<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Yang,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>You might indeed be right. Since you already have a testsystem - it would be great if you could file it as a bug in bugzilla.gromacs.org, and I'll fix it before releasing 3.3.1.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Erik</DIV><DIV><BR><DIV><DIV>On Oct 18, 2005, at 8:53 PM, Yang Ye wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"> 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> </BLOCKQUOTE> </BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use the<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV> </BLOCKQUOTE></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV>-----------------------------------------------------------</DIV><DIV>Erik Lindahl <<A href="mailto:lindahl@sbc.su.se">lindahl@sbc.su.se</A>></DIV><DIV>Assistant Professor, Stockholm Bioinformatics Center</DIV><DIV>Stockholm University, SE 106 91 Stockholm</DIV><DIV>Phone: +46 8 5537 8564 Fax: +46 8 5537 8214</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN> </DIV><BR></DIV></BODY></HTML>