hello gmx users,<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 id=":vp">-----------------------------------------<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 class="yj6qo ajU"><div id=":2" class="ajR" tabindex="0">
<img class="ajT" src="https://mail.google.com/mail/u/0/images/cleardot.gif"></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 class="h5"><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 class="HOEnZb"><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>
<br>--<br>
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