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 ? :) 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<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<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<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