AMBER Archive (2008)

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

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Sun Dec 21 2008 - 23:12:32 CST

Dear Balaji,
 
Thank you very much for your help. I have made such a stupid error.
 
Best regards,
 
Annie

From: balaji_sethu_at_hotmail.comTo: amber_at_scripps.eduSubject: RE: AMBER: Error: tutorial one for md simulation of DNADate: Mon, 22 Dec 2008 09:36:55 +0530

hai ! Catein Catherineyou load your prmtop fileand 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 ! balajiUOM

From: askamber23_at_hotmail.comTo: amber_at_scripps.eduSubject: AMBER: Error: tutorial one for md simulation of DNADate: 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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