From chemistry-request@ccl.net Tue Aug 4 23:08:06 1992 Date: Tue, 4 Aug 92 21:36 EDT From: Subject: Strange problem with SHAKE To: chemistry@ccl.net Status: R Hi, I have recently written molecular dynamics code implementing the leapfrog integration scheme. Under the AMBER potential function, this code works wonderfully with the leapfrog integration scheme and the energy varies within + or - 0.1 kcal when simulating a 10 residue alanine helix. However, if I incorporate SHAKE, the temperature rapidly rises and the energy rapidly increases and the simulation essentially goes haywire. The actual SHAKE section appears to function correctly and I have turned off all bond forces. I have looked at the temperature of various atoms and it appears that the amino hydrogens first heat up, then the amino nitrogens and then the whole thing explodes. I have tried 1.5, 1.0, and 0.5 femtosecond timesteps to no avail. SHAKE tolerance is set to 5.0e-04. Any ideas? Scott Le Grand --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Tue Aug 4 07:09:45 1992 Received: by oscsunb.ccl.net (5.65c+KVa/920330.1102) id AA21295; Tue, 4 Aug 1992 05:56:34 -0400 Received: from DARWIN.NTU.EDU.AU by oscsunb.ccl.net (5.65c+KVa/920330.1102) id AA20980; Tue, 4 Aug 1992 05:30:18 -0400 Date: Tue, 4 Aug 1992 18:58:56 GMT From: B_DUKE@DARWIN.NTU.EDU.AU (Brian Duke) Message-Id: <920804185856.22a05b69@DARWIN.NTU.EDU.AU> Subject: GAUSSIAN on IBM RISC 220 To: chemistry@ccl.net X-Vmsmail-To: SMTP%"chemistry@ccl.net" Sender: chemistry-request@ccl.net Errors-To: owner-chemistry@ccl.net Precedence: bulk Status: R Does anyone have any experience with G90 or g92 on a IBM RISC 6000 220? I know it runs like a dream on the 320H, but I seem to be failing in putting together enough cash for a 320H and I may have to buy the 220. What do people think? Please e-mail me. I will summarise to the group. Many thanks. Brian. Brian Salter-Duke (Brian Duke) School of Chemistry and Earth Sciences, Northern Territory University GPO Box 40146, Casuarina, NT 0811, Australia. Phone 089-466702 FAX 089-410460 E-mail B_DUKE@DARWIN.NTU.EDU.AU --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net ---