[AMBER] Problem with folding simulation

From: <moitrayee.mbu.iisc.ernet.in>
Date: Wed, 10 Apr 2013 07:37:43 +0530 (IST)

Dear Amber Users,
I am trying to follow the protocols in
http://ambermd.org/tutorials/basic/tutorial3 to obtain some conformational
sampling for a small peptide of my interest. It turns out that during the
heating stages (~250K), the total energy of the system becomes +ve. I am heating
it upto 310K and I have pasted below the snapshots from the last heating run. I
am following the protocol in the tutorial.

 NSTEP = 39950 TIME(PS) = 49.975 TEMP(K) = 310.94 PRESS = 0.0
 Etot = 221.9592 EKtot = 457.8622 EPtot = -235.9030
 BOND = 122.9774 ANGLE = 355.1161 DIHED = 464.4054
 1-4 NB = 122.0431 1-4 EEL = 1446.9111 VDWAALS = -166.7690
 EELEC = -2024.7384 EGB = -555.8486 RESTRAINT = 0.0000
 ------------------------------------------------------------------------------


   KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000

   Translational and rotational motion removed

   KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000

 NSTEP = 40000 TIME(PS) = 50.000 TEMP(K) = 306.34 PRESS = 0.0
 Etot = 222.0932 EKtot = 451.0901 EPtot = -228.9969
 BOND = 116.2790 ANGLE = 351.3472 DIHED = 469.2875
 1-4 NB = 118.3938 1-4 EEL = 1474.4917 VDWAALS = -165.3935
 EELEC = -2042.9887 EGB = -550.4139 RESTRAINT = 0.0000
 ------------------------------------------------------------------------------
Any comments would be greatly appreciated.

Many thanks and Best Regards,
Moitrayee


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 09 2013 - 19:00:03 PDT
Custom Search