[gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field
Thanks for the suggestions, Justin. I'm still having issues with instabilities and large fluctuations in unconstrained NPT simulations of the CHCl3 box, so I'll appreciate comments from the list on my run parameters. I think there is a problem with the pressure coupling, but I'm not sure what to change to fix it. I modified the topology, using the H-Cl and Cl-Cl as bonds, and the H-C and C-Cl bond distances as constraints: ---[chcl3.itp]--- [...] [ bonds ] 1 3 2gb_47 1 4 2gb_47 1 5 2gb_47 3 4 2gb_48 3 5 2gb_48 4 5 2gb_48 [ constraints ] 1 2 10.1100 2 3 10.1758 2 4 10.1758 2 5 10.1758 [...] ---[chcl3.itp]--- This prevented the grompp warning message about too many constraints to appear. I first minimized the 216-molecule box with the following mdp: ---[em.mdp]--- integrator = steep nsteps = 5 emtol = 100 emstep = 0.01 ; ;Electrostatics ; coulombtype = PME rlist = 1 rcoulomb= 1.0 ns_type = grid nstlist = 1 ; ;vdW ; rvdw= 1.0 ; ; PBC ; pbc= xyz ; ; constraints ; constraint_algorithm = lincs constraints = none lincs_iter= 1 lincs_order= 4 ---[em.mdp]--- This converged well: ---[em.log]--- Energies (kJ/mol) G96Bond G96AngleLJ (SR) Coulomb (SR) Coul. recip. 3.05135e+004.35449e-01 -5.41548e+03 -2.09196e+01 -2.57100e+01 Potential Pressure (bar) Cons. rmsd () -5.45863e+031.17031e+031.50663e-07 Steepest Descents converged to Fmax 100 in 297 steps Potential Energy = -5.45862698325888e+03 Maximum force = 9.95795243267423e+01 on atom 798 Norm of force = 3.22657158607021e+01 ---[em.log]--- Then, I heated the system to 300K in an NVT simulation: ---[nvt.mdp]--- ; ;NVT equilibration ; ; Run parameters integrator= md nsteps= 25000 dt= 0.002 ; Output control nstxout= 100 nstvout= 100 nstenergy= 100 nstlog= 100 ; Bond parameters continuation= no constraint_algorithm = lincs constraints= none lincs_iter= 1 lincs_order= 4 ; Neighborsearching ns_type= grid nstlist= 5 rlist= 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Electrostatics coulombtype= PME pme_order= 4 fourierspacing= 0.16 ; Temperature coupling is on tcoupl= V-rescale tau_t= 0.1 tc_grps= SYSTEM ref_t= 300 ; Pressure coupling is off pcoupl= no ; PBC pbc= xyz ; Dispersion correction DispCorr= EnerPres ; Velocity generation gen_vel= yes gen_temp= 300 gen_seed= -1 ---[nvt.mdp]--- This simulation yielded a temperature with large fluctuations: Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 298.89910.185710.1724 -0.0360483 -1.80249 The fluctuations look fairly large, but I'm not sure if these are reasonable for a 216-molecule system. I then applied pressure to the system: ---[npt.mdp]--- ; NPT equilibration ; Run parameters integrator= md nsteps= 5 dt= 0.002 ; Output control nstxout= 100 nstvout= 100 nstenergy= 100 nstlog= 100 ; Bond parameters continuation= yes constraint_algorithm = lincs constraints= none lincs_iter= 1 lincs_order= 4 ; Neighborsearching ns_type= grid nstlist= 5 rlist= 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Electrostatics coulombtype= PME pme_order= 4 fourierspacing= 0.16 ; Temperature coupling is on tcoupl= V-rescale tc-grps= SYSTEM tau_t= 0.1 ref_t= 300 ; Pressure coupling is on pcoupl= Parrinello-Rahman pcoupltype= isotropic tau_p= 2.0 ref_p= 1.0 compressibility = 1e-4 ; Periodic boundary conditions pbc= xyz ; Dispersion correction DispCorr= EnerPres ; Velocity generation gen_vel= no ---[npt.mdp]--- This simulation yields large fluctuations of temperature as well: I tried playing around with the value of tau_p: - tau_p = 5.0 == slow increase of density, not stable after 100 ps; temperature with similar fluctuations as NVT (300K, RMSD 9); pressure starts oscillating wildly after ~10 ps - tau_p = 2.0 == increase of density, not stable at end of simulation; huge fluctuations
[gmx-users] Aligning protein in bilayer with editconf
