http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php CHARMM forums: QM/MM discussions and questions CHARMM Forums - UBB.threads(tm) http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27741#Post27741 Posted by farawayyy:
Dear all, I just found out where the problem is. The auto-generated input files from CHARMM-GUI use "flex" option in "read parm" command. If I remove all "flex" options and join all rtf files into one big rtf file, this error disappeared. (w]]> Sun, 26 Jun 2011 00:49:39 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27698#Post27698 Posted by kuku:
Dear all, I am doing umbrella sampling and want to understand how the energy terms originate. DYNA DYN: Step Time TOTEner TOTKe ENERgy TEMPerature DYNA PROP: GRMS HFCTote HFCKe EHFCor ]]> Mon, 20 Jun 2011 22:56:52 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27523#Post27523 Posted by Milla:
Dear Lennart, Many thanks for the swift response. I just assumed that the warnings referred to the two parameters I was assigning and didn't have the fortran knowledge to realise what was going on from the code. thanks again. ]]> Mon, 23 May 2011 12:02:07 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27437#Post27437 Posted by eagle:
Dear all, Recently, I want to investigate a enzyme reaction using QM/MM (ES--TS--PS--P+S). Experimentally, the primary isotope effects on the kinetic constants and the effects of changes in solvent viscosity are consistent with product releas]]> Sat, 07 May 2011 00:57:25 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27209#Post27209 Posted by rmv:
Well, it does seem a bit looney to use BOMLEV -3 even in this case, since one can avoid the errors by using SHAKE after PERT, as suggested.]]> Fri, 15 Apr 2011 00:09:46 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27123#Post27123 Posted by eagle:
thank Lennart...]]> Tue, 12 Apr 2011 00:55:58 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=26821#Post26821 Posted by indian_user:
Hi, I'm running a simulation with one water molecule in a box using the squantum of CHARMM. I select this water molecule as a QM molecule. Just two questions, 1)Does the 'REMO' remove the electrostatic but not the Van der Waals interacti]]> Thu, 17 Mar 2011 20:35:38 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=26615#Post26615 Posted by mariangela:
In other words, with SQUANTUM one has to use REMO to avoid double-counting these energies,is this correct? Was the same true in the older QUANTUM module? Thanks, Mariangela]]> Wed, 23 Feb 2011 11:56:23 CST http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=26435#Post26435 Posted by ashley:
I have had a similar problem, which I posted about in the CHARMM/Q-Chem section. My theory is that when the pressure is calculated the QM atoms are not included at all and therefore it thinks there is a big hole in the middle of your box and should ]]> Thu, 03 Feb 2011 14:34:38 CST http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=26093#Post26093 Posted by radish:
BTW, when there's no solvent, but only QM part in the system, the minimization output shows: MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI QUANTUM: QMELec QMVDw ---------- --------- --------- ]]> Tue, 28 Dec 2010 13:44:00 CST