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 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 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 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 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 href="tel:%28%2B34%29868887434" value="+34868887434" target="_blank">(+34)868887434</a> </div>
</font></span></div>
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<fieldset></fieldset>
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<br>
<div>-- <br>
Javier CEREZO BASTIDA<br>
PhD Student<br>
Physical Chemistry<br>
Universidad de Murcia<br>
Murcia (Spain)<br>
Tel: <a href="tel:%28%2B34%29868887434" value="+34868887434" target="_blank">(+34)868887434</a>
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