Have you tried sander instead of pmemd?
On Fri, Feb 5, 2021, 4:20 AM 吴晓东 <18xdwu.stu.edu.cn> wrote:
> 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 - 04:00:02 PST
