AMBER Archive (2008)

Subject: RE: AMBER: Error: tutorial one for md simulation of DNA

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Sun Dec 21 2008 - 22:06:55 CST

hai !
Catein Catherine
you load your prmtop file
and then give .mdcrd
file and
in vmd in the determine file type
you give "Amber coordinates with periodic box "
and load it
and see
your problem is solved
all the best !
balaji
UOM
From: askamber23_at_hotmail.com
To: amber_at_scripps.edu
Subject: AMBER: Error: tutorial one for md simulation of DNA
Date: Mon, 22 Dec 2008 11:33:41 +0800

Dear Sir/madam,

 

I am trying to repeat the md simulation for DNA with explicit water. I downloaded the prmtop, in files and do the min1, min2 and md1, md2 calculations according to the tutorial one. The jobs finished without error message. However, when I try to open the mdcrd files with vmd, I found all the atoms becomes scattered lines. Should I view the conformational changes in the mdcrd file with vmd? If yes, did I do anything wrong for the calculation?

 

At the end of the md2 out file, the following results were obtained.

 

check COM velocity, temp: 0.002531 0.01(Removed)

 NSTEP = 50000 TIME(PS) = 120.000 TEMP(K) = 303.86 PRESS = 262.4
 Etot = -27630.7594 EK!
 tot = 5899.1449 EPtot = -33529.9044
 BOND = 163.6482 ANGLE = 356.2195 DIHED = 461.3867
 1-4 NB = 164.1768 1-4 EEL = -350.1289 VDWAALS = 4077.8193
 EELEC = -38403.0260 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 2672.8728 VIRIAL = 2131.6828 VOLUME = 95519.1218
                                                    Density = 1.0416
 !
 ;Ewald error estimate: &nb
sp; 0.1550E-03
 ------------------------------------------------------------------------------

      A V E R A G E S O V E R 50000 S T E P S

 NSTEP = 50000 TIME(PS) = 120.000 TEMP(K) = 300.06 PRESS = -82.5
 Etot = -27586.0309 EKtot = 5825.2866 EPtot = -33411.3174
 BOND = 154.8456 ANGLE = 341.0208 DIHED = 457.3059
 1-4 NB = 167.4940 1-4 EEL = -352.5464 VDWAALS = 3859.0566
 EELEC = -38038.4939 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 2679.1492 VIRIAL = 2866.2955 VOLUME = 96791.2622
                                                    Density =<
SPAN style="mso-spacerun: yes"> 1.0292
 Ewald error estimate: 0.1106E-03
 ------------------------------------------------------------------------------

      R M S F L U C T U A T I O N S

 NSTEP = 50000 TIME(PS) = 120.000 TEMP(K) = !
   3.06 PRESS = 308.1
 Etot = 252.3080 EKtot = 59.4670 EPtot = 231.2448
 BOND = 10.2171 ANGLE = &nbs
p; 14.4065 DIHED = 8.8177
 1-4 NB = 4.7542 1-4 EEL = 13.2158 VDWAALS = 91.2265
 EELEC = 288.2691 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 39.7943 VIRIAL = 679.3842 VOLUME = 3532.2646
      &nb!
 sp; Density = 0.0337
 Ewald error estimate: 0.8365E-04
 ------------------------------------------------------------------------------

 

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