Hi ALL, I am facing a strange problem, while aligning a protein molecule in a lipid bilayer. I am using the center coordinates of the lipid .gro file (values in the last line of .gro) with -box option of editconf to properly align the protein with the bilayer. Now the problem is that the protein is in the middle of the bilayer, but it is parallel to the bilayer. I need to rotate it by 90 degrees to make it perpendicular with the bilayer (which is normal with any protein-lipid complex.). But I am not able to do this with editconf or any other command. Please suggest how to do this. Any suggestion is welcome. Thanks a lot. Regards, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Aligning protein in bilayer with editconf
Anirban Ghosh wrote: Hi ALL, I am facing a strange problem, while aligning a protein molecule in a lipid bilayer. I am using the center coordinates of the lipid .gro file (values in the last line of .gro) with -box option of editconf to properly align the protein with the bilayer. Now the problem is that the protein is in the middle of the bilayer, but it is parallel to the bilayer. I need to rotate it by 90 degrees to make it perpendicular with the bilayer (which is normal with any protein-lipid complex.). But I am not able to do this with editconf or any other command. Please suggest how to do this. Any suggestion is welcome. Thanks a lot. So you're saying that editconf -rotate is not working? That's what it's designed to do. If you think something is broken, at least provide the command you're issuing so we can see if there's something wrong with it. -Justin Regards, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field
Pablo Englebienne wrote: Thanks for the suggestions, Justin. I'm still having issues with instabilities and large fluctuations in unconstrained NPT simulations of the CHCl3 box, so I'll appreciate comments from the list on my run parameters. I think there is a problem with the pressure coupling, but I'm not sure what to change to fix it. I modified the topology, using the H-Cl and Cl-Cl as bonds, and the H-C and C-Cl bond distances as constraints: ---[chcl3.itp]--- [...] [ bonds ] 1 3 2gb_47 1 4 2gb_47 1 5 2gb_47 3 4 2gb_48 3 5 2gb_48 4 5 2gb_48 [ constraints ] 1 2 10.1100 2 3 10.1758 2 4 10.1758 2 5 10.1758 [...] ---[chcl3.itp]--- This prevented the grompp warning message about too many constraints to appear. I first minimized the 216-molecule box with the following mdp: ---[em.mdp]--- integrator = steep nsteps = 5 emtol = 100 emstep = 0.01 ; ;Electrostatics ; coulombtype = PME rlist = 1 rcoulomb= 1.0 ns_type = grid nstlist = 1 ; ;vdW ; rvdw= 1.0 ; ; PBC ; pbc= xyz ; ; constraints ; constraint_algorithm = lincs constraints = none lincs_iter= 1 lincs_order= 4 ---[em.mdp]--- This converged well: ---[em.log]--- Energies (kJ/mol) G96Bond G96AngleLJ (SR) Coulomb (SR) Coul. recip. 3.05135e+004.35449e-01 -5.41548e+03 -2.09196e+01 -2.57100e+01 Potential Pressure (bar) Cons. rmsd () -5.45863e+031.17031e+031.50663e-07 Steepest Descents converged to Fmax 100 in 297 steps Potential Energy = -5.45862698325888e+03 Maximum force = 9.95795243267423e+01 on atom 798 Norm of force = 3.22657158607021e+01 ---[em.log]--- Then, I heated the system to 300K in an NVT simulation: ---[nvt.mdp]--- ; ;NVT equilibration ; ; Run parameters integrator= md nsteps= 25000 dt= 0.002 ; Output control nstxout= 100 nstvout= 100 nstenergy= 100 nstlog= 100 ; Bond parameters continuation= no constraint_algorithm = lincs constraints = none lincs_iter= 1 lincs_order= 4 ; Neighborsearching ns_type= grid nstlist= 5 rlist= 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Electrostatics coulombtype= PME pme_order= 4 fourierspacing= 0.16 ; Temperature coupling is on tcoupl= V-rescale tau_t= 0.1 tc_grps= SYSTEMref_t= 300 ; Pressure coupling is off pcoupl= no; PBC pbc= xyz ; Dispersion correction DispCorr= EnerPres ; Velocity generation gen_vel= yes gen_temp= 300 gen_seed= -1 ---[nvt.mdp]--- This simulation yielded a temperature with large fluctuations: Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 298.89910.185710.1724 -0.0360483 -1.80249 The fluctuations look fairly large, but I'm not sure if these are reasonable for a 216-molecule system. I then applied pressure to the system: ---[npt.mdp]--- ; NPT equilibration ; Run parameters integrator= md nsteps= 5 dt= 0.002 ; Output control nstxout= 100 nstvout= 100 nstenergy= 100 nstlog= 100 ; Bond parameters continuation= yes constraint_algorithm = lincs constraints= none lincs_iter= 1 lincs_order= 4 ; Neighborsearching ns_type= grid nstlist= 5 rlist= 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Electrostatics coulombtype= PME pme_order= 4 fourierspacing= 0.16 ; Temperature coupling is on tcoupl= V-rescale tc-grps= SYSTEM tau_t= 0.1 ref_t= 300 ; Pressure coupling is on pcoupl= Parrinello-Rahman pcoupltype= isotropic tau_p= 2.0 ref_p= 1.0 compressibility = 1e-4 ; Periodic boundary conditions pbc= xyz ; Dispersion correction DispCorr= EnerPres ; Velocity generation gen_vel= no ---[npt.mdp]--- This simulation yields large fluctuations of temperature as well: I tried playing around with the value of tau_p: - tau_p = 5.0 == slow increase of density, not stable after 100 ps; temperature with similar fluctuations as NVT (300K, RMSD 9); pressure starts oscillating wildly after ~10 ps - tau_p = 2.0 == increase of density, not stable at end of simulation; huge fluctuations in potential
Re: [gmx-users] Aligning protein in bilayer with editconf
Put your protein file in TMDET and it will align the protein for you perpendicular to Z axis and also the protein will be at origin in that case then you can use geom_center script provided in VMD to put the lipid in the origin and move it towards the protein. Hope it helps On Tue, Oct 27, 2009 at 8:00 AM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I am facing a strange problem, while aligning a protein molecule in a lipid bilayer. I am using the center coordinates of the lipid .gro file (values in the last line of .gro) with -box option of editconf to properly align the protein with the bilayer. Now the problem is that the protein is in the middle of the bilayer, but it is parallel to the bilayer. I need to rotate it by 90 degrees to make it perpendicular with the bilayer (which is normal with any protein-lipid complex.). But I am not able to do this with editconf or any other command. Please suggest how to do this. Any suggestion is welcome. Thanks a lot. So you're saying that editconf -rotate is not working? That's what it's designed to do. If you think something is broken, at least provide the command you're issuing so we can see if there's something wrong with it. -Justin Regards, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] .tpr problem
Hi, I try to run Gromacs using Cygwin emulator in a Windows XP. So, I received this error messenger: Program mdrun, VERSION 4.0.5 Source code file: gmxfio.c, line: 736 Can not open file: md300.tpr __ can someone help... would be some missing package cygwin install? Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] .tpr problem
Edilson Beserra wrote: Hi, I try to run Gromacs using Cygwin emulator in a Windows XP. So, I received this error messenger: Program mdrun, VERSION 4.0.5 Source code file: gmxfio.c, line: 736 Can not open file: md300.tpr __ can someone help... would be some missing package cygwin install? More likely the problem is what the error states - md300.tpr does not exist. Check the contents of your working directory, and any error messages from grompp that would have prevented the .tpr file from being created. -Justin Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] .tpr problem
Edilson Beserra wrote: Hi, I try to run Gromacs using Cygwin emulator in a Windows XP. So, I received this error messenger: Program mdrun, VERSION 4.0.5 Source code file: gmxfio.c, line: 736 Can not open file: md300.tpr __ can someone help... would be some missing package cygwin install? No. This error means what it says. You'll need to provide more information about what you're trying to do and the commands you used. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells
Hi ,
I am getting the following error when I try to run in parallel (I've
tried with 8 and 2 nodes and get the same).
Not all bonded interactions have been properly assigned to the domain
decomposition cells
But my simulation works when I run in serial.
I'm using gromacs 4.0.5. I am working on a mesoprous silica which I
define as a single residue (each atom is assigned to a single charge
group).
I've tried changing table_ext in the .mdp file (I first increased it
to 2.5 and then 30) following advice on previous forum posts but I
still get the same thing.
