[AMBER] RMS Fluctuation limit and difference in Temperature maximum Density (TMD)

From: Zafar,Muhammad Saqlain via AMBER <amber.ambermd.org>
Date: Tue, 18 Jul 2023 04:09:36 +0000

Hello Everyone,

I have been new to AMBER. i start simulating water model TIP4P-EW to calculate the Temperature maximum Density (TMD) .
While running NPT for 10ns with 512 water molecule i got the density out file (eq.out) with higher density than that of previous work already done

previous work TMD 0.998
My simulation result TMD 1.0656


  1. what could be the reason of this difference ?
  2. what is the RMS fluctuation limit for density, pressure & Temperature in NPT ? Below is my RMS fluctuation data comes from eq.out file after running 10ns NPT.


R M S F L U C T U A T I O N S

 NSTEP = 10000000 TIME(PS) = 10000.000 TEMP(K) = 4.14 PRESS = 511.8
 Etot = 153.9831 EKtot = 18.9400 EPtot = 155.3859
 BOND = 67.4032 ANGLE = 0.0000 DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 78.4465
 EELEC = 280.3686 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 14.0403 VIRIAL = 175.0029 VOLUME = 2899.7105
                                                    Density = 0.1092

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Received on Mon Jul 17 2023 - 21:30:02 PDT
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