The trr file has something wrong. Look at "Coords", it has 0 frames
You may have forgotten to set nstxout to a non-zero value?
Javier
El 09/05/12 16:10, Steven Neumann escribió:
I added one water molecule in my topology to all water molecules:
[ molecules ]
; Compound #mols
Alanine 40
SOL 724
Maybe I should add aditional line like:
[ molecules ]
; Compound #mols
Alanine 40
SOL 723
SOL 1
What do you think?
On Wed, May 9, 2012 at 3:04 PM, Steven Neumann <s.neuman...@gmail.com
<mailto:s.neuman...@gmail.com>> wrote:
Checking file md.trr
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
# Atoms 2569
Last frame 2000 time 100000.000
Item #frames Timestep (ps)
Step 2001 50
Time 2001 50
Lambda 2001 50
Coords 0
Velocities 2001 50
Forces 0
Box 2001 50
Well, it looks ok. Any suggestions?
On Wed, May 9, 2012 at 3:01 PM, Javier Cerezo <j...@um.es
<mailto:j...@um.es>> wrote:
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 <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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