Does anyone know why this is happening and how I can fix this? I could
run in serial but it would take too long.
I also get a NOTE: Periodic molecules: can not easily determine the
required minimum bonded cut-off, using half the non-bonded cut-off
Is this part of the same problem or a different thing altogether?
I've pasted my md.log file below
Thanks
010/AP_ready more md.log
Log file opened on Tue Oct 27 13:31:44 2009
Host: vlxbig20.see.ed.ac.uk pid: 6930 nodeid: 0 nnodes: 8
The Gromacs distribution was built Tue Jul 21 13:18:34 BST 2009 by
parameters of the run:
integrator = md
nsteps = 500
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 0
comm_mode= None
nstlog = 1000
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstenergy= 1000
nstxtcout= 1000
init_t = 0
delta_t = 0.001
xtcprec = 1000
nkx = 39
nky = 39
nkz = 64
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols= TRUE
bContinuation= FALSE
bShakeSOR= FALSE
etc = Nose-Hoover
epc = No
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1.5
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.5
vdwtype = Shift
rvdw_switch = 1.2
rvdw = 1.5
epsilon_r= 1
epsilon_rf = 1
tabext = 2.5
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = EnerPres
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall= 0
wall_type= 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre= No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter= 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Lincs
shake_tol= 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel= 0
deform (3x3):
deform[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
[gmx-users] Is anyone also using lammps?s
I am trying to simulate alkane melt and found out that gromacs and lammps gave different results, particularly the bonded interaction energy. I wonder if anyone has such experience. Thanks, ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] warning in editconf
Hi for making simulation box for pr-dna interaction I typyed [editconf -f -o -d 0.5] but this warning appeared: No boxtype specified - distance condition applied in each dimension. If the molecule rotates the actual distance will be smaller. You might want to use a cubic box instead, or why not try a dodecahedron today? please guide me. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Error during NVT equillibration with nvt.log file
Dear Justin, Thanks for your patience and suggestions, as I am new to gromacs, i had to confirm my results. Ram On Mon, Oct 26, 2009 at 4:28 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As per the suggestions, I have run NPT equillibration (without constraints) for 1ns and observed the average values and plots in the xmgrace as follows: 1) Pressure Energy Average RMSD Fluct. Drift Tot-Drift --- Pressure (bar) 0.967068315.557315.557 -0.00139934 -1.39934 In the pressure.xvg plot the pressure was the same through out the equilibration, that is no rise or fall in the graph, fluctuating in the same range. 2) Density Energy Average RMSD Fluct. Drift Tot-Drift --- Density (SI)1010.056.139124.17568 0.0155894 15.5894 In the density.xvg plot the density in the beginning was around 984 and then increased upto 500 ps then onwards was the same through out the equilibration, that is no rise or fall in the graph, fluctuating in the same range. 3) temperature Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 3231.689791.68965 7.75704e-05 0.0775705 Heat Capacity Cv: 12.4723 J/mol K (factor = 2.73692e-05) In the temperature.xvg plot the pressure was the same through out the equilibration, that is no rise or fall in the graph, fluctuating in the same range. 4) Box-x Statistics over 101 steps [ 0. thru 1000.0001 ps ], 1 data sets All averages are exact over 101 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Box-X 6.81637 0.00919707 0.00692067 -2.09829e-05 -0.0209829 In the box-x.xvg plot the value decreased from 6.82 - 6.84 to 6.79 - 6.81 after the 500 ps and then was the same through out the equilibration, that is no rise or fall in the graph, fluctuating in the same range. 5) Box-Y the trend was same as X dimension Energy Average RMSD Fluct. Drift Tot-Drift --- Box-Y 6.84395 0.00923428 0.00694867 -2.10678e-05 -0.0210678 5) Box-Z the trend was same as X dimension Statistics over 101 steps [ 0. thru 1000.0001 ps ], 1 data sets All averages are exact over 101 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Box-Z9.0932 0.0438719 0.036307 -8.53145e-05 -0.0853146 In the box-z.xvg plot the value started from 9.3 and decreased to 9.03 at the 500 ps and then the values were fluctuating around this value in the same run. Please suggest me are my equilibrated parameters ok for the MD production run or i have to look for some more parameters and is it ok if i run the production phase also without constraints and position restraints. You've presented six pieces of data that have all stabilized. You have to make the decision as