Dear Mark, & Chris, Thanks for your useful suggestions.
Yes Mark define = -DFLEXIBLE is the only difference in both the cases. Actually in my previous post I have pasted only small section of tip4p.itp file,(sorry if it created unnecessary confusions/doubt). This time I am pasting full tip4p.itp file. As you expected, it has more #ifdef statements. I have not modified this file. this is the original file and comes with the gromacs-3.2.1 distribution. I have cross checked it with the clean distribution. I have also compared the order of TIP4P atoms in my structure file (gro/pdb) and the same is pasted below as TIP4P.itp file. Order is same in both the files. TIP4P.itp File ################## ; ; Note the strange order of atoms to make it faster in gromacs. ; [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; id at type res nr residu name at name cg nr charge #ifdef _FF_OPLS 1 opls_115 1 SOL MW1 1 -1.04 2 opls_114 1 SOL HW2 1 0.52 3 opls_114 1 SOL HW3 1 0.52 4 opls_113 1 SOL OW4 1 0 #else #ifdef _FF_GROMOS96 1 IW 1 SOL MW1 1 -1.04 0.0 2 H 1 SOL HW2 1 0.52 1.008 3 H 1 SOL HW3 1 0.52 1.008 4 OWT4 1 SOL OW4 1 0 15.9994 #else 1 IW 1 SOL MW1 1 -1.04 2 HW 1 SOL HW2 1 0.52 3 HW 1 SOL HW3 1 0.52 4 OWT4 1 SOL OW4 1 0 #endif #endif #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 4 2 1 0.09572 502416.0 0.09572 502416.0 4 3 1 0.09572 502416.0 0.09572 502416.0 [ angles ] ; i j k funct angle force.c. 2 4 3 1 104.52 628.02 104.52 628.02 #else [ constraints ] ; i funct doh dhh 4 2 1 0.09572 4 3 1 0.09572 3 2 1 0.15139 [ exclusions ] 1 2 3 4 2 1 3 4 3 1 2 4 4 1 2 3 #endif ; The position of the dummy is computed as follows: ; ; O ; ; D ; ; H H ; ; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ] ; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ] ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1) [ dummies3 ] ; Dummy from funct a b 1 4 2 3 1 0.128012065 0.128012065 Best regards, Alok Jain > [EMAIL PROTECTED] wrote: >> Dear Mark, >> >> Thanks a lot for your reply. >> >> Default was 1.6 angstrom and when I change gradually till 2.5 angstrom >> then >> structure looks similar to original structure. >> >> I have again checked in my top and mdp files for include statement. >> >> I have define = -DFLEXIBLE in my mdp file > > Good, that's a material difference that you can use to find where the > problem occurs, since this is only present in your EM, not your > simulation. > >> in my top file I have included the tip4p.itp file as follow. >> #include "tip4p.itp" >> >> which must open the tip4p.itp file comes with the distribution which has >> following section > > This bears little resemblance to a tip4p.itp file I have in a 3.3.1 > distribution I had lying around. > >> ####################################################################### >> >> [ moleculetype ] >> ; molname nrexcl >> SOL 2 >> >> [ atoms ] >> ; id at type res nr residu name at name cg nr charge >> #ifdef _FF_OPLS >> 1 opls_115 1 SOL MW1 1 -1.04 >> 2 opls_114 1 SOL HW2 1 0.52 >> 3 opls_114 1 SOL HW3 1 0.52 >> 4 opls_113 1 SOL OW4 1 0 > > There should be more #ifdef regions here for various force fields, and > the atom order is changed from my file. I think this might introduce a > problem if the atom order in your water molecules in your structure file > differs, but I'm guessing here. > >> #ifdef FLEXIBLE >> [ bonds ] >> ; i j funct length force.c. >> 4 2 1 0.09572 502416.0 0.09572 502416.0 >> 4 3 1 0.09572 502416.0 0.09572 502416.0 > > These are well-formed, given the above, but if you've given the whole > tip4p.itp file then there are missing #endifs such that it isn't working > properly. > >> [ angles ] >> ; i j k funct angle force.c. >> 2 4 3 1 104.52 628.02 104.52 628.02 > > Likewise. > >> ######################################################## > > I'd start by finding out where you got this tip4p.itp file, and probably > hitting someone over the back of the head for messing around > unnecessarily with it. Or, if it was necessary to change it for some > purpose, hitting them over the back of the head for letting you have a > copy of this file, not a normal one :-) > > Then, I'd get a clean distribution, start from the beginning, check the > tip4p.itp file and see how it goes. > > Mark > _______________________________________________ > 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 > _______________________________________________ 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
