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David van der Spoel wrote:
<blockquote cite="mid1096882137.24197.6.camel@vangogh.bmc.uu.se"
type="cite">
<pre wrap="">On Mon, 2004-10-04 at 08:13, Hector Mrz-Seara Monne wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Thank you David for your help, I'm quite new in gromacs and many things
still lack on
my knowledge. Well I'm trying to reduce all the constants forces in the
*.itp file of my monomer.
By the way, the only constants that worry you where those of the
improper dihedral or also of the proper once
with the asterisk. And why PRODRG duplicate the colums of definitions
(c0 c1 m) (c0 c1 m)
, this is normal(this confuses me since the beginning)?
</pre>
</blockquote>
<pre wrap=""><!---->This has to do with free energy calculations where you go from one
definition to another. Does prodrg produce the m for impropers as well?
</pre>
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<br>
Hi david,<br>
<br>
All contants forces definition provide from PRODRG, the number 1673 is
the given by the program<br>
but for your coments is quite hight. Sorry, but for your answer I can't
know if you think I have also problems<br>
with the proper dihedral also, Can you clarify this point please. <br>
<br>
Thanks in advance for all your help.<br>
<br>
Hector
<blockquote cite="mid1096882137.24197.6.camel@vangogh.bmc.uu.se"
type="cite">
<pre wrap=""></pre>
<blockquote type="cite">
<pre wrap="">Thanks.
I've been looking for the configuration of my fonts and everything seems
to be allright. I'm using the netscape mail. I don't know
what is hapenning but I'll try to fix this problem in the near future
<a class="moz-txt-link-abbreviated" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> wrote:
</pre>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">Try equilibrating at lower temperature and/or with a shorter time step.
In particular since you describe this resonance thing. Could it be that
your force constants are too high? You should have roughly 20 time steps
in a complete period of the fastest motion.
</pre>
</blockquote>
<pre wrap="">Thanks in advance for all your help, it's been quite useful for me in
order to increase my knowledge on this suite.
I've been thinking in the last suggestion and I'm not sure about the
meaning. As I understand if I use high constants
for defining my proper dihedrals I have to reduce my time steep that
actually is quite small 1fs only or work at lower temperature.
Here the *.itp file of the monomer contain this lines that I have
specifically modify to have a planarity system.
</pre>
</blockquote>
<pre wrap="">First off, please turn off the weird fonts in your mail...
In the improper definition below there are too many force constants,
i.e. the thirs and sixth number (m) should go. Further the force
constant is ten times higher than usual which means vibrations will be
sqrt(10) times faster, which again means you will have to reduce the
timestep. Reducing the force constant by a factor of ten will be fine
too.
</pre>
<blockquote type="cite">
<pre wrap="">.....
[ dihedrals ]
;ai aj ak al fu c0 c1 m c0 c1 m
9 12 10 8 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBA CAD
CAE CAU
14 15 13 11 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBB NAV
CAF CAG
17 16 20 18 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBC NAW
CAH CAI
22 23 21 19 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBD OAY
CAJ CAK
27 26 29 28 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAZ CAT
OAX OAC
17 18 19 22 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBC CAI
CAK CBD
18 19 22 21 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAI CAK
CBD CAJ
19 22 21 20 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAK CBD
CAJ CAH
22 21 20 17 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBD CAJ
CAH CBC
21 20 17 18 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAJ CAH
CBC CAI
20 17 18 19 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAH CBC
CAI CAK
9 10 11 14 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBA CAE
CAG CBB
10 11 14 13 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAE CAG
CBB CAF
11 14 13 12 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAG CBB
CAF CAD
14 13 12 9 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBB CAF
CAD CBA
14 15 17 16 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBB NAV
CBC NAW
13 12 9 10 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAF CAD
CBA CAE
12 9 10 11 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAD CBA
CAE CAG
4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; DI
CAN CAM CAL CAA
.....
11 14 15 16 1 180.0 53.5 2 180.0 33.5 2 ; DI CAG CBB
NAV NAW *
15 16 17 20 1 180.0 53.5 2 180.0 33.5 2 ; DI NAV NAW
CBC CAH *
.....
25 26 27 29 1 0.0 0.4 6 0.0 0.4 6 ; DI CAR
CAT CAZ OAX
26 27 29 30 1 180.0 16.7 2 180.0 16.7 2 ; DI CAT CAZ
OAX HE2 *
Do you know if your advise works equally for both proper and improper
dihedrals? If not can you tell me the diference?
I think for your coment that the dihedral with the asterisk that are
the problematic? witch time step will you use, or do you know any
way to avoid the restriction that my system contain?
Thank you very much for taking your time to answer me, David. If you
think you need any other information or that is not clear what
I'm asking for just tell me and I can send you any indormation or
foles that you thing could be usefull to solve my actual problems
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