far. You can use a normal cutoff
> > or a shifted cutoff.
>
> One or two of the early PME papers describe implementation details for
> LJ PME, but I am not immediately aware of a modern MD code that
> implements it. If you want it, shop around.
>
> Mark
> _______________________________________________
> gmx-users mailing list [email protected]
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
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Message: 3
Date: Wed, 24 May 2006 17:13:09 +0200
From: "Alessandro Mattozzi" <[EMAIL PROTECTED]>
Subject: [gmx-users] Position restrain
To: <[email protected]>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Hi
How should my posres.itp look like? Is there any template available?
Thank
Regards
Alessandro Mattozzi
M.Phil., Ph.D. student
Dept. of Fibre and Polymer Technology
Royal Institute of Technology
Stockholm, Sweden
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------------------------------
Message: 4
Date: Wed, 24 May 2006 17:21:11 +0200
From: Xavier Periole <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Position restrain
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=us-ascii; format=flowed
Alessandro Mattozzi wrote:
> Hi
> How should my posres.itp look like? Is there any template available?
> Thank
> Regards
>
genpr does generate position rstrains ...
--
----------------------------------
Xavier Periole - Ph.D.
Dept. of Biophysical Chemistry / MD Group
Univ. of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands
Tel: +31-503634329
Fax: +31-503634398
email: [EMAIL PROTECTED]
web-page: http://md.chem.rug.nl/~periole
----------------------------------
------------------------------
Message: 5
Date: Wed, 24 May 2006 19:55:20 +0400
From: Oleg Stroganov <[EMAIL PROTECTED]>
Subject: [gmx-users] Stange results of bonds fep
To: [email protected]
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=us-ascii
Dear all,
I'm trying to calculate dG of transition between alpha and pi
conformation in some part of my protein. I indended to use fep and
perform this conversion in three steps: first, I want to fix alpha
conformation gradually by indroducing bonded interactions between
i'th H, i+4 and i+5'th O, then change equlibrium distances of these
bonds from alpha- to pi- state and finally remove bonds.
Surpringly, my system behaved in quite unusual way : at the first
steps of simulation (I used slow growth fep) distances between
perturbed atoms increased dramatically from 0.2nm and 0.45nm
(which are equlibrium distances for alpha-state) to 0.7 nm and
even further. No increase, however, was mentioned when fep was turned
off.
I succeeded to reproduce this strange behaviour on smaller systems by
cutting the piece of the protein, converting it into poly-cly chain
and performing the same simulation with following parameters f A and B
state:
[ atoms ]
...
16 opls_236 2 GLY O 4 -0.5 15.9994 ; qtot
1
...
23 opls_236 3 GLY O 6 -0.5 15.9994 ; qtot
1
...
46 opls_241 7 GLY H 13 0.3 1.008 ; qtot
0.8
...
[ bonds ]
...
23 46 1 0.20 0 0.20 1000
16 46 1 0.45 0 0.45 1000
At the and of 50 ps bd simulation from lambda=0 to lambda=1 distance
between 23 and 46 atoms increased from 0.196 to 0.448 nm, and distance
between 16 and 46 atoms increased form 0.496 to 0.73 nm.
Can anyone suggest, why results of fep are so strange? Is this a bug
or I'm missing something?
P.S. I run all these tests with gromacs 3.3.1
------------------------------
Message: 6
Date: Wed, 24 May 2006 12:02:43 -0500
From: "Arindam Ganguly" <[EMAIL PROTECTED]>
Subject: [gmx-users] POPC simulation
To: [email protected]
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Steffen,
thanks for the reply. this is what i have done. my topol.top looks
like this now
#inlcude ffgmx.itp
inlcude popc.itp.
as per your last reply i have copied the contents of lipid.itp to
ffgmxbon.itp and ffgmxnb.itp without removing the contents of the
respective file. basically just appended the files with the contents
of the lipid.itp .
now when i run grommp -v - -f em.mdp ,
it still says atom type "LC3" not found,.
i can't understand why this mistake in fact taking place. popc.itp
file the first 3 lines after [atom]
in fact mentions LC3. so where is the mistake. plx help. thanks.
arindam
------------------------------
Message: 7
Date: Wed, 24 May 2006 15:53:07 +0000 (UTC)
From: Yang Ye <[EMAIL PROTECTED]>
Subject: [gmx-users] Re: Simulating crystalls
To: [email protected]
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=us-ascii
Mark Abraham <[EMAIL PROTECTED]> writes:
>
> David van der Spoel wrote:
> > Gale, Ella wrote:
> >
> >>
> >> Thanks for the advice, but my force-field has no charges and hence no
> >> coulomb potential, so I want the atoms to interact with itself via the
> >> Van der Waals functions. I'm using 3.2.1 at the moment and there is no
> >> option to use any of the Ewald summation techniques. Is this something
> >> that has been added in the most recent version?
> >
> > Ewald variant are only for Coulomb so far. You can use a normal cutoff
> > or a shifted cutoff.
>
> One or two of the early PME papers describe implementation details for
> LJ PME, but I am not immediately aware of a modern MD code that
> implements it. If you want it, shop around.
>
> Mark
>
I got to read a note by Cheatham on PME for LJ VDW.
Look for question "Is there a PME algorithm also for the VDW interactions?"
in
http://amber.scripps.edu/Questions/ewald.html
Yang Ye
------------------------------
Message: 8
Date: Wed, 24 May 2006 14:39:10 -0400
From: Jim Fonseca <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] POPC simulation
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
Arindam,
I fixed this problem a while ago and it was pretty difficult to
figure out. I tinkered with so many things, once I got it to work I
didn't even know what steps I took to fix it!
Here's something to try: GROMACS doesn't like the fact popc.itp has
a four-character residue name (since protein residues are just three
characters). If you look at your .gro file, you'll probably see that
somewhere along the line, the POPC got truncated to POP. Try
changing all instances of 'POPC' to 'POP' in your setup--this should
probably just be in popc.itp (lots of occurrences) and topol.top(one
occurrence where you list the number of POP molecules.
Please let me know if that works.
Jim
On May 24, 2006, at 1:02 PM, Arindam Ganguly wrote:
> Hi Steffen,
> thanks for the reply. this is what i have done. my topol.top looks
> like this now
> #inlcude ffgmx.itp
> inlcude popc.itp.
>
> as per your last reply i have copied the contents of lipid.itp to
> ffgmxbon.itp and ffgmxnb.itp without removing the contents of the
> respective file. basically just appended the files with the contents
> of the lipid.itp .
>
> now when i run grommp -v - -f em.mdp ,
> it still says atom type "LC3" not found,.
>
> i can't understand why this mistake in fact taking place. popc.itp
> file the first 3 lines after [atom]
> in fact mentions LC3. so where is the mistake. plx help. thanks.
> arindam
> _______________________________________________
> gmx-users mailing list [email protected]
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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/mailing_lists/users.php
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