to whether or not your equilibration is sufficient; you can't rely on others who know nothing about your project or its goals to continually check it and tell you if it's right. -Justin The mdp file used for NPT is as below: title = NPT Equilibration define = -DPOSRES integrator = md nsteps = 100 dt = 0.001 nstxout = 100 nstvout = 100 nstenergy = 100 nstlog = 100 continuation= yes constraint_algorithm = lincs constraints = none lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = Nose-Hoover tc-grps = Protein DPPC SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 323 323 323 pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 ref_p = 1.0 1.0 compressibility = 4.5e-54.5e-5 pbc = xyz DispCorr= EnerPres gen_vel = no nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL- Thanks, Ram On Tue, Oct 20, 2009 at 7:59 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justion, When I executed the command g_energy -f anneal_npt1.edr, the output for temperature
Re: [gmx-users] warning in editconf
leila karami wrote: Hi for making simulation box for pr-dna interaction I typyed [editconf -f -o -d 0.5] but this warning appeared: No boxtype specified - distance condition applied in each dimension. If the molecule rotates the actual distance will be smaller. You might want to use a cubic box instead, or why not try a dodecahedron today? You either need to specify a box type (-bt) or use the -d flag such that it satisfies the minimum image convention in the case of your molecule rotating, as editconf has clearly warned you. http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention -Justin please guide me. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] What is the difference between LJ(SR) and LJ(LR)?
Besides Disper.-corr., what is the difference between LJ(SR) and LJ(LR) in the energy.xvg file? Thanks, ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Gromos Parameters for Heme bound Oxygen
Dear gmx users, I would like to know if any one has parameters for oxygen or carbonmonoxide bound to the heme in hemoglobin. I am running MD simulations on hemoglobin using the gromos force field G43a1 in gromacs, i had no problem when i used the pdb structure for pure hemoglobin, but when i try to convert the pdb structure files for the liganded hemoglobin (both oxy- and carbonmonoxy- ), there was complain of my oxy and carbomonoxy residue unknown i.e not defined in the .rtp file. so i would like to know if there is anyone with parameters for these kind of heme in gromacs or better still another reference of force field with parameters for them that can be use in gromacs. Thanks Kamil yusuff Deparment of Chemistry, University of Ibadan ,Nigeria. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Freezing a molecule
Hello, One quick questions... I have a structure for which I now want to freeze a portion. I already have a .top file where the entire structure is flexible (bond angles, stretches and torions defined). When freezing, do I need to delete all those bond stretches, angles and torsions associated with the frozen part from my .top file? (I am not using constraints on the frozen portion as I have seen this can cause problems). Will the bonding parameters all be set to zero when the these atoms are frozen or will their contribution be calculated if I leave these terms in. Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Gromos Parameters for Heme bound Oxygen
Olaniyi Yusuff wrote: Dear gmx users, I would like to know if any one has parameters for oxygen or carbonmonoxide bound to the heme in hemoglobin. I am running MD simulations on hemoglobin using the gromos force field G43a1 in gromacs, i had no problem when i used the pdb structure for pure hemoglobin, but when i try to convert the pdb structure files for the liganded hemoglobin (both oxy- and carbonmonoxy- ), there was complain of my oxy and carbomonoxy residue unknown i.e not defined in the .rtp file. so i would like to know if there is anyone with parameters for these kind of heme in gromacs or better still another reference of force field with parameters for them that can be use in gromacs. If it has been published, then perhaps the authors of that particular study will share them with you. If not, then realize what you are trying to do is certainly an expert topic, one that is not addressed easily: http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species -Justin Thanks Kamil yusuff Deparment of Chemistry, University of Ibadan ,Nigeria. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Freezing a molecule
