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 > <[EMAIL PROTECTED]> wrote: > > > >> From: Justin A. Lemkul <[EMAIL PROTECTED]> > >> Subject: Re: [gmx-users] segmentation fault with > lincs warning > >> To: [EMAIL PROTECTED] > >> Cc: gmx-users@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 > >> <[EMAIL PROTECTED]> wrote: > >>>> From: Justin A. Lemkul > <[EMAIL PROTECTED]> > >>>> Subject: Re: [gmx-users] segmentation > fault with > >> lincs warning > >>>> To: [EMAIL PROTECTED], > "Discussion > >> list for GROMACS users" > <gmx-users@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@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 > >>>> [EMAIL PROTECTED] > >>>>> 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 <[EMAIL PROTECTED]> > Subject: [gmx-users] switch potential function gromacs > 3.3.2 > To: gmx-users@gromacs.org > Message-ID: > <[EMAIL PROTECTED]> > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080721/17b78964/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: 21 Jul 2008 12:57:42 -0000 > From: "sarbani chattopadhyay" > <[EMAIL PROTECTED]> > Subject: [gmx-users] problem with charmm > To: "gmx_users" <gmx-users@gromacs.org> > Message-ID: > <[EMAIL PROTECTED]> > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080721/265771c4/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Mon, 21 Jul 2008 16:03:08 +0200 (CEST) > From: Michael Hirtz <[EMAIL PROTECTED]> > Subject: [gmx-users] Re: Simulation of silicon oxide > surfaces > To: <gmx-users@gromacs.org> > Message-ID: > <[EMAIL PROTECTED]> > > 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 > <[EMAIL PROTECTED] > >> 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@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 > [EMAIL PROTECTED] > >> 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 <[EMAIL PROTECTED]> > Subject: [gmx-users] How to modify code so that rlist > > rcoulomb > To: gmx-users@gromacs.org > Message-ID: > <[EMAIL PROTECTED]> > 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" <[EMAIL PROTECTED]> > Subject: [gmx-users] RE: problem with using VMD to view the > trajectory > To: gmx-users@gromacs.org > Message-ID: > <[EMAIL PROTECTED]> > 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: [EMAIL PROTECTED] > skype: vvchaban > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search > before posting! > > End of gmx-users Digest, Vol 51, Issue 77 > *****************************************
From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/ _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php