Sorry again, I just checked in case of TIP4P water molecules there is separate section [ constraints ] which is used if we do not use FLEXIBLE water. It does not uses SETTLE algorithm for constraining water molecules (correct me if I am wrong). Sorry for my previous mail.
Regards, Alok > 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 > > 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 > > ####################################################################### > > [ 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 > > > #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 > > ######################################################## > > I have also checked my tpr file using gmxdump and searched for SETTLE > term, but I did not observe any SETTLE term. it's means my include/define > statement are working fine and during minimization I am not using SETTLE > (please correct me if I am wrong). > > Actually in my previos mail I have pasted the link of plots > (http://i269.photobucket.com/albums/jj58/gromacs/hole-depth-atom1.jpg ) > which Chris had asked me to plot. These plots give the idea of the number > of atoms inside the hole created in the membrane and how deep these atoms > are > present after imposing the force by using modified version of mdrun > program, > which ultimetly validate my procure of mdrun_hole. I want to know my plots > look fine or not (for me it looks fine !!), but your expert comments will > give me confidence . > > Still I am at the same point, I am not able to resolve my problem :-( > > Best regards, > Alok > > > >> Alok wrote: >>> Dear Mark & Chris, >>> >>> Thanks a lot for your help. >>> >>> As both of you suggested I have increased the tolerence limit of the >>> bond (using VMD, as described by Chris), after increasing the Dynamic >>> bond lenth, the structure looks fine. >> >> How long did you have to make the O-H bonds before it looked like all of >> them were being "made"? >> >>> So it means that during >>> mimimization, position of water hydrogens are moved further to their >>> ideal limit. So what could be the possible reason for that? >> >> A broken water model, so check your .top, and the #include file with the >> water molecule topology, and pay attention to how the #ifdef mechanism >> is working in concert with anything in your "define = xxx" .mdp file >> entry. >> >>> Is this the >>> problem of my initial structure or that of mimimization parameters >>> (em.mdp)? >> >> Likely neither, except inasmuch as "define =" selects which bit of the >> topology file is being used. >> >>> what do you think about my plots from md_run data? Do they look fine or >>> that could be the root of the problem? >> >> Not sure what you mean here. >> >> 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 > _______________________________________________ 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
