[gmx-users] Re: gmx-users Digest, Vol 51, Issue 77
ANINDITA GAYEN
aninditagayen at yahoo.co.in
Tue Jul 22 06:26:50 CEST 2008
dear sir,
I am trying to do that you have said.
yours sincerely,
anindita
>
> ANINDITA GAYEN wrote:
> >
> > dear sir,
> >
> >
> >
> > I have tried to insert only one chaps in the bilayer
> and the problem arose after the minimisation when i started
> the MD. I have also tried to do a minimistaion using lincs,
> where the minimisation also failed to proceed. Can you
> please tell me is this shows that the topology is broken
> and therefore it cannot produce the actual geometry?
> >
>
> As I said before, EM is not guaranteed to remove all bad
> contacts. If your
> minimization fails with LINCS warnings, it is most likely
> due to the fact that
> you have bad steric clashes. Check the atom pairs that
> LINCS prints it; it will
> give you a clue as to where the problem lies.
>
> Other options include removing a different lipid; maybe the
> location you've
> selected is a bad one to try to disturb the bilayer.
>
> > I am also trying to take a last chance where i want to
> use the genbox command to place the chaps in the bilyer.
> But, one of my colleague have faced a problem that
> inserting one protein in a bilayer caused removal of about
> 9 lipid molecules. Will this cause a problem in the
> original bilayer property?
> >
>
> Well, what do you expect? If you need to place a large
> molecule in the bilayer,
> several lipids may have to be removed :)
>
> Sufficient equilibration (tens of ns under the appropriate
> conditions) should
> return bilayer properties to normal. Only after this time
> should you begin data
> collection. "Solvating" a single CHAPS molecule
> with your bilayer should not
> remove too many lipids, probably just one or two.
>
> > I am disturbing a number of times; but i am really
> helpless. If the minimisation with lincs fails for a
> molecule, i want to know is the topology totally incorrect?
> Then what shall i do?
> >
>
> Without seeing the topology, I have no idea. But
> that's not my job, or anyone's
> on the list. You've got to check your own work.
>
> -Justin
>
> > Can anyone please help me with the topology?
> >
> >
> > --- On Mon, 21/7/08, Justin A. Lemkul
> <jalemkul at vt.edu> wrote:
> >
> >> From: Justin A. Lemkul <jalemkul at vt.edu>
> >> Subject: Re: [gmx-users] segmentation fault with
> lincs warning
> >> To: aninditagayen at yahoo.co.in
> >> Cc: gmx-users at gromacs.org
> >> Date: Monday, 21 July, 2008, 6:26 AM
> >> ANINDITA GAYEN wrote:
> >>> Dear Sir,
> >>>
> >>> I have removed now one dmpc molecule
> from the
> >> bilayer, but the problem is the same. I have also
> tried
> >> using a downloaded pdb of chaps from pdb data
> bank, i.e.
> >> 1XU9. Why all the bonds of chaps are rotating more
> than 30
> >> degree when i have already minimised chaps to a
> reasonable
> >> potential value? Is there any problem in the
> topology?
> >> "Is the topology broken?" i have read
> that this
> >> type of problem may happen if i have problem in my
> topology
> >> file. This can be true as i have built the
> topology by hand
> >> using the toplogy file from prodrg2 server and
> oplsaa force
> >> field bonds, angles, and dihedrals.
> >> It sounds like your in vacuo minimization was
> successful,
> >> so I doubt that your
> >> topology is severely broken. There are plenty of
> pitfalls
> >> in converting a
> >> GROMOS topology from PRODRG to OPLS-AA, but I
> recall
> >> several discussions on this
> >> topic a while back, so my comments are the same as
> those
> >> I've already given.
> >>
> >>> Can you tell me what will be the rpoblem if i
> use
> >> oplsUA atom descriptions for chaps? Are OPLSUA
> atom and
> >> geometry definintion that are defined in the
> OPPLSAA itp
> >> files in the gromacs ff library totally
> uncompatible with
> >> OPLSAA?
> >> I know nothing about OPLS-UA, but my knee-jerk
> reaction to
> >> this question is
> >> "absolutely not." One cannot represent,
> say,
> >> nonbonded interactions under (for
> >> example) OPLS-UA, then apply bonded parameters
> from
> >> OPLS-AA, or vice versa, or
> >> some hybrid of both.
> >>
> >> I don't think that messing with the force
> field
> >> representation of CHAPS is going
> >> to substantially change things.
