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no. I suspect there is a bug in grompp. I have specified comb-rule 3
for my FF but grompp used rule 1.<br>
<br>
Yang Ye<br>
<br>
David wrote:
<blockquote
cite="mid1129661017.5916.6.camel@217-208-143-88-o1123.tbon.telia.com"
type="cite">
<pre wrap="">On Wed, 2005-10-19 at 02:34 +0800, Yang Ye wrote:
</pre>
<blockquote type="cite">
<pre wrap="">After checking, I found that grompp has used comb-rule 1 for
generating LJ.
</pre>
</blockquote>
<pre wrap=""><!---->So problem solved?
</pre>
<blockquote type="cite">
<pre wrap="">Yang Ye
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 no 0.5 0.833333
Erik Lindahl wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Yang,
Please include the header [defaults] section from your forcefield.
The number of columns is flexible, since both atomic number and
bonded_atomtype fields are optional.
Cheers,
Erik
On Oct 18, 2005, at 7:25 PM, Yang Ye wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
I have found that 3.3's grompp generates drastically different
LJ_SR and LJ14 parameters for one of my self-defined forcefield
(converted from AMBER).
>From gmxdump,
(3.3's tpr) tpx version 40
ntypes=72
functype[0]=LJ_SR, c6= 2.24468820e-20, c12=
3.18825866e-35
functype[1]=LJ_SR, c6= 1.61870333e-32, c12= 0.00000000e
+00
functype[2]=LJ_SR, c6= 1.43123863e-20, c12=
1.22953165e-35
functype[3]=LJ_SR, c6= 1.17580789e-26, c12= 0.00000000e
+00
...
They should be
(3.3b's tpr) tpx version 32
ntypes=72
functype[0]=LJ_SR, c6= 3.35273775e-03, c12=
3.95092275e-06
functype[1]=LJ_SR, c6= 8.76983977e-05, c12=
8.89523299e-09
functype[2]=LJ_SR, c6= 3.08322068e-03, c12=
4.16509010e-06
functype[3]=LJ_SR, c6= 4.73846623e-04, c12=
2.59686658e-07
...
My ffambernb.itp is
[ atomtypes ]
;name mass charge ptype c6 c12
H 1.008 0.000 A 3.9229141156e-07
5.8568793913e-13
HO 1.008 0.000 A 0.0000000000e+00 0.0000000000e
+00
...
[ nonbond_params ]
; i j func c6 c12
H H 1 3.9229141156e-07 5.8568793913e-13
H HO 1 0.0000000000e+00 0.0000000000e+00
H HS 1 3.9229141156e-07 5.8568793913e-13
...
[ nonbond_params ]
; i j func c6 c12
H H 1 3.9229141156e-07 5.8568793913e-13
H HO 1 0.0000000000e+00 0.0000000000e+00
H HS 1 3.9229141156e-07 5.8568793913e-13
...
I found that FF provided by gromacs has different column width. Is
this the reason?
Thanks.
Yang Ye
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</pre>
</blockquote>
<pre wrap="">-----------------------------------------------------------
Erik Lindahl <a class="moz-txt-link-rfc2396E" href="mailto:lindahl@sbc.su.se"><lindahl@sbc.su.se></a>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564 Fax: +46 8 5537 8214
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</pre>
</blockquote>
<pre wrap="">--
Regards,
Yang Ye
Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Singapore
Tel: 6316-2884
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</pre>
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