Sorry, I saw now the command line you've posted. Did you check your trr
with gmxcheck?
El 09/05/12 15:49, Steven Neumann escribió:
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
<mailto: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 <tel:%28%2B34%29868887434>
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--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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