Thanks alot Justin I will do it in the way you suggested.
On Wed, 02 Jul 2008 Justin A.Lemkul wrote : > > >minnale wrote: >> >> >> >>Thanks to Justin for comment about my problem >>I will tell you clearly >>1. Initially POPC bilayer taken from Tieleman website and run the simulation >>for 5ns. >>2. Protein also has taken and simulated for 9ns actually this contain 10 >>helices among that 10 helices two helices have taken, because i want only 2 >>and generated .top file for 2 helices by using *pdb2gmx command. >>3. By using VMD orient 2 helices properly in POPC bilayer >>4. BY using genbox command these helices embedded into POPC >>5. Minimisation has done, it ran fine without error but it didnt reach >>FMAX<1000 >>6. Ran restarin with fc1000 showed the abnrmal POPC and water molecules >>stucture. >> > >All of that seems reasonable enough. There are two possibilities that come to >mind for things that might be of issue: > >1. Run the simulation longer (see my previous message). >2. I have previously helped another user determine that their system was of >insufficient size, i.e. the water layer above and below the bilayer was too >small, and they were seeing artefacts of periodic boundaries (the lipid >headgroups were "seeing" each other and were distorting accordingly. > >Assure that your system is of adequate dimensions to eliminate possibility #2, >and otherwise just run a few ns of MD and see if the lipids equilibrate. > >-Justin > >> Earlier I have run similar system with ffgmx FF with similar time 50 ps >> restrain that structure pretty fine.The idea of simulating system with short >> time is if it runs fine with short time I will give long step. >> >>Toplogy file is >> >>; Include forcefield parameters >>#include "ffoplsaa.itp" >>#include "popc.itp" >> >>[ moleculetype ] >>; Name nrexcl >>Protein 3 >> >>[ atoms ] >>; nr type resnr residue atom cgnr charge mass typeB >>chargeB massB >> 1 opls_287 1 ALA N 1 -0.3 14.0067 ; qtot -0.3 >> 2 opls_290 1 ALA H1 1 0.33 1.008 ; qtot 0.03 >> 3 opls_290 1 ALA H2 1 0.33 1.008 ; qtot 0.36 >> 4 opls_290 1 ALA H3 1 0.33 1.008 ; qtot 0.69 >> 5 opls_293B 1 ALA CA 1 0.25 12.011 ; qtot 0.94 >> 6 opls_140 1 ALA HA 1 0.06 1.008 ; qtot 1 >> 7 opls_135 1 ALA CB 2 -0.18 12.011 ; qtot 0.82 >> 8 opls_140 1 ALA HB1 2 0.06 1.008 ; qtot 0.88 >> 9 opls_140 1 ALA HB2 2 0.06 1.008 ; qtot 0.94 >> 10 opls_140 1 ALA HB3 2 0.06 1.008 ; qtot 1 >> 11 opls_235 1 ALA C 3 0.5 12.011 ; qtot 1.5 >> 12 opls_236 1 ALA O 3 -0.5 15.9994 ; qtot 1 >> 13 opls_238 2 VAL N 4 -0.5 14.0067 ; qtot 0.5 >> 14 opls_241 2 VAL H 4 0.3 1.008 ; qtot >> 0.8 >> 15 opls_224B 2 VAL CA 4 0.14 12.011 ; qtot 0.94 >> 16 opls_140 2 VAL HA 4 0.06 1.008 ; qtot 1 >> . >> . >> . >> . >> . >> . >> . >> . >> . >> . >>; Include Position restrain protein >>#ifdef POSRES_PROTEIN >>#include "posre.itp" >>#endif >> >>;Include Position restrain lipid >>#ifdef POSRES_LIPID >>#include "lip_posre.itp" >>#endif >> >>; Include water topology >>#include "spc.itp" >> >>#ifdef POSRES_WATER >>; Position restraint for each water oxygen >>[ position_restraints ] >>; i funct fcx fcy fcz >> 1 1 1000 1000 1000 >>#endif >> >>; Include generic topology for ions >>#include "ions.itp" >> >>[ system ] >>; Name >>GROtesk MACabre and Sinister in water >> >>[ molecules ] >>; Compound #mols >>Protein 1 >>POPC 94 >>SOL 2434 >>CL- 3 >> >>Any comments wiill be appreciated. >> >>Thanks in advance >> >> >> >> >> >>On Tue, 01 Jul 2008 Justin A.Lemkul wrote : >> > >> > >> >minnale wrote: >> >> >> >> >> >> So I dont boughter about those sentences because I confirmed in list >> >> archives that I can proceed further steps and moreover em.gro file is >> >> fine, so I went for restrain, here I am getting abnormal POPC structure >> >>means POPC tails are tilting, water molecules structure also disturbed. >> >> >> >>Could you please tell me where iam doing mistake? >> >> >> > >> >Not really. You haven't told us much. What parameters are you using (for >> >the protein and the lipids)? How did you insert your protein? >> > >> >Also realize that 50 ps is *extremely* short in the realm of membrane >> >protein MD. Even after several hundred picoseconds things may look a bit >> >strange. Prevailing wisdom is that between 25-30 ns of MD are required for >> >the lipids to reach equilibrium (although they should look reasonable after >> >just a few ns, but parameters like area per headgroup may not level off for >> >a while). >> > >> >-Justin >> > >> >>my pr.mdp filetitle = protein in popc restrained >> >>define = -DPOSRES_protein >> >>constraints = all-bonds >> >>integrator = md >> >>dt = 0.002 ; ps ! >> >>nsteps = 10000 ; total 50 ps. >> >>nstcomm = 1 >> >>nstxout = 50 >> >>nstvout = 1000 >> >>nstfout = 0 >> >>nstlog = 10 >> >>nstenergy = 10 >> >>nstlist = 10 >> >>ns_type = grid >> >>rlist = 0.9 >> >>coulombtype = PME >> >>rcoulomb = 0.9 >> >>rvdw = 1.4 >> >>pbc = xyz >> >>; Berendsen temperature coupling is on in three groups >> >>Tcoupl = Berendsen >> >>tc-grps = POPC Protein SOL_CL- >> >>tau_t = 0.1 0.1 0.1 >> >>ref_t = 310 310 310 >> >>; Anisotropic pressure coupling is now on >> >>Pcoupl = berendsen >> >>pcoupltype = anisotropic >> >>tau_p = 1.0 1.0 1.0 0 0 0 >> >>compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 >> >>ref_p = 1.0 1.0 1.0 0 0 0 >> >>; Energy monitoring >> >>energygrps = POPC Protein SOL_CL- >> >>; Generate velocites is on at 300 K. >> >>gen_vel = yes >> >>gen_temp = 310.0 >> >>gen_seed = 173529 >> >> >> >>Thanks in advance. >> >> >> >> >>------------------------------------------------------------------------ >> >> >> >>_______________________________________________ >> >>gmx-users mailing list [email protected] >> >>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 >> > >> >======================================== >> > >> >> >> >>------------------------------------------------------------------------ >> >>_______________________________________________ >>gmx-users mailing list [email protected] >>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 > >======================================== >
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