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The trr file has something wrong. Look at "Coords", it has 0 frames<br>
<br>
You may have forgotten to set nstxout to a non-zero value?<br>
<br>
Javier<br>
<br>
El 09/05/12 16:10, Steven Neumann escribió:
<blockquote
cite="mid:CAKZJqQHPsWfJdVUoKJ=46Xxzwo_oLsFaFZxPZo-sd9NOTZDmTg@mail.gmail.com"
type="cite">I added one water molecule in my topology to all water
molecules:<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
Alanine 40<br>
SOL 724<br>
<br>
Maybe I should add aditional line like:<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
Alanine 40<br>
SOL 723<br>
SOL 1<br>
<br>
What do you think?<br>
<br>
<br>
<div class="gmail_quote">On Wed, May 9, 2012 at 3:04 PM, Steven
Neumann <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Checking
file md.trr<br>
trn version: GMX_trn_file (single precision)<br>
Reading frame 0 time 0.000<br>
# Atoms 2569<br>
Last frame 2000 time 100000.000<br>
<br>
<br>
Item #frames Timestep (ps)<br>
Step 2001 50<br>
Time 2001 50<br>
Lambda 2001 50<br>
Coords 0<br>
Velocities 2001 50<br>
Forces 0<br>
Box 2001 50<br>
<br>
Well, it looks ok. Any suggestions?
<div class="HOEnZb">
<div class="h5">
<br>
<br>
<div class="gmail_quote">
On Wed, May 9, 2012 at 3:01 PM, Javier Cerezo <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:jcb1@um.es" target="_blank">jcb1@um.es</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Sorry, I saw
now the command line you've posted. Did you check
your trr with gmxcheck?
<div><br>
<br>
El 09/05/12 15:49, Steven Neumann escribió: </div>
<blockquote type="cite">hello gmx users,
<div>
<div><br>
<br>
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:<br>
<br>
title = Test Particle Insertion<br>
; Run parameters<br>
integrator = tpi <br>
nsteps = 50000000 ; 100 ns<br>
dt = 0.002 ; 2 fs<br>
; Output control<br>
nstxout = 0 ; suppress .trr
output ; output coordinates every 25 ps<br>
nstvout = 25000 ; velocities to output
every 25000 steps<br>
nstenergy = 1000 ; save energies every
2 ps<br>
nstlog = 1000 ; update log file
every 2 ps<br>
nstxtcout = 100000 ; suppress
(tlumic) xtc trajectory<br>
energygrps = System<br>
continuation = no ; first
dynamics run<br>
constraint_algorithm = lincs ; holonomic
constraints <br>
constraints = all-bonds ; all bonds
(even heavy atom-H bonds) constrained<br>
lincs_iter = 1 ; accuracy of
LINCS<br>
lincs_order = 4 ; also related
to accuracy<br>
; Neighborsearching<br>
ns_type = grid ; search neighboring
grid cells<br>
nstlist = 5 ; 10 fs<br>
vdwtype = Switch<br>
rvdw-switch = 1.0<br>
rlist = 1.4 ; short-range
neighborlist cutoff (in nm)<br>
rcoulomb = 1.4 ; short-range
electrostatic cutoff (in nm)<br>
rvdw = 1.2 ; short-range van der
Waals cutoff (in nm)<br>
ewald_rtol = 1e-5 ; relative strenght of
the Ewald-shifted potential rcoulomb<br>
; Electrostatics<br>
coulombtype = PME ; Particle Mesh
Ewald for long-range electrostatics<br>
pme_order = 4 ; cubic
interpolation<br>
fourierspacing = 0.12 ; grid spacing for
FFT<br>
; Temperature coupling is on<br>
tcoupl = V-rescale ;
modified Berendsen thermostat<br>
tc_grps = System ; two
coupling groups - more accurate<br>
tau_t = 0.1
; time constant, in ps<br>
ref_t = 318 ;
reference temperature, one for each group, in
K<br>
; Pressure coupling is on<br>
pcoupl = Parrinello-Rahman ;
pressure coupling is on for NPT<br>
pcoupltype = isotropic ;
uniform scaling of box vectors<br>
tau_p = 2.0 ;
time constant, in ps<br>
ref_p = 1.0 ;
reference pressure, in bar<br>
compressibility = 4.5e-5 ;
isothermal compressibility of water, bar^-1<br>
; Periodic boundary conditions<br>
pbc = xyz ; 3-D PBC<br>
