[gmx-users] Cyclohexane simulation problem
Thank you Justin for prompt reply.I have been used coulombtype = Cut-off in my mdp file for Cyclohexane energy minimization but the results sound odd.I used cyclohexane density (0.824 g/ml) for calculating number of CHX molecules in a 10 nm3 (about 56 molecules). Then I used following command to make a box.gmx insert-molecules -ci chx.gro -nmol 56 -box 2.154434 2.154434 2.154434 -o chx_box.grochx.gro and chx.itp that I used are: =chx.itp ==; ; ; This file was generated by PRODRG version AA100323.0717 ; PRODRG written/copyrighted by Daan van Aalten ; and Alexander Schuettelkopf ; ; Questions/comments to d...@davapc1.bioch.dundee.ac.uk ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. ; ; [ moleculetype ] ; Name nrexcl chx 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH1 1 chx CAA 1 0.000 14.0270 2 CH1 1 chx CAB 1 0.000 14.0270 3 CH1 1 chx CAE 1 0.000 14.0270 4 CH1 1 chx CAF 1 0.000 14.0270 5 CH1 1 chx CAD 1 0.000 14.0270 6 CH1 1 chx CAC 1 0.000 14.0270 [ bonds ] ; ai aj fu c0, c1, ... 1 2 2 0.152 543.0 0.152 543.0 ; CAA CAB 1 6 2 0.152 543.0 0.152 543.0 ; CAA CAC 2 3 2 0.152 543.0 0.152 543.0 ; CAB CAE 3 4 2 0.152 543.0 0.152 543.0 ; CAE CAF 4 5 2 0.152 543.0 0.152 543.0 ; CAF CAD 5 6 2 0.152 543.0 0.152 543.0 ; CAD CAC [ pairs ] ; ai aj fu c0, c1, ... 1 4 1 ; CAA CAF 2 5 1 ; CAB CAD 3 6 1 ; CAE CAC [ angles ] ; ai aj ak fu c0, c1, ... 2 1 6 2 109.5 520.0 109.5 520.0 ; CAB CAA CAC 1 2 3 2 109.5 520.0 109.5 520.0 ; CAA CAB CAE 2 3 4 2 109.5 520.0 109.5 520.0 ; CAB CAE CAF 3 4 5 2 109.5 520.0 109.5 520.0 ; CAE CAF CAD 4 5 6 2 109.5 520.0 109.5 520.0 ; CAF CAD CAC 1 6 5 2 109.5 520.0 109.5 520.0 ; CAA CAC CAD [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 3 2 1 6 1 0.0 5.9 3 0.0 5.9 3 ; dih CAE CAB CAA CAC 5 6 1 2 1 0.0 5.9 3 0.0 5.9 3 ; dih CAD CAC CAA CAB 4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih CAF CAE CAB CAA 5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih CAD CAF CAE CAB 6 5 4 3 1 0.0 5.9 3 0.0 5.9 3 ; dih CAC CAD CAF CAE 1 6 5 4 1 0.0 5.9 3 0.0 5.9 3 ; dih CAA CAC CAD CAF =chx.gro PRODRG COORDS 6 1chx C AA 1 0.155 0.105 0.177 1chx C AB 2 0.100 0.247 0.184 1chx C AE 3 0.182 0.344 0.100 1chx C AF 4 0.330 0.339 0.137 1chx C AD 5 0.385 0.196 0.130 1chx C AC 6 0.303 0.100 0.214 0.48500 0.44400 0.31400=== Then I minimized the energy of generated box as follows:gmx grompp -f minim.mdp -c chx_box.gro -p chx_box.top -o em.tpr -maxwarn 1gmx mdrun -deffnm em -v The warning I got in grompp runing was WARNING 1 [file chx_box.top, line 58]: 336 non-matching atom names atom names from chx_box.top will be used atom names from chx_box.gro will be ignored Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 56 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 1005.00 This run will generate roughly 2 Mb of data There was 1 note There was 1 warning --- Program gmx, VERSION 5.0.4 Source code file: /home/mohsen/Downloads/gromacs-5.0.4/src/gromacs/gmxpreprocess/grompp.c, line: 2087 Fatal error: Too many warnings (1), gmx terminated. So I used -maxwarn 1 The chx_box ITP is==chx_box.itp=; ; File 'topol.top' was generated ; By user: mohsen (1000) ; On host: mohsen-All-Series ; At date: Wed May 20 12:09:46 2015 ; ; This is a standalone topology file
[gmx-users] Cyclohexane simulation problem
