[gmx-users] NVT and NVE

[JMandumpal]

Dear David,

I post the input file for the NVE run.

I use SHAKE, Would it be better if I use LINCS?

title                    = NVE
cpp                      = /usr/bin/cpp
; RUN CONTROL PARAMETERS
integrator               = md
; Start time and timestep in ps
tinit                    = 500
dt                       = 0.0015;
nsteps                   = 360000; 540 ps
; For exact run continuation or redoing part of a run
init_step                = 0
; number of steps for center of mass motion removal
nstcomm                  = 1
; group(s) for center of mass motion removal
comm-grps                = SOL
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
; Checkpointing helps you continue after crashes
nstcheckpoint            = 1000
; Output frequency for energies to log file and energy file
nstlog                   = 100000
nstenergy                = 1000
; Output frequency and precision for xtc file
nstxtcout                = 0
xtc-precision            = 1000
; select multiple groups. By default all atoms will be written.
; NEIGHBORSEARCHING PARAMETERS
nstlist                  = 10
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions:
pbc                      = xyz
; nblist cut-off
rlist                    = 1.0
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = pme
rcoulomb                 = 1.0
ewald_rtol               = 1e-5  ; since erfc(sigma*rcutoff)=ewald_rtol
optimize_fft             = yes
; Relative dielectric constant for the medium
epsilon_r                = 1  ; for water
; Method for doing Van der Waals
vdw-type                 = cut-off
rvdw                     = 1.0
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12 ;
; EWALD/PME/PPPM parameters
pme_order                = 4
ewald_geometry           = 3d
epsilon_surface          = 0
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl                   = no
Pcoupl                   = no
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = no
gen-temp                 = 300
gen-seed                 = 173529
; OPTIONS FOR BONDS
constraints              = all-bonds
constraint_algorithm     = shake
shake_tol                = 0.0001
morse                    = no
                                                                                                                                                                                                                                  

rgds,
Jes



On Fri, 28 Mar 2008 David van der Spoel wrote :
>JMandumpal wrote:
>>Dear list,
>>
>>         These are the energy I obtained running 60ps NVE of 500 TIP5P water molecules- I still wonder why the energy has not been converged even having run for 160 ps in total (100 NVT + 60 NVE).
>>
>>
>it is difficult to run NVE.
>what constraint settings etc. do you use and what cutoffs.
>
>>   100.000000  -15887.623027
>>   101.500000  -15887.961065
>>   103.000000  -15894.289055
>>   104.500000  -15898.915859
>>   106.000000  -15903.562196
>>   107.500000  -15906.540627
>>   109.000000  -15912.662455
>>   110.500000  -15915.571468
>>   112.000000  -15917.889520
>>   113.500000  -15923.955612
>>   115.000000  -15929.135491
>>   116.500000  -15932.507824
>>   118.000000  -15937.882055
>>   119.500000  -15941.562218
>>   121.000000  -15945.644608
>>   122.500000  -15949.063632
>>   124.000000  -15953.389791
>>   125.500000  -15957.524802
>>   127.000000  -15962.299775
>>   128.500000  -15967.579640
>>   130.000000  -15972.576889
>>   131.500000  -15975.427574
>>   133.000000  -15980.852975
>>   134.500000  -15985.584201
>>   136.000000  -15988.488715
>>   137.500000  -15993.295989
>>   139.000000  -15997.867767
>>   140.500000  -16000.630051
>>   142.000000  -16005.100451
>>   143.500000  -16009.649201
>>   145.000000  -16014.842764
>>   146.500000  -16019.498233
>>   148.000000  -16022.975477
>>   149.500000  -16027.677441
>>   151.000000  -16032.965475
>>   152.500000  -16036.043976
>>   154.000000  -16039.844112
>>   155.500000  -16044.836132
>>   157.000000  -16047.992186
>>   158.500000  -16052.196926
>>   160.000000  -16056.946593
>>
>>
>>-----------------------
>>I corrected these variables to:
>>tinit                    = 100
>>
>>init_step                = 0
>>
>>Where could be the problem, then? Or should I run for even longer?
>>
>>regards,
>>Jes
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