Dear Chris, Thanks for your help. I have also tried the "comm_grps = System" option, and did energy minimization but after that also water molecular looked like the previous case (Figure-B, in my previous post).
Regards, Alok > >Dear All, > > > >I am doing the simulation of POPE lipid + Protein, I did my system > setup using mdrun_hole program. It looks fine to me > http://i269.photobucket.com/albums/jj58/gromacs/all-three_final.gif > (Figure-A). When I was doing energy minimization (using steepest decent > and conjugant gradient algorithm), water molecules diffuse a lot, > structure looks very weird (Figure-B). But only after 1ps mdrun (NVT > ensemble) it comes back to its normal (Figure-C). But during this 1ps I > got lots of LINCE warning, all for water molecules. If I continue my > simulation (till now ~5ns production run) I do not get any > problem/warning. > > > >So I just want to know should I proceed further, or I have to come > back to my initial state and resolve this problem? > >Previously I tried different options by changing value of emtol but I > could not resolve this problem. So I proceeded. By this mail, I am > requesting expert comments from you people. Is it normal to Membrane > simulation or there is some problem in my system? Till now I have not > encountered any problems/warning. > > > >Eagerly waiting for your reply, > > > >Best regards, > >Alok Jain > > > > > >@Mark: > >Thanks a lot for your reply/comments and time. I am using TIP4P water > model, and I really could not understand why it happens, Some of the > bonds of the water molecules are broken down, and after 1ps MD they > make bonds again. Is it not very strange? I have tried to visualize in > different visualization tool but still problem was persisting. I was not > able to implement your suggestion regarding tolerance limit of the > visualization software, I used rasmol, chimera, insightII but could not > found any such option. I am still trying for that, if I could found it, > I will inform you the result after that. I am really worried about > temporary LINCE warning > >which I was getting. Is there any way to resolve this issue? > > Use VMD and set your representation to "dynamic bonds", then there is a > sliding bar that determines how to detect bonds. > Easier yet, load your initial (presumable ok) structure from figure A > into VMD, then load in the figure B structure as a new frame > in the original structure. This will draw the representation of fig B > using the topology as determined from fig A. > > > > >I am pasting the em.mdp and my top file below. > > > >@chris: Thanks for your time spent on investigating on my problem. > Thanks for creating the public album. I am sorry to say I could not get > your statement "In the worst case scenario that I can imagine, temporary > lincs warning could represent a chiral inversion that will never be > resolved and never give you any more warning messages, but would > definitely give you the wrong answer." could you please explain it a > little more (in layman term) because as I think there is no Chiral > center in water so what it > >means by chiral inversion. > > Yes, water has no chiral center. But your protein does. In the midst of > all those LINCS warnings, > you might have had one about your protein, and it is even possible that > only the first N LINCS errors > are reported (you could ask a developer about that) so possibly you have > protein angles rotating > too much during minimization steps without knowing it. > > Regarding what I mean by a chiral inversion... If forces get too high in > EM, it is entirely possible that > totally unphysical things can happen. To give an MD example, a long time > ago (using CHARMM) I was doing > simulated annealing and taking my structure up to 5000K. At that > temperature, I had some strange rearrangements > where the Ca of a Trp had a "chiral inversion" (perhaps not the correct > term?) in which my L-Trp became D-Trp. > Then upon cooling, the molecule no longer had enough energy to overcome > this L to D barrier of the improper and > note that impropers do not enforce L amino acids, they just hinder L->D > or D->L conversions. > > >I have also plotted the two plots to validate my final structure of > mdrun_hole program and uploaded these plots at > http://i269.photobucket.com/albums/jj58/gromacs/hole-depth-atom1.jpg As > I pasted below my em.mdp file. I was using FLEXIBLE TIP4P water molecules. > > > > > > > > > >em.mdp > >---------- > > > >define = -DFLEXIBLE > >constraints = none > >integrator = steep > >nsteps = 10000 > >; > >; Energy minimizing stuff > >; > >emtol = 100 > >emstep = 0.001 > >nstcgsteep = 1000 > > > >comm_mode = Linear > >nstcomm = 1 > >comm_grps = Protein_POP SOL > >ns_type = grid > >rlist = 0.9 > >coulombtype = PME > >rcoulomb = 0.9 > >vdw-type = Cut-off > >rvdw = 1.2 > >fourierspacing = 0.12 > >pme_order = 4 > >ewald_rtol = 1e-5 > >optimize_fft = yes > >Tcoupl = no > >Pcoupl = no > >gen_vel = no > > > > > > Are you sure about "comm_grps = Protein_POP SOL" ?? > Try with "comm_grps = System" > > Chris. > > > > > >top file: > >-------------- > > > >; Include forcefield parameters > >#include "/home/lysine/ffoplsaa.itp" > > > >; Include chain topologies > >#include "Protein_A.itp" > >#include "Protein_B.itp" > >#include "Protein_C.itp" > >#include "Protein_D.itp" > > > >#include "pope_opls.itp" > > > >; Include water topology > >#include "tip4p.itp" > > > > > >#ifdef POSRES_WATER > >; Position restraint for each water oxygen > >[ position_restraints ] > >; i funct fcx fcy fcz > > 1 1 10000 10000 10000 > >#endif > > > >; Include generic topology for ions > >#include "ions.itp" > > > >[ system ] > >; Name > >protein + POPE + TIP4P water molecules > > > >[ molecules ] > >; Compound #mols > >Protein_A 1 > >Protein_B 1 > >Protein_C 1 > >Protein_D 1 > >POPE 269 > >SOL 13800 > > > > > > _______________________________________________ > 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. 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