[gmx-users] POPC simulation
Jim Fonseca
jf163201 at ohiou.edu
Thu May 25 00:27:47 CEST 2006
You said you appended the info in lipid.itp into ffgmxbon.itp and
ffgmxnb.itp. Did you copy the different values (atomtypes,
nonbdon_params) into their respective positions or did you just
concatenate the files?
Also, I looked at my ffgmxbon.itp and I don't believe I edited it
from the standard gromacs version. I think I only made two changes
to the standard gromacs files in the /top/directory. One was to
replace ffgmx.atp (which you said you did) with contribution version.
The other was to copy the lipid.itp information into ffgmx.itp.
Also could you post your whole topol.top?
On May 24, 2006, at 4:11 PM, Arindam Ganguly wrote:
> 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, gmx-users-request at gromacs.org <gmx-users-
> request at gromacs.org> 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 <Mark.Abraham at anu.edu.au>
>> Subject: [gmx-users] CHARMM force field in GROMACS
>> To: Gromacs Users <gmx-users at gromacs.org>
>> Message-ID: <44745E06.9020901 at anu.edu.au>
>> 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" <karamyog.singh at gmail.com>
>> Subject: Re: [gmx-users] Simulating crystalls
>> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>> Message-ID:
>> <f8a1ae850605240806v1135211eoc551ba4ed28cb486 at mail.gmail.com>
>> 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 <Mark.Abraham at anu.edu.au> 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 gmx-users at gromacs.org
>> > http://www.gromacs.org/mailman/listinfo/gmx-users
>> > Please don't post (un)subscribe requests to the list. Use the
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>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >
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>>
>> ------------------------------
>>
>> Message: 3
>> Date: Wed, 24 May 2006 17:13:09 +0200
>> From: "Alessandro Mattozzi" <Alessandro at polymer.kth.se>
>> Subject: [gmx-users] Position restrain
>> To: <gmx-users at gromacs.org>
>> Message-ID:
>> <B190919A5A0D684E9AC628C8574166521CFFD3 at kvaser2.mimer.kth.se>
>> 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 <x.periole at rug.nl>
>> Subject: Re: [gmx-users] Position restrain
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <447479E7.1090901 at rug.nl>
>> 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: x.periole at rug.nl
>> web-page: http://md.chem.rug.nl/~periole
>> ----------------------------------
>>
>>
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Wed, 24 May 2006 19:55:20 +0400
>> From: Oleg Stroganov <stroganov at belozersky.msu.ru>
>> Subject: [gmx-users] Stange results of bonds fep
>> To: gmx-users at gromacs.org
>> Message-ID: <1156912725.20060524195520 at belozersky.msu.ru>
>> 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" <arindamganguly at gmail.com>
>> Subject: [gmx-users] POPC simulation
>> To: gmx-users at gromacs.org
>> Message-ID:
>> <fb688b860605241002j1f0682e1rf9c18b87e190a22d at mail.gmail.com>
>> 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 <leafyoung81-group at yahoo.com>
>> Subject: [gmx-users] Re: Simulating crystalls
>> To: gmx-users at gromacs.org
>> Message-ID: <loom.20060524T175131-656 at post.gmane.org>
>> Content-Type: text/plain; charset=us-ascii
>>
>> Mark Abraham <Mark.Abraham at ...> 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 <jf163201 at ohiou.edu>
>> Subject: Re: [gmx-users] POPC simulation
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <3A81B630-1453-43AA-8B8F-0CC866F5D8CC at ohiou.edu>
>> 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 gmx-users at gromacs.org
>> > 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 gmx-users-request at gromacs.org.
>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>> ------------------------------
>>
>> _______________________________________________
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>>
>> End of gmx-users Digest, Vol 25, Issue 93
>> *****************************************
>>
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