> >>
> >>> If yes, then what is the way? how can i insert
> chaps
> >> in the bilayer?
> >> Alright, so you removed one lipid from your DMPC
> bilayer,
> >> but that does not
> >> guarantee that all steric clashes are resolved.
> Are you
> >> still trying to fit 4
> >> CHAPS into the bilayer, as in your quoted message
> below, or
> >> just one molecule?
> >> The latter case would probably be the best one.
> >>
> >> Also, is this crash occurring during minimization,
> >> equilibration, or MD? Be
> >> aware also that even if you pass through
> minimization, not
> >> all unfavorable
> >> clashes will necessarily be resolved by energy
> >> minimization. EM just provides a
> >> "reasonable" starting structure for the
> >> simulation.
> >>
> >> If manual removal of a single DMPC does not allow
> for
> >> appropriate insertion of
> >> CHAPS, try another methodology, such as using
> genbox or
> >> InflatGRO to prepare the
> >> input structure.
> >>
> >> -Justin
> >>
> >>> Sincerely
> >>> yours,
> >>> Anindita Gayen
> >>>
> >>>
> >>> --- On Mon, 14/7/08, Justin A. Lemkul
> >> <jalemkul at vt.edu> wrote:
> >>>> From: Justin A. Lemkul
> <jalemkul at vt.edu>
> >>>> Subject: Re: [gmx-users] segmentation
> fault with
> >> lincs warning
> >>>> To: aninditagayen at yahoo.co.in,
> "Discussion
> >> list for GROMACS users"
> <gmx-users at gromacs.org>
> >>>> Date: Monday, 14 July, 2008, 4:40 PM
> >>>> ANINDITA GAYEN wrote:
> >>>>> Dear all,
> >>>>>
> >>>>>
> >>>>> I have an dmpc bilayer equilibrated
> for 12 ns.
> >> I have
> >>>> built a CHAPS molecule in the OPLSAA force
> field
> >> and
> >>>> inserted it in the equilibrated bilayer.
> There was
> >> no
> >>>> problem till the minimisation, but when i
> started
> >> the MD,
> >>>> the job escaped out with a lincs error
> >>>>> Initializing LINear Constraint Solver
> >>>>> number of constraints is 6572
> >>>>> average number of constraints
> coupled to one
> >>>> constraint is 3.3
> >>>>> Rel. Constraint Deviation: Max
> between
> >> atoms
> >>>> RMS
> >>>>> Before LINCS 0.817519
> 4126
> >> 4128
> >>>> 0.017115
> >>>>> After LINCS 30.145958
> 17066
> >> 17068
> >>>> 1.789056
> >>>>> Step -2, time -0.004 (ps) LINCS
> WARNING
> >>>>> relative constraint deviation after
> LINCS:
> >>>>> max 30.145958 (between atoms 17066 and
> 17068)
> >> rms
> >>>> 1.789056
> >>>>> bonds that rotated more than 30
> degrees:
> >>>>> atom 1 atom 2 angle previous,
> current,
> >> constraint
> >>>> length
> >>>>> 4128 4129 31.1 0.1571
> 0.1600
> >> 0.1530
> >>>>> 16859 16858 36.1 0.1529
> 0.1022
> >> 0.1529
> >>>>> 16858 16859 36.1 0.1529
> 0.1022
> >> 0.1529
> >>>>> 16897 16858 49.2 0.1523
> 0.1495
> >> 0.1529
> >>>>> [all the atoms and bonds in the error
> list are
> >> for
> >>>> CHAPS]
> >>>>> Do i have the problem in the topology
> file? I
> >> have
> >>>> inserted 4 chaps mole cules without
> replacing the
> >> dmpc
> >>>> molecules, i.e. 4 chaps with 128 dmpc
> molecules in
> >> the
> >>>> bilayer. Is this causing any steric
> problem?
> >>>> This is a *very* common problem, and a lot
> of
> >> potential
> >>>> solutions are in the
> >>>> list archive and wiki site. As such, I
> won't
> >> list them
> >>>> here, but you can
> >>>> certainly find them within a few minutes
> (or
> >> seconds) of
> >>>> searching.
> >>>>
> >>>> If you have a pre-equilibrated bilayer,
> and
> >> inserted
> >>>> molecules into it without
> >>>> removing any lipids, you probably have
> very severe
> >> atomic
> >>>> overlap. But as I
> >>>> said, search the archive and try the
> things you
> >> find there.
