hello gmx users,
I am sorry for bothering you but I was searching mailing list and no
results. I have a problem with my test particle insertion as I run the
workflow I described previously with my mdp:
title = Test Particle Insertion
; Run parameters
integrator = tpi
nsteps = 50000000 ; 100 ns
dt = 0.002 ; 2 fs
; Output control
nstxout = 0 ; suppress .trr output ; output coordinates every
25 ps
nstvout = 25000 ; velocities to output every 25000 steps
nstenergy = 1000 ; save energies every 2 ps
nstlog = 1000 ; update log file every 2 ps
nstxtcout = 100000 ; suppress (tlumic) xtc trajectory
energygrps = System
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
vdwtype = Switch
rvdw-switch = 1.0
rlist = 1.4 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
ewald_rtol = 1e-5 ; relative strenght of the Ewald-shifted potential
rcoulomb
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; 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 = 318 ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; pressure coupling is on for
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 = yes ; assign velocities from Maxwell distribution
gen_temp = 318 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
Then My log file:
The temperature for test particle insertion is 318.000 K
Started Test Particle Insertion on node 0 Wed May 9 14:18:18 2012
Will insert 3 atoms with partial charges
Will insert 50000000 times in each frame of md318.trr
Will use the same neighborlist for 5 insertions in a sphere of radius
0.050000
<V> = -nan nm^3
<mu> = -nan kJ/mol
No MEGA Flopsen this time
R E A L C Y C L E A N D T I M E A C C O U N T I N G
Computing: Nodes Number G-Cycles Seconds %
------------------------------
-----------------------------------------
Rest 4 5.218 1.9 100.0
-----------------------------------------------------------------------
Total 4 5.218 1.9 100.0
-----------------------------------------------------------------------
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 0.485 0.485 100.0
(Mnbf/s) (MFlops) (steps/hour)
Performance: 0.000 0.000 0.0
Finished mdrun on node 0 Wed May 9 14:18:19 2012
Files are empty. Do you have any clue what is happening?
Thank you for your time,
Steven
On Wed, May 9, 2012 at 1:45 PM, Javier Cerezo <j...@um.es> wrote:
> Hi Steven
>
> As I remember, TPI is based on the calculation of the potential at every
> conformation from the already computed simulation (inserting the particle
> in every snapshot), so velocities are not used.
>
> Anyway, use both and see if there are any differences.
>
> Javier
>
> El 09/05/12 11:27, Steven Neumann escribió:
>
> Dear Gmx Users,
>
> I am running TPI of the water in the system containing free amino acids.
> Steps:
>
> 1. I run the NPT simulation of 100 ns to equilibrate the system.
> 2. I added 1 extra water molecule to the final pdb file (converted from
> gro) and to topology
> 3. I creaded tpi.tpr using grompp using new pdb file with extra water
> molecule
> 4. mdrun –s tpi298.tpr -rerun md298.trr -deffnm tpi298 -tpi tpi298.xvg
> -tpid tpid298.xvg
>
> My question: Is it better generate new velocities in my mdp file
> (continuation = yes, gen_vel = no, tpi integrator) for a pdb file or use
> velocities from previous simulations (gro file)?
> If the second option is more appropriate what velocity shall I adjust to
> the extra water molecule?
>
> I will appreciate your reply.
>
> Steven
>
>
>
> --
> Javier CEREZO BASTIDA
> PhD Student
> Physical Chemistry
> Universidad de Murcia
> Murcia (Spain)
> Tel: (+34)868887434
>
> --
> gmx-users mailing list gmx-users@gromacs.org
> 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 gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
