Mark,<br><div class="gmail_quote"><br><br>My restrains on topology consist of the next section<br><br>; Include Position restraint file<br>#ifdef POSRES<br>#include "posre.itp"<br>#endif<br><br>[ dihedral_restraints ]<br>
; ai aj ak al type label phi dphi kfac power<br>; Chi N - CA - CB - CG<br> 2908 2910 2911 2912 1 1 180 0 1 2<br><br>[ distance_restraints ]<br>; ai aj type index type’ low up1 up2 fac<br>
1097 3201 1 1 1 0.796 0.841 0.900 1.0<br> 2948 3201 1 2 1 0.796 0.841 0.900 1.0<br> 1097 2948 1 3 1 0.796 0.841 0.900 1.0<br> 1097 2999 1 4 1 0.800 1.000 1.100 1.0<br> 1098 2034 1 5 1 0.800 1.000 1.100 1.0<br>
1098 2042 1 6 1 0.800 1.000 1.100 1.0<br> 1098 2067 1 7 1 0.800 1.000 1.100 1.0<br> 1130 3241 1 8 1 0.540 0.630 0.700 1.0<br> 546 3393 1 9 1 1.162 1.725 1.800 1.0<br> 628 3460 1 10 1 1.438 2.067 2.100 1.0<br>
637 3460 1 11 1 0.700 1.238 1.300 1.0<br> 648 2791 1 12 1 1.788 2.152 2.200 1.0<br> 648 3376 1 13 1 1.736 2.061 2.150 1.0<br> 2292 2743 1 14 1 0.200 0.300 0.350 1.0<br> 1258 2203 1 15 1 0.200 0.300 0.350 1.0<br>
<br>Also I've attached my md.mdp file.<br><br>I have no problems with that system on my home desktop.<br><br>On cluster with installed MPI I've lunch my simulation by means of below command<br><br>grompp -f md.mdp -c nvtWprotonated.gro -p topol.top -n index.ndx -o md_50ns.tpr<br>
<br>mpiexec -np 24 mdrun_mpi_d.openmpi -v -deffnm md_50ns<br><br><br>I'll be very thankful if you show me what's wrong could be with my initial systems because I have no any problems with my systems on my home desktop. On the other hand on Cluster some of my jobs ends with the errors ( something wrong with PME order or the error wich I've shown you with the ensembles of restrains)<br>
<br>It was installed the same last version of Gromacs on cluster like on my desctop ( difference only in double precission with lack on my home desctop but present on cluster)<br><br>Could you tell me in what log files I could obtain more detailed information of the source of such erors? I've checked only md.log as well as name_of_the_simulation.log. Besides there are files gromacs.err wich contain information about crashed simulation.<div class="im">
<br>
<br><br>Thanks for help again,<br><br><br>James<br><br></div><div class="gmail_quote">14 марта 2012 г. 16:10 пользователь Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> написал:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div class="im"><div>
You're probably doing something wrong, but in the absence of a
command line and your .top file fragment, we can't possibly know.</div><div><br>
<br></div></div><div><div class="h5"><span><font color="#888888">
Mark</font></span><div><div><br>
<br>
<blockquote type="cite">
<br>
Thanks for help again,<br>
<br>
<br>
James<br>
<br>
<div class="gmail_quote">14 марта 2012 г. 10:50 пользователь James
Starlight <span dir="ltr"><<a href="mailto:jmsstarlight@gmail.com" target="_blank">jmsstarlight@gmail.com</a>></span>
написал:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Mark, thanks
for explanation.<br>
<br>
So if I understood that graph correctly I must define R1=1 and
R2=2 values from my example 1<Rij<2 to obtain quadratic
restrain forces done in my distance range ( from 1 to 2
angstr). In other words this would restrains the i and j atom
to the desired distance by the force wich would increased by
the quadratic progresion upon distance will increased up to 2.
Does it correct ?<br>
<br>
So the value R0 ( no forces= no restraints) must correspond to
the values above and below my range. How the same range value
for R0 could be defined ?<br>
<br>
<br>
JAmes<br>
<br>
<div class="gmail_quote">14 марта 2012 г. 3:42 пользователь
Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
написал:
<div>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
<br>
I can't think of a clearer way to explain the functional
form of the distance restraint than the given equation
with an example graph of it nearby. You have some
distance range that you want to see happen based on some
external information. You need to choose the distance
constants for that functional form to reproduce that in
a way that you judge will work, given your initial
distance. The linear regime above r_2 is useful for not
having forces that are massively large (from a quadratic
potential) far from the region of zero potential.
Whether this is important depends on your starting
configuration.
<div>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I already answered this.<br>
<a href="http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html</a><br>
</blockquote>
I've found only theoretical explanation of such
possibility (<br>
gradually increasing force constant during
simulation). But I<br>
intresting in practical implementation. Could I do
it in scope of<br>
single MDrun by some options in mdm fle or should I
do step-by-step<br>
series of simulation with gradually changing forces
appplied on the<br>
disres in each MDrun?<br>
</blockquote>
<br>
</div>
Only step by step. Something like simulated annealing is
only available for temperature variation.<br>
<br>
Mark<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
James<br>
</blockquote>
<div>
<div>
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