[gmx-users] Packmol starting .pdb and proper equilibration
Dr. Vitaly Chaban
vvchaban at gmail.com
Wed Oct 29 20:00:51 CET 2014
I do not believe it is because of packmol or because of equilibration.
What about trying a different number of cores per job? Sometimes,
certain number of cores do not want to work correctly for certain
systems.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Wed, Oct 29, 2014 at 7:07 PM, Ioanna Styliari
<paxids at nottingham.ac.uk> wrote:
> Dear Gromacs users,
>
> I am simulating a system that contains a drug nanoparticle in amorphous state, surrounded by water and the water is also surrounded by acetone (imagine 2 concentric spheres for the first two inside one big box for the acetone).
>
> I used to build the system using gromacs editconf and more precisely building one box at a time and running em, nvt and npt equilibration for each one of the extra box-layers I was adding. However this was a very tedious procedure so I have started recently building the system using Packmol. Once I get the pdb from packmol I edit it to add the box dimensions with editconf and then go through an em, nvt, npt (usually 100ps) for the whole system.
> I have already run 4-5 simulations of 50ns and 100ns and they were running fine (they are running on parallel in a cluster). However in my last one I got the following error:
>
> Fatal error:
> 1 particles communicated to PME node 20 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y.
>
> I know this means that the system is not well equilibrated but after the nvt and npt the T and P are converged. I have reduced the time step to 1fs but I am also worried that the equilibration is not the correct one. It is also worth saying that I had similar errors even with my previous building procedure using gromacs.
>
> Any suggestions/experiences with using Packmol? I am also attaching my mdp options below just in case.
>
> Thank you very much for your time in advance,
>
> Ioanna Styliari
>
> EM:
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 10.0 ; Stop minimization when the maximum force < 10.0 kJ/mol/nm
> emstep = 0.001 ; Energy step size
> nsteps = 500000 ; Maximum number of (minimization) steps to perform
>
> ; Parameters describing how to find the neighbours of each atom and how to calculate the interactions
> Nstlist = 1 ; Frequency to update the neighbour list and long range forces
> ns_type = grid ; Method to determine neighbour list (simple, grid)
> rlist = 1.0 ; Cut-off for making neighbour list (short range forces)
> coulombtype = PME ; Treatment of long range electrostatic interactions
> rcoulomb = 1.0 ; Short-range electrostatic cut-off
> vdw-type = Cut-off
> rvdw = 1.0 ; Short-range Van der Waals cut-off
> pbc = xyz ; Periodic Boundary Conditions
> NVT
> title = pol1-box NVT
> ; Run parameters
> integrator = md ;
> nsteps = 100000 ; 100 ps
> dt = 0.001 ; 1 fs
> ; Bond parameters
> continuation = no ; first dynamics run
> ; Neighborsearching
> ns_type = grid ; search neighboring grid cells
> nstlist = 5 ;
> rlist = 1.0 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.16 ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl = V-rescale ; modified Berendsen thermostat
> tc-grps = system ;
> tau_t = 0.1 ; time constant, in ps
> ref_t = 300 ; reference temperature, one for each group, in K
> ; Pressure coupling is off
> pcoupl = no ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
> ; Dispersion correction
> DispCorr = EnerPres ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = yes ; assign velocities from Maxwell distribution
> gen_temp = 300 ; temperature for Maxwell distribution
> gen_seed = -1 ; generate a random seed
>
> constraints = none
>
> NPT
> title = pol1-box NPT
> ; Run parameters
> integrator = md
> nsteps = 100000
> dt = 0.001
> ; Bond parameters
> continuation = yes ; Restarting after NVT
> ; Neighborsearching
> ns_type = grid ; search neighbouring grid cells
> nstlist = 5 ; fs
> rlist = 1.0 ; short-range neighbourlist cutoff (in nm)
> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.16 ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl = V-rescale ; modified Berendsen thermostat
> tc-grps = system ;
> tau_t = 0.1 ; time constant, in ps
> ref_t = 300 ; reference temperature, one for each group, in K
> ; Pressure coupling is on
> pcoupl = berendsen ; Pressure coupling on in NPT
> pcoupltype = isotropic ; uniform scaling of box vectors
> tau_p = 2.0 ; time constant, in ps
> ref_p = 1.0 ; reference pressure, in bar
> compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
> refcoord_scaling = com
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
> ; Dispersion correction
> DispCorr = EnerPres ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = no ; Velocity generation is off
>
>
> and then MD:
>
> title = pol1-box first 2 ns MD
> ; Run parameters
> integrator = md ;
> nsteps = 2000000 ;
> dt = 0.001 ; fs
> ; Bond parameters
> continuation = yes ; Restarting after NPT
> ; Neighborsearching
> ns_type = grid ; search neighboring grid cells
> nstlist = 5 ; fs
> rlist = 1.0 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.16 ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl = V-rescale ; modified Berendsen thermostat
> tc-grps = system ; two coupling groups - more accurate
> tau_t = 0.1 ; time constant, in ps
> ref_t = 300 ; reference temperature, one for each group, in K
> ; Pressure coupling is on
> pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
> pcoupltype = isotropic ; uniform scaling of box vectors
> tau_p = 2.0 ; time constant, in ps
> ref_p = 1.0 ; reference pressure, in bar
> compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
> ; Dispersion correction
> DispCorr = EnerPres ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = no ; Velocity generation is off
>
>
> This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
>
>
>
> This message has been checked for viruses but the contents of an attachment
>
> may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
>
>
>
>
>
>
>
>
>
> --
> 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-request at gromacs.org.
More information about the gromacs.org_gmx-users
mailing list