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From the output it looks like you forgot the --without-qmmm-gaussian
flag while compiling.<br>
<br>
Micha<br>
On 07/11/11 14:42, xi zhao wrote:
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<div>When remove these lines, the errros still :Fatal
error:<br>
Invalid QMMM input: 1 groups 0 basissets and 0 methods;</div>
<div>when put something there, (<br>
QMmethod =rhf;QMbasis =sto-3g), <br>
<br>
grompp_a -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o
pyp_qm.tpr -maxwarn 10</div>
<div> </div>
<div>mpirun -np 8 mdrun_a -v -s pyp_qm.tpr </div>
<div>......</div>
<div>Back Off! I just backed up md.log to ./#md.log.7#<br>
Getting Loaded...<br>
Reading file pyp_qm.tpr, VERSION 4.5.3 (double
precision)<br>
Loaded with Money</div>
<div>QM/MM calculation requested.<br>
QM/MM calculation requested.<br>
QM/MM calculation requested.<br>
QM/MM calculation requested.<br>
QM/MM calculation requested.<br>
QM/MM calculation requested.<br>
there we go!<br>
QM/MM calculation requested.<br>
QM/MM calculation requested.<br>
there we go!<br>
there we go!<br>
there we go!<br>
there we go!<br>
there we go!<br>
there we go!<br>
there we go!<br>
Layer 0<br>
nr of QM atoms 22<br>
QMlevel: RHF/STO-3G</div>
<div>number of CPUs for gaussian = 1<br>
memory for gaussian = 50000000<br>
accuracy in l510 = 8<br>
NOT using cp-mcscf in l1003<br>
Level of SA at start = 0<br>
-----------------------------------------------------------------------------<br>
One of the processes started by mpirun has exited with a
nonzero exit<br>
code. This typically indicates that the process
finished in error.<br>
If your process did not finish in error, be sure to
include a "return<br>
0" or "exit(0)" in your C code before exiting the
application.</div>
<div>PID 11786 failed on node n0 (127.0.0.1) due to signal
11.</div>
<div> </div>
<div>how to deal with?</div>
<div><a moz-do-not-send="true" class="plink"
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--- <b>11年11月7日，周一, Gerrit Groenhof <i><a class="moz-txt-link-rfc2396E" href="mailto:ggroenh@gwdg.de"><ggroenh@gwdg.de></a></i></b>
写道：<br>
</div>
<blockquote style="BORDER-LEFT: rgb(16,16,255) 2px solid;
PADDING-LEFT: 5px; MARGIN-LEFT: 5px"><br>
发件人: Gerrit Groenhof <a class="moz-txt-link-rfc2396E" href="mailto:ggroenh@gwdg.de"><ggroenh@gwdg.de></a><br>
主题: [gmx-users] Re 1. orca and qm/mm (xi zhao)<br>
收件人: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
日期: 2011年11月7日,周一,下午9:23<br>
<br>
<div class="plainMail">Try to remove these lines, or put
something there. The input is ignored, but since
strings are used as input (for use in multui-layer
oniom), leaving blank causes an error.<br>
<br>
Gerrit<br>
On 7 Nov 2011, at 14:21, <a moz-do-not-send="true"
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wrote:<br>
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> 1. orca and qm/mm (xi zhao)<br>
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----------------------------------------------------------------------<br>
> <br>
> Message: 1<br>
> Date: Mon, 7 Nov 2011 20:54:04 +0800 (CST)<br>
> From: xi zhao <<a moz-do-not-send="true"
href="http://cn.mc151.mail.yahoo.com/mc/compose?to=zhaoxiitc2002@yahoo.com.cn"
ymailto="mailto:zhaoxiitc2002@yahoo.com.cn">zhaoxiitc2002@yahoo.com.cn</a>><br>
> Subject: [gmx-users] orca and qm/mm<br>
> To: <a moz-do-not-send="true"
href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org"
ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> Message-ID:<br>
> <<a moz-do-not-send="true"
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> Content-Type: text/plain; charset="utf-8"<br>
> <br>
> All users:<br>
> <br>
> <br>
> According to <a moz-do-not-send="true"
href="http://wwwuser.gwdg.de/%7Eggroenh/qmmm.html#code"
target="_blank">http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code</a>,
I want to build qm/mm calculation by using gromacs
4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH
and BASENAME.ORCAINFO as told in the instruction. <br>
> BASENAME=pyp_qm<br>
> here is the BASENAME.ORCAINFO file:<br>
> ! RKS B3LYP/G SV(P) TightSCF Opt<br>
> <br>
> here is the md file:<br>
> integrator = md<br>
> tinit = 0<br>
> dt = 0.001<br>
> nsteps = 500<br>
> nstcomm = 1<br>
> comm_grps = system<br>
> <br>
> emtol = 100.0<br>
> emstep = 0.001<br>
> nstcgsteep = 50<br>
> <br>
> nstxout = 1<br>
> nstvout = 1<br>
> nstfout = 1<br>
> nstlog = 1<br>
> nstenergy = 1<br>
> nstxtcout = 1<br>
> xtc_grps = system<br>
> energygrps = QMatoms rest_Protein
SOL<br>
> <br>
> nstlist = 10<br>
> ns_type = grid<br>
> pbc = xyz<br>
> rlist = 1.0<br>
> <br>
> coulombtype = cut-off<br>
> rcoulomb = 1.4<br>
> epsilon_r = 1<br>
> vdwtype = Cut-off<br>
> rvdw = 1.4<br>
> <br>
> tcoupl = berendsen<br>
> tc-grps = rest_Protein SOL
QMatoms<br>
> tau_t = 0.1 0.1 0 ; QM atoms
are uncoupled<br>
> ref_t = 300 300 300<br>
> Pcoupl = Berendsen<br>
> pcoupltype = isotropic<br>
> tau_p = 1.0<br>
> compressibility = 4.5e-5<br>
> ref_p = 1.0<br>
> <br>
> free_energy = no<br>
> init_lambda = 0<br>
> delta_lambda = 0<br>
> QMMM = yes<br>
> QMMM-grps = QMatoms<br>
> QMmethod =<br>
> QMbasis =<br>
> QMMMscheme = normal<br>
> QMcharge = -1<br>
> CASelectrons =<br>
> CASorbitals =<br>
> SH =<br>
> <br>
> gen_vel = no<br>
> gen_temp = 300<br>
> gen_seed = 173529<br>
> <br>
> constraints = all-bonds<br>
> constraint_algorithm = LINCS<br>
> unconstrained_start = yes<br>
> shake_tol = 0.0001<br>
> lincs_order = 4<br>
> lincs_warnangle = 30<br>
> morse = no<br>
> According to the instruction “In the
ORCAINFO-file the method, basis set and all other
ORCA-specific keywords must be given. (This also means
that QMmethod and QMbasis from the mdp-file are
ignored).”, the QMmethod and QMbasis are blank, <br>
> But When grompp<br>
> grompp_c -f pyp.mdp -c pyp.gro -p pyp.top -n
pyp.ndx -o pyp_qm.tpr<br>
> ……….<br>
> Fatal error:<br>
> Invalid QMMM input: 1 groups 0 basissets and 0
methods.<br>
> <br>
> How to deal with it? Please help me!<br>
> <br>
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