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After checking, I found that grompp has used comb-rule 1 for generating
LJ.<br>
<br>
Yang Ye<br>
<br>
<tt>[ defaults ]<br>
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>
1 3 no 0.5 0.833333</tt><br>
<br>
Erik Lindahl wrote:
<blockquote cite="midB962A89D-0BE8-4473-A84B-BB65AF4E947D@sbc.su.se"
type="cite">Hi Yang, <br>
<br>
Please include the header [defaults] section from your forcefield. <br>
<br>
The number of columns is flexible, since both atomic number and
bonded_atomtype fields are optional. <br>
<br>
Cheers, <br>
<br>
Erik <br>
<br>
On Oct 18, 2005, at 7:25 PM, Yang Ye wrote: <br>
<br>
<blockquote type="cite">Hi, <br>
<br>
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). <br>
<br>
>From gmxdump, <br>
(3.3's tpr) tpx version 40 <br>
ntypes=72 <br>
functype[0]=LJ_SR, c6= 2.24468820e-20, c12= 3.18825866e-35 <br>
functype[1]=LJ_SR, c6= 1.61870333e-32, c12= 0.00000000e+00 <br>
functype[2]=LJ_SR, c6= 1.43123863e-20, c12= 1.22953165e-35 <br>
functype[3]=LJ_SR, c6= 1.17580789e-26, c12= 0.00000000e+00 <br>
... <br>
<br>
They should be <br>
(3.3b's tpr) tpx version 32 <br>
ntypes=72 <br>
functype[0]=LJ_SR, c6= 3.35273775e-03, c12= 3.95092275e-06 <br>
functype[1]=LJ_SR, c6= 8.76983977e-05, c12= 8.89523299e-09 <br>
functype[2]=LJ_SR, c6= 3.08322068e-03, c12= 4.16509010e-06 <br>
functype[3]=LJ_SR, c6= 4.73846623e-04, c12= 2.59686658e-07 <br>
... <br>
<br>
My ffambernb.itp is <br>
[ atomtypes ] <br>
;name mass charge ptype c6 c12 <br>
H 1.008 0.000 A 3.9229141156e-07 5.8568793913e-13 <br>
HO 1.008 0.000 A 0.0000000000e+00 0.0000000000e+00 <br>
... <br>
[ nonbond_params ] <br>
; i j func c6 c12 <br>
H H 1 3.9229141156e-07 5.8568793913e-13 <br>
H HO 1 0.0000000000e+00 0.0000000000e+00 <br>
H HS 1 3.9229141156e-07 5.8568793913e-13 <br>
... <br>
[ nonbond_params ] <br>
; i j func c6 c12 <br>
H H 1 3.9229141156e-07 5.8568793913e-13 <br>
H HO 1 0.0000000000e+00 0.0000000000e+00 <br>
H HS 1 3.9229141156e-07 5.8568793913e-13 <br>
... <br>
<br>
I found that FF provided by gromacs has different column width. Is
this the reason? <br>
<br>
Thanks. <br>
<br>
Yang Ye <br>
<br>
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<br>
</blockquote>
<br>
----------------------------------------------------------- <br>
Erik Lindahl <a class="moz-txt-link-rfc2396E"
href="mailto:lindahl@sbc.su.se"><lindahl@sbc.su.se></a> <br>
Assistant Professor, Stockholm Bioinformatics Center <br>
Stockholm University, SE 106 91 Stockholm <br>
Phone: +46 8 5537 8564 Fax: +46 8 5537 8214 <br>
<br>
<br>
<br>
<br>
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</blockquote>
<br>
<div class="moz-signature">-- <br>
<i>Regards,</i><br>
Yang Ye<br>
<small><i>Computational Biology Lab<br>
School of Biological Sciences<br>
Nanyang Technological University<br>
Singapore<br>
Tel: 6316-2884<br>
</i></small>
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