Mark,
due to hight density the volume of my system have been slightly increased and during NPT phase I've obtained error Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. I'm using 0.9 for electrostatic and 1.4 for vdw cutofs and the dimensions of my box was 6.5 3 3 on the initial step and 6.6 3 3.3 before crush :) I want prevent such expansion of my system by increasing of pressure and/ or compressibility but I have not found exact sollution yet. James 2012/2/14 Mark Abraham <mark.abra...@anu.edu.au> > On 14/02/2012 11:01 PM, James Starlight wrote: > > This also was solved by the some extra minimisation steps. > > > I've forced with another problem :D > > During npt equilibration my system have slightly expanded so my desired > volume and density were perturbed. > > I've noticed the below options in npt wich could help me > > ref_p = 1 1 > compressibility = 4.5e-5 > > i'm using this compressibility value because I'm modelling the > lipid-like environment so I think that I must increase pressure. Could you > remind me the dependence of pressure from density and volume for liquids ? > :) > > > Your forcefield, simulation cell contents and .mdp settings will determine > the equilibrium density. Whether you need to do anything depends on whether > you've made a statistically significant post-equilibration measurement of > your average density. Haphazardly increasing the reference pressure for the > coupling will reduce the volume, but now you are simulating at that > pressure. See http://www.gromacs.org/Documentation/Terminology/Pressurefor > background info. > > Mark > > > > James > > > > 2012/2/14 James Starlight <jmsstarli...@gmail.com> > >> It seems that I've fixed that problem by reduce vdv radii for Cl during >> defining of my box >> >> Eventually I've obtained box with the desired density >> than I've delete vdvradii.dat for my wor dir >> >> by when I've launched equilibration I've oibtained >> >> Fatal error: >> Too many LINCS warnings (1598) >> If you know what you are doing you can adjust the lincs warning threshold >> in your mdp file >> >> I've never seen this before >> >> I'm using 1.o cutoff for pme and 1.4 for vdv >> my LINKS parameters are >> >> ; Bond parameters >> continuation = no ; first dynamics run >> constraint_algorithm = lincs ; holonomic constraints >> constraints = all-bonds ; all bonds (even heavy atom-H bonds) >> constrained >> lincs_iter = 1 ; accuracy of LINCS >> lincs_order = 4 ; also related to accuracy >> >> How I could solve it? >> >> >> James >> >> >> 2012/2/14 James Starlight <jmsstarli...@gmail.com> >> >>> Mark, >>> >>> I've checked only density value >>> >>> with 500 molecules Ccl4 I have density that is twisely less that I need >>> ( in accordance to the literature ). Also I've checked my box visually and >>> found that the box is not properly tightly packed so I dont know why genbox >>> didnt add some extra mollecules :( >>> >>> In other words I wounder to know if there is any way to add some extra >>> molecules to the pre defined box to make my system more tighly packed ( to >>> short distance between existing molecules and place new ones in the new >>> space ) ? >>> >>> James >>> >>> >>> 2012/2/14 Mark Abraham <mark.abra...@anu.edu.au> >>> >>>> On 14/02/2012 4:57 PM, James Starlight wrote: >>>> >>>>> Justin, >>>>> >>>>> Firstly I've created the box of desired size with only 500 molecules ( >>>>> I need 1000) >>>>> >>>>> Than I've tried to add extra 200 molecules by means of Genbox >>>>> >>>>> genbox -cp super_box.gro -ci Ccl4.gro -nmol 200 -o new_solv.gro >>>>> >>>>> but no molecules have been added >>>>> Added 0 molecules (out of 200 requested) of Cl4 >>>>> >>>> >>>> ... then there are no gaps large enough to insert your molecules. >>>> Either make gaps, or check out genbox -h for advice on defining the radii. >>>> >>>> >>>> >>>>> also I've tried >>>>> >>>>> genbox -cp super_box.gro -cp Ccl4.gro -nmol 200 -o new_solv.gro >>>>> >>>> >>>> Two -cp options is not what you want, and -nmol probably only works >>>> with -ci. >>>> >>>> >>>> >>>>> but system were crashed with message >>>>> >>>>> Reading solute configuration >>>>> God Rules Over Mankind, Animals, Cosmos and Such >>>>> Containing 2500 atoms in 500 residues >>>>> Initialising van der waals distances... >>>>> >>>>> WARNING: masses and atomic (Van der Waals) radii will be determined >>>>> based on residue and atom names. These numbers can deviate >>>>> from the correct mass and radius of the atom type. >>>>> >>>>> Reading solvent configuration >>>>> "God Rules Over Mankind, Animals, Cosmos and Such" >>>>> solvent configuration contains 5 atoms in 1 residues >>>>> >>>>> >>>>> Is there any ways to add extra mollecules to the pre defined box ? >>>>> >>>> >>>> Yes - but there has to be room for them. >>>> >>>> Mark >>>> >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> Please don't post (un)subscribe requests to the list. Use the www >>>> interface or send it to gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>> >>> >> > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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