[gmx-users] NVT equalibriation
Hello i have been performed NVT equalibriation for three time each time i got a note . Is this not is harmful? NOTE: Detected invalid cycle counts, probably because threads moved between CPU cores that do not have synchronized cycle counters. Will not print the cycle accounting. Core t (s) Wall t (s)(%) Time:76515.00819128.752 400.0 5h18:48 (ns/day)(hour/ns) Performance:0.452 53.134 GROMACS reminds you: "If You Touch Me, You'll Get Shocked" (Beastie Boys) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Hi During simulation of protein after giving grompp ions command i got a note what should i do. NOTE 3 [file ions2.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] NVT problem
hello i am trying to simulating a protein after run NVT md run i got a not what i will do. is this not show any problem. Back Off! I just backed up nvt.edr to ./#nvt.edr.1# starting mdrun 'TUBULIN ALPHA CHAIN' 5 steps,100.0 ps. step 49900, remaining wall clock time:35 s Writing final coordinates. step 5, remaining wall clock time: 0 s NOTE: Detected invalid cycle counts, probably because threads moved between CPU cores that do not have synchronized cycle counters. Will not print the cycle accounting. Core t (s) Wall t (s)(%) Time:70001.93417500.483 400.0 4h51:40 (ns/day)(hour/ns) Performance:0.494 48.611 GROMACS reminds you: "Uh-oh Right Again" (Laurie Anderson) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] problem
hello i am simulating tubulin heterodimer . after giving command for solvent adding i got a warning on screen what should i do. Initialising inter-atomic 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. NOTE: From version 5.0 gmx solvate uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. PLEASE READ AND CITE THE FOLLOWING REFERENCE A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 --- Thank You --- Generating solvent configuration Will generate new solvent configuration of 7x7x7 boxes Solvent box contains 202791 atoms in 67597 residues Removed 17799 solvent atoms due to solvent-solvent overlap Removed 10800 solvent atoms due to solute-solvent overlap Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 58064 residues Generated solvent containing 174192 atoms in 58064 residues Writing generated configuration to 1jff_solv.gro Output configuration contains 182636 atoms in 58902 residues Volume : 1882.42 (nm^3) Density: 1006.94 (g/l) Number of solvent molecules: 58064 Processing topology Adding line for 58064 solvent molecules with resname (SOL) to topology file (topol.top) Back Off! I just backed up topol.top to ./#topol.top.1# GROMACS reminds you: "She's Not Bad, She's Just Genetically Mean" (Captain Beefheart) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] (no subject)
thanks for reply On Fri, Sep 14, 2018 at 5:09 PM Justin Lemkul wrote: > > > On 9/14/18 6:48 AM, AKANXA TIWARI wrote: > > i am getting a warning after converting pdb2gmx and then applying force > > field what i will do. please help me.i get this on screen. > > WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was > > mapped > > to an entry in the topology database, but the atom H used in > > an interaction of type angle in that entry is not found in the > > input file. Perhaps your atom and/or residue naming needs to be > > fixed. > > > > > > > > WARNING: WARNING: Residue 374 named PHE of a molecule in the input file > was > > mapped > > to an entry in the topology database, but the atom O used in > > an interaction of type angle in that entry is not found in the > > input file. Perhaps your atom and/or residue naming needs to be > > fixed. > > > > pdb2gmx is just being a bit too noisy here. Termini are being patched, > which means some atoms get deleted, replaced, or added. Here, an > existing atom is being deleted and replaced with another at both the N- > and C-termini. There is no problem, as you see the message below about > successful completion. > > -Justin > > > Before cleaning: 6050 pairs > > Before cleaning: 7868 dihedrals > > Making cmap torsions... > > There are 2709 dihedrals, 1833 impropers, 5404 angles > >6050 pairs, 3705 bonds and 0 virtual sites > > Total mass 40604.576 a.m.u. > > Total charge 11.000 e > > Writing topology > > > > Back Off! I just backed up posre.itp to ./#posre.itp.1# > > > > Writing coordinate file... > > > > Back Off! I just backed up actin_asp_processed.gro to > > ./#actin_asp_processed.gro.1# > > - PLEASE NOTE > > You have successfully generated a topology from: actin_asp_clean.pdb. > > The Gromos54a7 force field and the spce water model are used. > > - ETON ESAELP > > > > GROMACS reminds you: "Miggida-Miggida-Miggida-Mac" (Kriss Kross) > > > > akanxa@akanxa-HP-Notebook:~/Documents/aasp$ > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
i am getting a warning after converting pdb2gmx and then applying force field what i will do. please help me.i get this on screen. WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 374 named PHE of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 6050 pairs Before cleaning: 7868 dihedrals Making cmap torsions... There are 2709 dihedrals, 1833 impropers, 5404 angles 6050 pairs, 3705 bonds and 0 virtual sites Total mass 40604.576 a.m.u. Total charge 11.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.1# Writing coordinate file... Back Off! I just backed up actin_asp_processed.gro to ./#actin_asp_processed.gro.1# - PLEASE NOTE You have successfully generated a topology from: actin_asp_clean.pdb. The Gromos54a7 force field and the spce water model are used. - ETON ESAELP GROMACS reminds you: "Miggida-Miggida-Miggida-Mac" (Kriss Kross) akanxa@akanxa-HP-Notebook:~/Documents/aasp$ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