Quoting Jennifer Williams jennifer.willi...@ed.ac.uk: Hello, One quick questions... I have a structure for which I now want to freeze a portion. I already have a .top file where the entire structure is flexible (bond angles, stretches and torions defined). When freezing, do I need to delete all those bond stretches, angles and torsions associated with the frozen part from my .top file? No. Just select the freeze group and say yes (Y) in the directions you want your molecule to be frozen (in the mdp-file). I also choose an energy_group exclusion for the frozen part, though I don't know whether that's necessary. (I am not using constraints on the frozen portion as I have seen this can cause problems). Will the bonding parameters all be set to zero when the these atoms are frozen or will their contribution be calculated if I leave these terms in. Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] nans in g_anaeig
Hi all! I run into a problem trying to project trajectory on the eigenvector(s) (with g_anaeig -proj ) from covariace matrix - all projections are nan. The eigenvalues are OK, the g_anaeig -comp -v2 -eig2 -over options works OK so eigenvectors seems are OK (but g_anaeig -2d fails to nan too). I am using gromacs-4.0.5 on x86-64 CentOS5 (compiled with gcc-34). What can help me to project it properly? Regards, Alex. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] nans in g_anaeig
Hi Alex, Can you paste the actual sequence of commands you used? Cheers, Tsjerk 2009/10/27 alexander yakovenko yakovenk...@ukr.net: Hi all! I run into a problem trying to project trajectory on the eigenvector(s) (with g_anaeig -proj ) from covariace matrix - all projections are nan. The eigenvalues are OK, the g_anaeig -comp -v2 -eig2 -over options works OK so eigenvectors seems are OK (but g_anaeig -2d fails to nan too). I am using gromacs-4.0.5 on x86-64 CentOS5 (compiled with gcc-34). What can help me to project it properly? Regards, Alex. ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 66, Issue 174
Thank you, Tsjerk, for replay. my commands: g_covar_d -f sss_mdsi_1000.trr -s sss_mdsi_1000.tpr -n sss.ndx -o sss_1000_eigenval.xvg -xpm sss_1000_covar.xpm -v sss_1000_eigenvec.trr -mwa -l ... Option Filename Type Description -f sss_mdsi_1000.trr Input Trajectory: xtc trr trj gro g96 pdb cpt -s sss_mdsi_1000.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -n sss.ndx Input, Opt! Index file -o sss_1000_eigenval.xvg Output xvgr/xmgr file -v sss_1000_eigenvec.trr Output Full precision trajectory: trr trj cpt -av average.pdb Output Structure file: gro g96 pdb -l covar.log Output Log file -ascii covar.dat Output, Opt. Generic data file -xpm sss_1000_covar.xpm Output, Opt! X PixMap compatible matrix file -xpma covara.xpm Output, Opt. X PixMap compatible matrix file Option Type Value Description -- -[no]h bool no Print help info and quit -nice int 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: ps, fs, ns, us, ms or s -[no]xvgr bool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -[no]fit bool yes Fit to a reference structure -[no]ref bool no Use the deviation from the conformation in the structure file instead of from the average -[no]mwa bool yes Mass-weighted covariance analysis -last int -1 Last eigenvector to write away (-1 is till the last) -[no]pbc bool yes Apply corrections for periodic boundary conditions Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision) Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision) Choose a group for the least squares fit Group 0 ( System) has 31748 elements ... Group 20 ( active_site) has 54 elements Select a group: 20 Selected 20: 'active_site' Choose a group for the covariance analysis Group 0 ( System) has 31748 elements ... Group 20 ( active_site) has 54 elements Select a group: 20 Selected 20: 'active_site' Calculating the average structure ... trn version: GMX_trn_file (double precision) Last frame 2000 time 2000.000 Constructing covariance matrix (162x162) ... Last frame 2000 time 2000.000 Read 2001 frames Trace of the covariance matrix: 6.22756 (u nm^2) 100% Diagonalizing ... Sum of the eigenvalues: 6.22756 (u nm^2) Writing eigenvalues to sss_1000_eigenval.xvg Writing reference, average structure eigenvectors 1--162 to sss_1000_eigenvec.trr Wrote the log to covar.log gcq#86: Shake Barrels Of Whisky Down My Throat (Throwing Muses) g_anaeig_d -v sss_1000_eigenvec.trr -eig sss_1000_eigenval.xvg -v2 sss_1000_eigenvec.trr -eig2 sss_1000_eigenval.xvg -f sss_mdsi_1000.trr -s sss_mdsi_1000.tpr -first 1 -last 10 -n sss.ndx -proj -over ... Option Filename Type Description -v sss_1000_eigenvec.trr Input Full precision trajectory: trr trj cpt -v2 sss_1000_eigenvec.trr Input, Opt! Full precision trajectory: trr trj cpt -f sss_mdsi_1000.trr Input, Opt! Trajectory: xtc trr trj gro g96 pdb cpt -s sss_mdsi_1000.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb -n sss.ndx Input, Opt! Index file -eig sss_1000_eigenval.xvg Input, Opt! xvgr/xmgr file -eig2sss_1000_eigenval.xvg Input, Opt! xvgr/xmgr file -comp eigcomp.xvg Output, Opt. xvgr/xmgr file -rmsf eigrmsf.xvg Output, Opt. xvgr/xmgr file -proj proj.xvg Output, Opt! xvgr/xmgr file -2d 2dproj.xvg Output, Opt. xvgr/xmgr file -3d 3dproj.pdb Output, Opt. Structure file: gro g96 pdb -filt filtered.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -extr extreme.pdb Output, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -over overlap.xvg Output, Opt! xvgr/xmgr file -inpr inprod.xpm Output, Opt. X PixMap compatible matrix file Option Type Value Description -- -[no]h bool no Print help info and quit -nice int 19 Set the nicelevel -b time 0 First