> >>>> -Justin
> >>>>
> >>>>> Please suggest a way to get out of the
> >> problem. If you
> >>>> want, i can upload my topology and mdp
> files in
> >> the next
> >>>> mail.
> >>>>> Yours truly,
> >>>>> anindita gayen
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> Unlimited freedom, unlimited
> storage.
> >> Get it
> >>>> now, on
> >>>>
> >>
> http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/
> >> _______________________________________________
> >>>>> gmx-users mailing list
> >> gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >>>>> Please search the archive at
> >>>> http://www.gromacs.org/search before
> posting!
> >>>>> 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
> >>>> --
> >>>> ========================================
> >>>>
> >>>> Justin A. Lemkul
> >>>> Graduate Research Assistant
> >>>> Department of Biochemistry
> >>>> Virginia Tech
> >>>> Blacksburg, VA
> >>>> jalemkul[at]vt.edu | (540) 231-9080
> >>>>
> >>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>>> ========================================
> >>>
> >>> Bring your gang together. Do your thing.
> Find
> >> your favourite Yahoo! group at
> >> http://in.promos.yahoo.com/groups/
> >>>
> >> --
> >> ========================================
> >>
> >> Justin A. Lemkul
> >> Graduate Research Assistant
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>
> >> ========================================
> >
> >
> > Share files, take polls, and make new friends -
> all under one roof. Go to
> http://in.promos.yahoo.com/groups/
> >
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 21 Jul 2008 13:26:05 +0000 (GMT)
> From: Claus Valka <lastexile7gr at yahoo.de>
> Subject: [gmx-users] switch potential function gromacs
> 3.3.2
> To: gmx-users at gromacs.org
> Message-ID:
> <756806.12989.qm at web26601.mail.ukl.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello,I would like to know the switching potential
> function.In the manual the potential function is Phi(r).
> Yet, this function has 1/nm**6 or 1/nm**12 units. So this
> potential should be multiplied by a factor. I supposed that
> this factor should be 6*4*epsilon*sigma**6 for the
> attractive part and 12*4*epsilon*sigma**12 for the
> dispersion part, similar to what gromacs does for the tail
> correction. Yet, in the file tables.c I have seen a swi
> function which doesn't seem to be the same as the one I
> describe. I'm not so accustomed to c++ language, so your
> help would be greatly appreciated.Thank you,Nikos
>
>
>
> __________________________________________________________
> Gesendet von Yahoo! Mail.
> Dem pfiffigeren Posteingang.
> http://de.overview.mail.yahoo.com
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> ------------------------------
>
> Message: 3
> Date: 21 Jul 2008 12:57:42 -0000
> From: "sarbani chattopadhyay"
> <sarbani_c84 at rediffmail.com>
> Subject: [gmx-users] problem with charmm
> To: "gmx_users" <gmx-users at gromacs.org>
> Message-ID:
> <20080721125742.12002.qmail at f5mail-236-230.rediffmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> hi,
> I have followed the process as told by Yuguan Mu.But
> while using the comman "pdb2gmax"
> I get the following error
> Source code file: ter_db.c, line: 85
>
> Fatal error:
> Reading Termini Database: expected 3 items of atom data in
> stead of 1 on line
> N NH3 14.0027 -0.3000
> I am not being able to fix this problem.
>
> Thanks in advance
>
> Sarbani
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> ------------------------------
>
> Message: 4
> Date: Mon, 21 Jul 2008 16:03:08 +0200 (CEST)
> From: Michael Hirtz <hirtz at uni-muenster.de>
> Subject: [gmx-users] Re: Simulation of silicon oxide
> surfaces
> To: <gmx-users at gromacs.org>
> Message-ID:
> <permail-20080721140308f0889e8400003d6d-hirtz at message-id.uni-muenster.de>
>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Diego, hello other gmx-users participants,
>
> > Hi Michael, look for the bionano tutorial at VMD site.
> It will
> > instruct you how to use TCL to build your SiO surface
> from an "unit
> > cell".
> > In a near future they will release the "inorganic
> builder plugin" that
> > will make things a LOT easier.
>
> Thanks for your reply! I haven't seen the tutorial
> before, so that gave me
> already some good background for the creation of
> substrates. But my main
> problem was not so much to get the structure (as pdb or
> similar) at all but to
> translate it to a GROMACS topography (like they used
> scripts for to generate a
> .psf in the bionano tutorial). I had found the inorganic
> builder plugin before
> (you can already download and install it to vmd), but still
> only end up with a
> .pdb that of course cannot be translated by pdb2gmx because
> it doesn't
> recognize the residues.
