Thank you Dr. Dallas. Yes I think the issue is that the starting conformation is linear, as I want to study its folding properties. I tried the same with helical starting conformation, and got around 110000 water molecules, which is still ok. I am trying to find a way to simulate a 89 aa peptide in linear starting conformation such that the simulation is practically feasible.
On Tue, May 14, 2013 at 10:45 AM, Dallas Warren <[email protected]>wrote: > >From the box volume printed in the script output it appears you have a > box that is approximately a 28nm cube. And that size box requires a > significant number of water molecules to fill up, so that number you have > in there (~770,000) seems about correct. > > If you want to have less water molecules, then you will need to make the > simulation cell smaller. Whether that is possible or not depends on what > you are looking to observe, how big the molecule you are solvating is etc. > > Catch ya, > > Dr. Dallas Warren > Drug Discovery Biology > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > [email protected] > +61 3 9903 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > > -----Original Message----- > > From: [email protected] [mailto:gmx-users- > > [email protected]] On Behalf Of Nikunj Maheshwari > > Sent: Tuesday, 14 May 2013 3:04 PM > > To: Discussion list for GROMACS users > > Subject: [gmx-users] Large number of solvent molecules > > > > Dear all, > > > > I am trying to see the folding of a 89 aa peptide. So I am setting up > > the > > system from linear conformation. > > I gave the following commands to build the box and add the solvent > > molecules. > > > > editconf -f output.gro -c -d 1.0 -bt dodecahedron -o outbox.gro > > > > genbox -cp outbox.gro -cs spc216.gro -p topol.top -o outh2o.gro > > > > Reading solute configuration > > Go Rough, Oppose Many Angry Chinese Serial killers > > Containing 1440 atoms in 89 residues > > Initialising van der waals distances... > > > > WARNING: Masses and atomic (Van der Waals) radii will be guessed > > based on residue and atom names, since they could not be > > definitively assigned from the information in your input > > files. These guessed numbers might deviate from the mass > > and radius of the atom type. Please check the output > > files if necessary. > > > > Reading solvent configuration > > "216H2O,WATJP01,SPC216,SPC- > > MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984" > > solvent configuration contains 648 atoms in 216 residues > > > > Initialising van der waals distances... > > Will generate new solvent configuration of 18x18x13 boxes > > Generating configuration > > Sorting configuration > > Found 1 molecule type: > > SOL ( 3 atoms): 909792 residues > > Calculating Overlap... > > box_margin = 0.315 > > Removed 324522 atoms that were outside the box > > Neighborsearching with a cut-off of 0.48 > > Table routines are used for coulomb: FALSE > > Table routines are used for vdw: FALSE > > Cut-off's: NS: 0.48 Coulomb: 0.48 LJ: 0.48 > > System total charge: 0.000 > > Grid: 73 x 73 x 51 cells > > Successfully made neighbourlist > > nri = 3007232, nrj = 82473964 > > Checking Protein-Solvent overlap: tested 36005 pairs, removed 1653 > > atoms. > > Checking Solvent-Solvent overlap: tested 7152003 pairs, removed 73182 > > atoms. > > Added 776673 molecules > > Generated solvent containing 2330019 atoms in 776673 residues > > Writing generated configuration to outh2o.gro > > > > Back Off! I just backed up outh2o.gro to ./#outh2o.gro.1# > > Go Rough, Oppose Many Angry Chinese Serial killers > > > > Output configuration contains 2331459 atoms in 776762 residues > > Volume : 23276.3 (nm^3) > > Density : 1001.32 (g/l) > > Number of SOL molecules: 776673 > > > > Processing topology > > Adding line for 776673 solvent molecules to topology file (topol.top) > > > > > > Later on, I used -d 0.5. I still get around 710000 water molecules in > > the > > system. > > > > Then, I used g_mindist for both cases (d 1.0 and d 0.5). It is around 9 > > A > > and 8.4 A respectively. > > > > I need to know if I have done something wrong in setting up the system. > > Is > > there any way to get feasible number of solvent molecules? > > > > Thanks.... > > Nikunj > > -- > > gmx-users mailing list [email protected] > > 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 [email protected]. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
