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Hi Steven<br>
<br>
You've tried with "constraints = none", but that still keeps
constraints over water molecules through SETTLE algorithm. Maybe you
can try a minimization with "define = -DFLEXIBLE" to remove settle
over water and then try again a constraint (settle) minimization.<br>
<br>
Javier<br>
<br>
El 18/05/12 12:58, Steven Neumann escribió:
<blockquote
cite="mid:CAKZJqQEeZNZ1siNZ+ekDq_zfUnnNqcLhnrvGAhVqfezDoUeHjQ@mail.gmail.com"
type="cite">Dear Gmx Users,<br>
<br>
My system consists of a Tube made of Oxygen, Hydrogen and ions.
These atoms are not connected via bonds. I try tu run EM:<br>
<br>
; minim.mdp - used as input into grompp to generate em.tpr<br>
; Parameters describing what to do, when to stop and what to save<br>
<br>
integrator = steep ; Algorithm (steep = steepest descent
minimization)<br>
emtol = 1000.0 ; Stop minimization when the maximum
force < 1000.0 kJ/mol/nm<br>
emstep = 0.001 <br>
nsteps = 50000 ; Maximum number of (minimization) steps
to perform<br>
nstxout = 1<br>
; Parameters describing how to find the neighbors of each atom and
how to calculate the interactions<br>
nstlist = 1 ; Frequency to update the neighbor list and
long range forces<br>
ns_type = grid ; Method to determine neighbor list
(simple, grid)<br>
rlist = 1.4 ; Cut-off for making neighbor list
(short range forces)<br>
coulombtype = PME ; Treatment of long range
electrostatic interactions<br>
rcoulomb = 1.4 ; Short-range electrostatic cut-off<br>
rvdw = 1.4 ; Short-range Van der Waals cut-off<br>
pbc = xyz ; Periodic Boundary Conditions (yes/no)<br>
<br>
freezegrps = TUB<br>
freezedim = Y Y Y<br>
<br>
<br>
Then a lot of errors "water molecule on atom X cannot be settled".
I tried:<br>
<br>
1. constraints = none<br>
<br>
2. remove those water molecules - then other water molecules have
the same error<br>
<br>
3. using nstxout =1 in VMD, I could observe that some of the
molecules facing this error split in one frame (hydrogens 7A away
from oxygen) or spin around 180 degrees - it depends.<br>
<br>
4. I tried increase vdwradii of the atoms which form my Tube so
they wont overlap with water<br>
<br>
<br>
If you have any suggestions I will really appreciate,<br>
<br>
Steven<br>
<br>
<br>
<br>
<br>
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<br>
</blockquote>
<br>
<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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