>
> When I look at the .psf for the SiN membrane of the
> tutorial, it seems that
> the whole substrate is introduced as one molecule. Of
> course I could build
> something similar in a GROMACS topography and define all
> necessary bonds, but
> what atomtypes should be used and what for the other
> parameters ([pairs],
> [angles] and [dihedrals]).
>
> Or would it be feasible to use single position restraint Si
> and O atoms (or
> maybe better SiO2 molecules) to build up the substrate?
> Since I only need the
> surface and it doesn't matter whether it's
> crystaline or amorphous I guess
> that would be also ok...
>
> Any comments/suggestions , anyone?
>
> Thanks,
> Michael
>
>
> > On Tue, Jul 15, 2008 at 9:37 AM, Michael Hirtz
> <hirtz at uni-muenster.de
> >> wrote:
> >> Hello,
>
> >> I want to set up a silicon oxide surface with
> varying -OH surface group
> >> for my simulation. Does anybody know a tool that
> could do that or maybe
> >> even has a topology I could start on and alter
> manually?
>
> >> Thanks for any sugesstions,
> >> Michael
> >> --
> >> http://www.defux.de
> >> _______________________________________________
> >> gmx-users mailing list gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> http://www.gromacs.org/search before posting!
> >> 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
> > --
> > Diego Enry B. Gomes
> > Laborat�rio de Modelagem e Dinamica
> Molecular
> > Universidade Federal do Rio de Janeiro - Brasil.
> --
> http://www.defux.de
>
>
> ------------------------------
>
> Message: 5
> Date: Sat, 19 Jul 2008 16:38:59 -0400
> From: Jeetain Mittal <jeetain at gmail.com>
> Subject: [gmx-users] How to modify code so that rlist >
> rcoulomb
> To: gmx-users at gromacs.org
> Message-ID:
> <33039E78-D420-4C2D-AECE-8552393604B4 at gmail.com>
> Content-Type: text/plain; charset=US-ASCII; format=flowed;
> delsp=yes
>
> Hi All,
>
> I want to simulate a system for which rvdw > rcoulomb
> and to account
> for LJ interactions correctly rlist should be greater than
> rvdw (if
> nstist != 1). For current gromacs setup rlist should be
> equal to
> rcoulomb. I searched the mailing list and there has been
> several
> discussions related to this issue such as,
>
> http://www.gromacs.org/pipermail/gmx-users/2006-July/022804.html
>
> I was wondering if anyone has implemented something already
> so that a
> system with, rlist > rvdw > rcoulomb, can be
> simulated without any
> problem. Can anyone please guide me what files / variables
> should be
> changed to implement this.
>
> Thanks,
> Jeetain
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 21 Jul 2008 03:17:58 -0700
> From: "Vitaly Chaban" <vvchaban at gmail.com>
> Subject: [gmx-users] RE: problem with using VMD to view the
> trajectory
> To: gmx-users at gromacs.org
> Message-ID:
> <7138ee40807210317v423b2414r7322fbbf3c3b2a4f at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> > I am a new user of gromacs. Recently, I have installed
> the gromacs-3.3.3 software package on my computer. After
> installation was complete, I run the example of water in
> > the online reference manual. The trajectory file is OK
> for the first time. But when I run it for the second time,
> and used vmd to look at the trajectory, I found that the
> trajetory is >disordered, the frames in the VMD main are
> equal to 2, and the output file .gro seems ok. What's
> worry with my gromacs? I don't know what to do now and
> how can I overcome >this. Could you help me?
>
> If the trajectory was OK for the first time everything is
> very well
> with your example. I would suggest just to rerun your task
> and pay
> particular attention to the type of file you submit to VMD
> (trr, xtc).
>
> What means "trajectory is disordered"? Is
> everything OK with your
> settings of PBC?
>
> --
> Vitaly V. Chaban
> School of Chemistry
> National University of Kharkiv
> Svoboda sq., 4, Kharkiv 61077, Ukraine
> email: chaban at univer.kharkov.ua
> skype: vvchaban
>
>
> ------------------------------
>
> _______________________________________________
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> Please search the archive at http://www.gromacs.org/search
> before posting!
>
> End of gmx-users Digest, Vol 51, Issue 77
> *****************************************
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