After running this minimization when i did gmxcheck i got this output<br><br>trn version: GMX_trn_file (single precision)<br>Reading frame 0 time 9.000 <br># Atoms 4113<br>Reading frame 3 time 57.000 <br>
Timesteps at t=31 don't match (12, 26)<br>Reading frame 4 time 69.000 <br>Timesteps at t=57 don't match (26, 12)<br>Reading frame 14 time 192.000 <br>Timesteps at t=184 don't match (13, 8)<br>
Last frame 14 time 192.000 <br><br><br>Item #frames<br>Step 15<br>Time 15<br>Lambda 15<br>Coords 15<br>Velocities 0<br>Forces 0<br>Box 15<br>
<br><br>why is it saying that Timesteps at t=31 don't match (12, 26). <br><br><br><div class="gmail_quote">On Fri, Oct 21, 2011 at 12:25 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">On 21/10/2011 5:09 PM, aiswarya pawar wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi users,<br>
<br>
Iam running a minimization on protein complex in vacuum. i have set the parameters as following-<br>
<br>
; Lines starting with ';' ARE COMMENTS<br>
; Everything following ';' is also comment<br>
<br>
title = Energy Minimization ; Title of run<br>
<br>
; The following line tell the program the standard locations where to find certain files<br>
cpp = /lib/cpp ; Preprocessor<br>
<br>
<br>
; Define can be used to control processes<br>
define = -DFLEXIBLE<br>
<br>
; Parameters describing what to do, when to stop and what to save<br>
integrator = steepest ; Algorithm (steep = steepest descent minimization)<br>
emtol = 1000.0 ; Stop minimization when the maximum force < 1.0 kJ/mol<br>
emstep = 0.01<br>
nsteps = 50000 ; Maximum number of (minimization) steps to perform<br>
nstenergy = 1 ; Write energies to disk every nstenergy steps<br>
energygrps = Protein ; Which energy group(s) to write to disk<br>
<br>
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions<br>
nstxout = 1<br>
nstlist = 10 ; Frequency to update the neighbor list and long range forces<br>
ns_type = grid ; Method to determine neighbor list (simple, grid)<br>
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)<br>
coulombtype = cutoff ; Treatment of long range electrostatic interactions<br>
rcoulomb = 1.0 ; long range electrostatic cut-off<br>
rvdw = 1.4 ; long range Van der Waals cut-off<br>
constraints = none ; Bond types to replace by constraints<br>
pbc = no ; Periodic Boundary Conditions (yes/no)<br>
<br>
But from this i could write only 2 frames i need to increase the time frames, what is to be changed in the parameters.<br>
</blockquote>
<br></div></div>
This will write every frame of the EM, but if it only has two steps...<br>
<br>
Mark<br><font color="#888888">
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