[AMBER] RAMD question (Xiaodong Wu)

From: <18xdwu.stu.edu.cn>
Date: Fri, 5 Feb 2021 09:19:57 +0000

Dear all,
I run RAMD by using Amber 20. And the input file was shown as follow. However, in my output file, I can't see any information of "RAMD".(As shown in RESULTS) I don't know if my input file is written correctly. In addition, when I write keyword "ramdprotmask", the system will remind me that "Fortran runtime error: Cannot match namelist object name ramdprotmask". These problems make me confused about RAMD. At last, the command I used for RAMD is "pmemd.cuda -O -i sander.in6 -o sander.out6 -p prmtop -c mdrest5 -r mdrest6 -x mdcrd6".

RAMD input file (sander.in6 file):

Production 10 ns
  &cntrl
   irest=1,ntx=5,
   nstlim=5000000,dt=0.002,
   temp0=300.0,ntt=3,gamma_ln=2.0,
   ntc=2,ntf=2,
   cut=8.0,
   ntpr=1,ntwx=2000,ntwv=0,ntwe=0,ntxo=1,iwrap=1,
   ntb=2,ntp=1,pres0=1.0,taup=1.0,
   ipol=0,igb=0,
   ramdboost=1,ramdmaxdist=12,ramdligmask=":484",
  &end

Output file:

   4. RESULTS
--------------------------------------------------------------------------------


 NSTEP = 1 TIME(PS) = 140.002 TEMP(K) = 302.00 PRESS = -26.8
 Etot = -177479.4708 EKtot = 44538.7031 EPtot = -222018.1739
 BOND = 1426.7920 ANGLE = 3707.7449 DIHED = 5935.2323
 1-4 NB = 1670.6042 1-4 EEL = 17671.6822 VDWAALS = 26333.7407
 EELEC = -278763.9704 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 19459.9489 VIRIAL = 19877.3290 VOLUME = 720868.8133
                                                    Density = 1.0216
 ------------------------------------------------------------------------------


 NSTEP = 2 TIME(PS) = 140.004 TEMP(K) = 306.70 PRESS = -68.3
 Etot = -177516.1147 EKtot = 45231.9414 EPtot = -222748.0561
 BOND = 1315.2206 ANGLE = 3539.3545 DIHED = 5913.0637
 1-4 NB = 1666.0066 1-4 EEL = 17666.0559 VDWAALS = 26288.0099
 EELEC = -279135.7674 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 19498.5145 VIRIAL = 20561.1439 VOLUME = 720867.0247
                                                    Density = 1.0216



Thanks,
Xiaodong

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Received on Fri Feb 05 2021 - 01:30:02 PST
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