Re: [gmx-users] Is anyone also using lammps?s
Peng Yi wrote: I am trying to simulate alkane melt and found out that gromacs and lammps gave different results, particularly the bonded interaction energy. I wonder if anyone has such experience. Thanks, Even two installations of the same version of GROMACS can give different results. The question is whether when using comparable model physics you observe the same ensemble averages. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] What is the difference between LJ(SR) and LJ(LR)?
Peng Yi wrote: Besides Disper.-corr., what is the difference between LJ(SR) and LJ(LR) in the energy.xvg file? Thanks, Look in the manual for twin-range cutoffs Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells
Jennifer Williams wrote:
Hi ,
I am getting the following error when I try to run in parallel (I've
tried with 8 and 2 nodes and get the same).
Not all bonded interactions have been properly assigned to the domain
decomposition cells
But my simulation works when I run in serial.
I'm using gromacs 4.0.5. I am working on a mesoprous silica which I
define as a single residue (each atom is assigned to a single charge
group).
How many atoms in what size simulation cell? What are your v-sites?
I've tried changing table_ext in the .mdp file (I first increased it to
2.5 and then 30) following advice on previous forum posts but I still
get the same thing.
Does anyone know why this is happening and how I can fix this? I could
run in serial but it would take too long.
I also get a NOTE: Periodic molecules: can not easily determine the
required minimum bonded cut-off, using half the non-bonded cut-off
Is this part of the same problem or a different thing altogether?
My random guess is that there's a single problem with the interaction
of parallel DD, PBC, vsites, periodic molecules and/or constraints. Berk did
fix a bug earlier this month whose git commit description is
fixed v-site pbc bug with charge groups consisting ofonly multiple v-sites
but I do not know if this is at all applicable.
Compiling the git release-4-0-patches branch and trying to run with that
may help.
See bottom of text also.
I've pasted my md.log file below
Thanks
010/AP_ready more md.log
Log file opened on Tue Oct 27 13:31:44 2009
Host: vlxbig20.see.ed.ac.uk pid: 6930 nodeid: 0 nnodes: 8
The Gromacs distribution was built Tue Jul 21 13:18:34 BST 2009 by
parameters of the run:
integrator = md
nsteps = 500
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 0
comm_mode= None
nstlog = 1000
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstenergy= 1000
nstxtcout= 1000
init_t = 0
delta_t = 0.001
xtcprec = 1000
nkx = 39
nky = 39
nkz = 64
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols= TRUE
bContinuation= FALSE
bShakeSOR= FALSE
etc = Nose-Hoover
epc = No
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1.5
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.5
vdwtype = Shift
rvdw_switch = 1.2
rvdw = 1.5
epsilon_r= 1
epsilon_rf = 1
tabext = 2.5
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = EnerPres
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall= 0
wall_type= 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre= No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter= 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Lincs
[gmx-users] some prolem about genbox genconf and editconf
Hi everybody, I have come across some problem when using genbox, genconf and editconf try to make a box with a certain density and a certain number of polymer chains. First, I use genbox to have one polymer chain filled in the box without any solvent.Then I use genconf to pile up 27 polymer chains ,after that I use editconf to designate a density of 0.3 g/ml to attain the final goal. When I finish it, i find that all the bond that connect the atoms are gone and all the atoms disperse in the box. In another try, I first use a pdb file which contains only one polymer chain to genconf a box with 27polymer chain, and then use editconf to designate the density, but finally I get a box with lots of bonds that might not present in a normal structure, like a carbon was bonded with a 3 or 4 or even more atoms distance long and the bonds connect with it is overcount. What is the prolem? How can I fix it? Thanks in advance, Celeste ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] some prolem about genbox genconf and editconf