; Dispersion correction<br>
DispCorr = EnerPres ; account for cut-off
vdW scheme<br>
; Velocity generation<br>
gen_vel = yes ; assign velocities
from Maxwell distribution<br>
gen_temp = 318 ; temperature for
Maxwell distribution<br>
gen_seed = -1 ; generate a random
seed<br>
<br>
Then My log file:<br>
<br>
<br>
The temperature for test particle insertion
is 318.000 K<br>
<br>
Started Test Particle Insertion on node 0 Wed
May 9 14:18:18 2012<br>
<br>
Will insert 3 atoms with partial charges<br>
<br>
Will insert 50000000 times in each frame of
md318.trr<br>
Will use the same neighborlist for 5
insertions in a sphere of radius 0.050000<br>
<br>
<V> = -nan nm^3<br>
<mu> = -nan kJ/mol<br>
No MEGA Flopsen this time<br>
<br>
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<br>
<br>
Computing: Nodes Number
G-Cycles Seconds %<br>
------------------------------
<div>-----------------------------------------<br>
Rest 4
5.218 1.9 100.0<br>
-----------------------------------------------------------------------<br>
Total 4
5.218 1.9 100.0<br>
-----------------------------------------------------------------------<br>
<br>
Parallel run - timing based on
wallclock.<br>
<br>
NODE (s) Real (s) (%)<br>
Time: 0.485 0.485 100.0<br>
(Mnbf/s) (MFlops)
(steps/hour)<br>
Performance: 0.000
0.000 0.0<br>
Finished mdrun on node 0 Wed May 9 14:18:19
2012<br>
<br>
<br>
<br>
Files are empty. Do you have any clue what
is happening?<br>
<br>
Thank you for your time,<br>
<br>
Steven
<div>
<div> <img moz-do-not-send="true" src=""></div>
</div>
</div>
<br>
<br>
<div class="gmail_quote">On Wed, May 9, 2012
at 1:45 PM, Javier Cerezo <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:jcb1@um.es" target="_blank">jcb1@um.es</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi
Steven<br>
<br>
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.<br>
<br>
Anyway, use both and see if there are
any differences.<br>
<br>
Javier<br>
<br>
El 09/05/12 11:27, Steven Neumann
escribió:
<div>
<div>
<blockquote type="cite">Dear Gmx
Users,<br>
<br>
I am running TPI of the water in
the system containing free amino
acids. Steps:<br>
<br>
1. I run the NPT simulation of 100
ns to equilibrate the system.<br>
2. I added 1 extra water molecule
to the final pdb file (converted
from gro) and to topology<br>
3. I creaded tpi.tpr using grompp
using new pdb file with extra
water molecule<br>
4. mdrun –s tpi298.tpr -rerun
md298.trr -deffnm tpi298 -tpi
tpi298.xvg -tpid tpid298.xvg<br>
<br>
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)? <br>
If the second option is more
appropriate what velocity shall I
adjust to the extra water
molecule?<br>
<br>
I will appreciate your reply.<br>
<br>
Steven<br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div>
</div>
<span><font color="#888888">
<div>-- <br>
Javier CEREZO BASTIDA<br>
PhD Student<br>
Physical Chemistry<br>
Universidad de Murcia<br>
Murcia (Spain)<br>
Tel: <a moz-do-not-send="true"
href="tel:%28%2B34%29868887434"
value="+34868887434"
target="_blank">(+34)868887434</a>
</div>
</font></span></div>
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<div>
<div> <br>
<div>-- <br>
Javier CEREZO BASTIDA<br>
PhD Student<br>
Physical Chemistry<br>
Universidad de Murcia<br>
Murcia (Spain)<br>
Tel: <a moz-do-not-send="true"
href="tel:%28%2B34%29868887434"
value="+34868887434" target="_blank">(+34)868887434</a>
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<div class="moz-signature">-- <br>
Javier CEREZO BASTIDA<br>
PhD Student<br>
Physical Chemistry<br>
Universidad de Murcia<br>
Murcia (Spain)<br>
Tel: (+34)868887434
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