AMBER Archive (2001)

Subject: error in sander

From: rathinavelan thenmalarchelvi (thenmalarvelan_at_hotmail.com)
Date: Wed Mar 21 2001 - 06:12:23 CST

Hello!,
  I am geting the following error while using "sander" of amber 6 in HP machine:
 
" vlimit exceeded for step  269334; vmax =   NAN

     COORDINATE RESETTING (SHAKE) WAS NOT ACCOMPLISHED
     WITHIN 3000 ITERATIONS "
(at 956.6ps)
 
 When I restarted the programe using the last restart file (955.0 ps) the program runs without any problem. I like to know whether I am using correct input for sander. Here is my input:
 

step13-PRODUCTION RUN
 &cntrl
 timlim=999999., nmropt=0,
 ntx=7,          irest=1,      ntrx=1,       ntxo=1,
 ntpr=100,       ntwx=500,     ntwv=0,       ntwe=10000,
 ioutfm=0,
 ntwprt=0,ntwr=500,

 ntf  =2,        ntb=2,        dielc=1.0,
 cut  =9.0,      nsnb=10,   
 scnb=2.0,       scee=1.2,    


 ipol=0,

 ibelly=0,       ntr=0,
 
 imin=0,
 maxcyc=1000,
 ncyc=5000,
 ntmin=1,        dx0=0.1,      dxm=0.5,       drms=0.0001

 nstlim=300000,
 ndfmin=0,       ntcm=1,       nscm=5000,
 t=0,            dt=0.002,

 temp0=300.0,    tempi=300.0,
 ig=71277,       heat=0.0,
 ntt=1,          dtemp=0.0,
 tautp=1.0,    
 vlimit=20.0,

 ntp=1,          pres0=1.0,    comp=44.6,
 taup=1.0,       npscal=1,
 
 ntc=2,          tol=0.000001,
 
 jfastw=0,

 ivcap=0,        matcap=0,     fcap=1.5,

 &end
 &ewald
 a=45.5184083,b=47.1546576,c=66.1120648,
 alpha=90.0, beta= 90.0,gamma= 90.0,
 order=4, ischrgd= 0, verbose=  0, ew_type=  0,
 dsum_tol=0.00001,nbtell=1,vdwmeth=1,nbflag=0,
 &end
  I will be verymuch thanmful  if anybody help me to solve the problem.

Thanks in advance

Thenmalar


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From ???@??? Wed Mar 21 11:56:13 2001 Received: from doves.llnl.gov (doves.llnl.gov [128.115.17.203]) by popcorn.llnl.gov (8.8.8/LLNL-3.0.2/pop.llnl.gov-5.2) with ESMTP id HAA14227 for ; Wed, 21 Mar 2001 07:41:03 -0800 (PST) Received: from pierce.llnl.gov (pierce.llnl.gov [128.115.41.100] (may be forged)) by doves.llnl.gov (8.9.3/LLNL-4.0) with ESMTP id HAA78299 for ; Wed, 21 Mar 2001 07:41:02 -0800 (PST) Received: from smtp-in-1.llnl.gov (smtp-in-1.llnl.gov [128.115.249.71]) by pierce.llnl.gov (8.8.8/LLNL-3.0.2/llnl.gov-5.1) with ESMTP id HAA08045 for ; Wed, 21 Mar 2001 07:40:56 -0800 (PST) Received: from socrates.cgl.ucsf.edu (localhost [127.0.0.1]) by smtp-in-1.llnl.gov (8.9.3/8.9.3/LLNL-gateway-1.0) with ESMTP id HAA00518 for ; Wed, 21 Mar 2001 07:40:55 -0800 (PST) Received: from cgl.ucsf.edu (cgl.ucsf.edu [128.218.27.20]) by socrates.cgl.ucsf.edu (8.9.3/8.9.3/GSC1.7) with ESMTP id HAA139436 for ; Wed, 21 Mar 2001 07:14:32 -0800 (PST) Received: from ccmailer.iitd.ac.in (IDENT:root@ccmailer.iitd.ac.in [202.141.68.10]) by cgl.ucsf.edu (8.9.3/8.9.3/GSC1.7) with ESMTP id HAA489898 for ; Wed, 21 Mar 2001 07:14:27 -0800 (PST) Received: from netearth.iitd.ac.in (IDENT:root@netearth.iitd.ac.in [10.10.2.4]) by ccmailer.iitd.ac.in (8.9.3/8.9.3) with ESMTP id UAA24024; Wed, 21 Mar 2001 20:46:17 +0530 Received: from localhost (adas@localhost) by netearth.iitd.ac.in (8.9.3/8.9.3) with ESMTP id UAA00973; Wed, 21 Mar 2001 20:46:15 +0530 Date: Wed, 21 Mar 2001 20:46:15 +0530 (IST) From: Achintya Das X-Sender: adas@netearth.iitd.ac.in To: "Sanjeev B.S." cc: The AMBER Mail Reflector , David Skinner Subject: RE: AMBER6 on IBMSP3 Installation In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-UIDL: 13fc8bad79c10ed8f7d2d71c9bfdeadc Replace the "&end" in your input file with a "/" IBM uses the slash to end namelists. -ad On Tue, 20 Mar 2001, Sanjeev B.S. wrote: > Dear Spraggins, > Thanks for your interest. I tried with this option but no > success... Is there anythingelse I might try? > > Best wishes, > -Sanjeev > > ___________________________________________________________________________ > > > NAMELIST is kind of strange with IBM's Fortran. There's an "old" format and > a "new" one. I believe you want the old one; the deafult is the new one. > > Try setting an environment variable: > > export XLFRTEOPTS="namelist=old" > > to force the run-time system to use the old format. There's also a > SETRTEOPTS call one can make in a program, but I've never tried that. > > Hope this helps. > > Tom Spraggins > tas@virginia.edu > > -----Original Message----- > From: Sanjeev B.S. [mailto:sanjeev@mbu.iisc.ernet.in] > Sent: Tuesday, March 20, 2001 9:07 AM > To: The AMBER Mail Reflector; David Skinner > Subject: AMBER6 on IBMSP3 Installation > > > Hello, > While trying to compile on IBM SP3 (with different MACHINE files > that I got from the mailing list), I face this typical problem. As I start > sander, it comes out with the error: > > --- > 1525-090 The NAMELIST READ statement cannot be completed because an > incorrect character was encountered in a NAMELIST group name or item name. > The program will recover by discontinuing further processing of the READ > statement. > --- > > It does one step in sander and then stops! Can anyone kindly let me know > how to go about this please? > > The input tested aganist AMBER5 succesfully (on SGI-Power Challange) was > used to test AMBER6 compilation. Also, with test runs with the sample > files that come with AMBER6, it gives the same error. So I presume that > this is not a problem with my input. > > Thanking you in advance, > -Sanjeev >