How are you visualizing the system? Using VMD? In that case, bonds are determined by how far apart the atoms are, it guesses what the bonding is, since a .gro file (or a pdb) doesn't have any bonding information in it. So what you are seeing is simply the fact you have scaled the box, increasing or decreasing the distance between the atoms. After a quick EM the atoms will return to their correct spacing. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of DreamCatcher Sent: Wednesday, 28 October 2009 1:50 PM To: gmx-users@gromacs.org Subject: [gmx-users] some prolem about genbox genconf and editconf Hi everybody, I have come across some problem when using genbox, genconf and editconf try to make a box with a certain density and a certain number of polymer chains. First, I use genbox to have one polymer chain filled in the box without any solvent.Then I use genconf to pile up 27 polymer chains ,after that I use editconf to designate a density of 0.3 g/ml to attain the final goal. When I finish it, i find that all the bond that connect the atoms are gone and all the atoms disperse in the box. In another try, I first use a pdb file which contains only one polymer chain to genconf a box with 27polymer chain, and then use editconf to designate the density, but finally I get a box with lots of bonds that might not present in a normal structure, like a carbon was bonded with a 3 or 4 or even more atoms distance long and the bonds connect with it is overcount. What is the prolem? How can I fix it? Thanks in advance, Celeste ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] some prolem about genbox genconf and editconf
DreamCatcher wrote: Hi everybody, I have come across some problem when using genbox, genconf and editconf try to make a box with a certain density and a certain number of polymer chains. First, I use genbox to have one polymer chain filled in the box without any solvent.Then I use genconf to pile up 27 polymer chains ,after that I use editconf to designate a density of 0.3 g/ml to attain the final goal. When I finish it, i find that all the bond that connect the atoms are gone and all the atoms disperse in the box. In another try, I first use a pdb file which contains only one polymer chain to genconf a box with 27polymer chain, and then use editconf to designate the density, but finally I get a box with lots of bonds that might not present in a normal structure, like a carbon was bonded with a 3 or 4 or even more atoms distance long and the bonds connect with it is overcount. What is the prolem? How can I fix it? As a side issue, read http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds Your scaling by density isn't working. I'd guess that editconf is using share/gromacs/top/atommass.dat to guess the atom masses and that your polymer's residue and atom names are not present there. Copy that file to your working directory, add suitable entries to the end and see how you go. I think editconf should be confirming which atommass.dat file it might be using - read it carefully. It should also be warning you if it doesn't find suitable masses! Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] some prolem about genbox genconf and editconf
Dallas B. Warren wrote: How are you visualizing the system? Using VMD? In that case, bonds are determined by how far apart the atoms are, it guesses what the bonding is, since a .gro file (or a pdb) doesn’t have any bonding information in it. So what you are seeing is simply the fact you have scaled the box, increasing or decreasing the distance between the atoms. After a quick EM the atoms will return to their correct spacing. I haven't used this feature of editconf, but if the scaling is truly over all coordinates, then Dallas's EM procedure will be necessary. It may also be necessary to scale in smallish increments, lest the EM be poorly conditioned with large forces. Mark Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *DreamCatcher *Sent:* Wednesday, 28 October 2009 1:50 PM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] some prolem about genbox genconf and editconf Hi everybody, I have come across some problem when using genbox, genconf and editconf try to make a box with a certain density and a certain number of polymer chains. First, I use genbox to have one polymer chain filled in the box without any solvent.Then I use genconf to pile up 27 polymer chains ,after that I use editconf to designate a density of 0.3 g/ml to attain the final goal. When I finish it, i find that all the bond that connect the atoms are gone and all the atoms disperse in the box. In another try, I first use a pdb file which contains only one polymer chain to genconf a box with 27polymer chain, and then use editconf to designate the density, but finally I get a box with lots of bonds that might not present in a normal structure, like a carbon was bonded with a 3 or 4 or even more atoms distance long and the bonds connect with it is overcount. What is the prolem? How can I fix it? Thanks in advance, Celeste ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
