[AMBER] RAMD simulation (Xiaodong)

From: <18xdwu.stu.edu.cn>
Date: Sun, 7 Feb 2021 07:00:28 +0000

Dear all,
I run RAMD by using Amber 20. In my inputfile, I have set some parameters of RAMD to tell Amber run RAMD.(As shown below) Then, in the output file, this simulation can be run successfully. However, in the output file, I can't find any information about "RAMD". I want to know if this simulation runs ramd successfully.

Input 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=500,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=20,ramdligmask=":484",
   ramdproteinmask=":ALA,GLY,SER,THR,LEU,ILE,VAL,ASN,GLN,ARG,HID,HIE,HIP,TRP,PHE,TYR,GLU,ASP,LYS,LYN,PRO,CYS,CYX,MET,ASH,GLH,CYM,HYP",
   ramdint=0,ramdboostfreq=0,ramdboostrate=0,
  &end


Output file:

          -------------------------------------------------------
          Amber 20 PMEMD 2020
          -------------------------------------------------------

| PMEMD implementation of SANDER, Release 18

| Compiled date/time: Tue Apr 28 09:19:54 2020
| Run on 02/07/2021 at 09:21:20

| Executable path: pmemd.cuda_DPFP
| Working directory: /home/Xiaodong/RAMD
| Hostname: Unknown
  [-O]verwriting output

File Assignments:
| MDIN: sander.in6
| MDOUT: sander.out6
| INPCRD: mdrest4
| PARM: prmtop
| RESTRT: mdrest5
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd5
| MDINFO: mdinfo
| MDFRC: mdfrc


 Here is the input 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=500,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=20,ramdligmask=":484",
   ramdproteinmask=":ALA,GLY,SER,THR,LEU,ILE,VAL,ASN,GLN,ARG,HID,HIE,HIP,TRP,PH
   ramdint=0,ramdboostfreq=0,ramdboostrate=0,
  &end


Note: ig = -1. Setting random seed to 867421 based on wallclock time in
      microseconds.
| irandom = 1, using AMBER's internal random number generator (default).

|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 18.0.0
|
| 03/25/2018
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
|
| Version 18 performance extensions by:
| David Cerutti (Rutgers)
|
| Precision model in use:
| [DPFP] - Double Precision Forces, 64-bit Fixed point
| Accumulation.
|
|--------------------------------------------------------

|----------------- CITATION INFORMATION -----------------
|
| When publishing work that utilized the CUDA version
| of AMBER, please cite the following in addition to
| the regular AMBER citations:
|
| - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
| Poole; Scott Le Grand; Ross C. Walker "Routine
| microsecond molecular dynamics simulations with
| AMBER - Part II: Particle Mesh Ewald", J. Chem.
| Theory Comput., 2013, 9 (9), pp3878-3888,
| DOI: 10.1021/ct400314y.
|
| - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
| Duncan Poole; Scott Le Grand; Ross C. Walker
| "Routine microsecond molecular dynamics simulations
| with AMBER - Part I: Generalized Born", J. Chem.
| Theory Comput., 2012, 8 (5), pp1542-1555.
|
|--------------------------------------------------------

|------------------- GPU DEVICE INFO --------------------
|
| CUDA_VISIBLE_DEVICES: 0
| CUDA Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: Quadro GP100
| CUDA Device Global Mem Size: 16275 MB
| CUDA Device Num Multiprocessors: 56
| CUDA Device Core Freq: 1.44 GHz
|
|--------------------------------------------------------


| Conditional Compilation Defines Used:
| PUBFFT
| BINTRAJ
| CUDA
| EMIL

| Largest sphere to fit in unit cell has radius = 39.941

| New format PARM file being parsed.
| Version = 1.000 Date = 01/19/21 Time = 23:06:42

| Note: 1-4 EEL scale factors are being read from the topology file.

| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals

| Duplicated 0 dihedrals

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

 getting new box info from bottom of inpcrd
 NATOM = 72310 NTYPES = 30 NBONH = 68501 MBONA = 3887
 NTHETH = 8329 MTHETA = 5262 NPHIH = 17285 MPHIA = 16374
 NHPARM = 0 NPARM = 0 NNB = 127595 NRES = 22097
 NBONA = 3887 NTHETA = 5262 NPHIA = 16374 NUMBND = 94
 NUMANG = 205 NPTRA = 213 NATYP = 53 NPHB = 1
 IFBOX = 2 NMXRS = 40 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Coordinate Index Table dimensions: 19 19 19
| Direct force subcell size = 5.1492 5.1492 5.1492

     BOX TYPE: TRUNCATED OCTAHEDRON

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

default_name

General flags:
     imin = 0, nmropt = 0

Nature and format of input:
     ntx = 5, irest = 1, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 500, ntrx = 1, ntwr = 5000000
     iwrap = 1, ntwx = 2000, ntwv = 0, ntwe = 0
     ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0

Potential function:
     ntf = 2, ntb = 2, igb = 0, nsnb = 25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 8.00000, intdiel = 1.00000

Frozen or restrained atoms:
     ibelly = 0, ntr = 0

Molecular dynamics:
     nstlim = 5000000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00200, vlimit = -1.00000

Langevin dynamics temperature regulation:
     ig = 867421
     temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000

Pressure regulation:
     ntp = 1
     pres0 = 1.00000, comp = 44.60000, taup = 1.00000

SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00001

| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1

| Energy averages sample interval:
| ene_avg_sampling = 500

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, netfrc = 1
     Box X = 97.835 Box Y = 97.835 Box Z = 97.835
     Alpha = 109.471 Beta = 109.471 Gamma = 109.471
     NFFT1 = 100 NFFT2 = 100 NFFT3 = 100
     Cutoff= 8.000 Tol =0.100E-04
     Ewald Coefficient = 0.34864
     Interpolation order = 4
--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

default_name
 begin time read from input coords = 140.000 ps


 Number of triangulated 3-point waters found: 21607

     Sum of charges from parm topology file = 0.00299974
     Forcing neutrality...

| Dynamic Memory, Types Used:
| Reals 2913592
| Integers 2778866

| Nonbonded Pairs Initial Allocation: 12077577

| GPU memory information (estimate):
| KB of GPU memory in use: 570617
| KB of CPU memory in use: 160121

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

 NSTEP = 500 TIME(PS) = 141.000 TEMP(K) = 299.96 PRESS = -74.7
 Etot = -177371.8208 EKtot = 44236.9545 EPtot = -221608.7752
 BOND = 1505.1627 ANGLE = 3801.7341 DIHED = 5919.6088
 1-4 NB = 1702.5714 1-4 EEL = 17752.2083 VDWAALS = 26404.2343
 EELEC = -278694.2949 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 19400.0442 VIRIAL = 20562.6493 VOLUME = 721153.0535
                                                    Density = 1.0212
 ------------------------------------------------------------------------------


 NSTEP = 1000 TIME(PS) = 142.000 TEMP(K) = 299.22 PRESS = -117.8
 Etot = -177539.0189 EKtot = 44129.0930 EPtot = -221668.1119
 BOND = 1438.2046 ANGLE = 3811.6772 DIHED = 5947.7667
 1-4 NB = 1727.1129 1-4 EEL = 17717.1514 VDWAALS = 26203.3344
 EELEC = -278513.3590 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 19417.7681 VIRIAL = 21251.4537 VOLUME = 721152.4244
                                                    Density = 1.0212
 ------------------------------------------------------------------------------


Thanks,
Xiaodong
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Received on Sat Feb 06 2021 - 23:30:02 PST
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