Dear All, I am interested in simulation of cyclohexane box based on Lemkul tutorial. At first I built a box using following commandgmx insert-molecules -ci chx.gro -nmol 500 -box 2.154434 2.154434 2.154434 -o chx_box.gro (I want a box with 10 nm3 volume)after run several times and convergence I have a box with 88 CHX. then I minimized energy using following mdp file:; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 100.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1 ; Short-range electrostatic cut-off rvdw = 1 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no)== OOPS!! I got following fatal error = GROMACS: gmx grompp, VERSION 5.0.4 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx grompp -f minim.mdp -c chx_box.gro -p chx_box.top -o em.tpr Back Off! I just backed up mdout.mdp to ./#mdout.mdp.41# NOTE 1 [file minim.mdp]: With Verlet lists the optimal nstlist is = 10, with GPUs = 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 1763529642 Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'chx' Warning: atom name 1 in chx_box.top and chx_box.gro does not match (CAA - AA) Warning: atom name 2 in chx_box.top and chx_box.gro does not match (CAB - AB) Warning: atom name 3 in chx_box.top and chx_box.gro does not match (CAE - AE) Warning: atom name 4 in chx_box.top and chx_box.gro does not match (CAF - AF) Warning: atom name 5 in chx_box.top and chx_box.gro does not match (CAD - AD) Warning: atom name 6 in chx_box.top and chx_box.gro does not match (CAC - AC) Warning: atom name 7 in chx_box.top and chx_box.gro does not match (CAA - AA) Warning: atom name 8 in chx_box.top and chx_box.gro does not match (CAB - AB) Warning: atom name 9 in chx_box.top and chx_box.gro does not match (CAE - AE) Warning: atom name 10 in chx_box.top and chx_box.gro does not match (CAF - AF) Warning: atom name 11 in chx_box.top and chx_box.gro does not match (CAD - AD) Warning: atom name 12 in chx_box.top and chx_box.gro does not match (CAC - AC) Warning: atom name 13 in chx_box.top and chx_box.gro does not match (CAA - AA) Warning: atom name 14 in chx_box.top and chx_box.gro does not match (CAB - AB) Warning: atom name 15 in chx_box.top and chx_box.gro does not match (CAE - AE) Warning: atom name 16 in chx_box.top and chx_box.gro does not match (CAF - AF) Warning: atom name 17 in chx_box.top and chx_box.gro does not match (CAD - AD) Warning: atom name 18 in chx_box.top and chx_box.gro does not match (CAC - AC) Warning: atom name 19 in chx_box.top and chx_box.gro does not match (CAA - AA) Warning: atom name 20 in chx_box.top and chx_box.gro does not match (CAB - AB) (more than 20 non-matching atom names) WARNING 1 [file chx_box.top, line 58]: 528 non-matching atom names atom names from chx_box.top will be used atom names from chx_box.gro will be ignored Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 88 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 1581.00 WARNING 2 [file minim.mdp]: You are using full electrostatics treatment PME for a system without charges. This costs a lot of performance for just processing zeros, consider using Cut-off instead. Calculating fourier grid dimensions for X Y Z Using a fourier grid of 20x20x20, spacing 0.108 0.108 0.108 Estimate for the relative computational load of the PME mesh part: 0.23 This run will generate roughly 2 Mb of data There was 1 note There were 2 warnings --- Program gmx, VERSION 5.0.4 Source code file: /home/mohsen/Downloads/gromacs-5.0.4/src/gromacs/gmxpreprocess/grompp.c, line: 2087 Fatal error: Too many warnings (2), gmx terminated. If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at
[gmx-users] Simulation of Ethanol
Dear All,I am intending to simulate the pure ethanol box. I considered density of natural ethanol (789 kg / m3) and generate a box of pure ethanol using gmx genconf. after ending MD production, with NPT ensemble and P = 1 bar and T = 298, I have encountered a strange behavior, The average density value of system is about 1610 kg /m3!!!. the box size is changed and is smaller than starting box and nvt box. Mohsen -- 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.
