<P>
Dear David,<BR>
<BR>
I post the input file for the NVE run.<BR>
<BR>
I use SHAKE, Would it be better if I use LINCS?<BR>
<BR>
title = NVE<BR>
cpp = /usr/bin/cpp<BR>
; RUN CONTROL PARAMETERS<BR>
integrator = md<BR>
; Start time and timestep in ps<BR>
tinit = 500<BR>
dt = 0.0015;<BR>
nsteps = 360000; 540 ps<BR>
; For exact run continuation or redoing part of a run<BR>
init_step = 0<BR>
; number of steps for center of mass motion removal<BR>
nstcomm = 1<BR>
; group(s) for center of mass motion removal<BR>
comm-grps = SOL<BR>
; OUTPUT CONTROL OPTIONS<BR>
; Output frequency for coords (x), velocities (v) and forces (f)<BR>
nstxout = 0<BR>
nstvout = 0<BR>
nstfout = 0<BR>
; Checkpointing helps you continue after crashes<BR>
nstcheckpoint = 1000<BR>
; Output frequency for energies to log file and energy file<BR>
nstlog = 100000<BR>
nstenergy = 1000<BR>
; Output frequency and precision for xtc file<BR>
nstxtcout = 0<BR>
xtc-precision = 1000<BR>
; select multiple groups. By default all atoms will be written.<BR>
; NEIGHBORSEARCHING PARAMETERS<BR>
nstlist = 10<BR>
; ns algorithm (simple or grid)<BR>
ns_type = grid<BR>
; Periodic boundary conditions:<BR>
pbc = xyz<BR>
; nblist cut-off<BR>
rlist = 1.0<BR>
; OPTIONS FOR ELECTROSTATICS AND VDW<BR>
; Method for doing electrostatics<BR>
coulombtype = pme<BR>
rcoulomb = 1.0<BR>
ewald_rtol = 1e-5 ; since erfc(sigma*rcutoff)=ewald_rtol<BR>
optimize_fft = yes<BR>
; Relative dielectric constant for the medium<BR>
epsilon_r = 1 ; for water<BR>
; Method for doing Van der Waals<BR>
vdw-type = cut-off<BR>
rvdw = 1.0<BR>
; Spacing for the PME/PPPM FFT grid<BR>
fourierspacing = 0.12 ;<BR>
; EWALD/PME/PPPM parameters<BR>
pme_order = 4<BR>
ewald_geometry = 3d<BR>
epsilon_surface = 0<BR>
; OPTIONS FOR WEAK COUPLING ALGORITHMS<BR>
; Temperature coupling<BR>
Tcoupl = no<BR>
Pcoupl = no<BR>
; GENERATE VELOCITIES FOR STARTUP RUN<BR>
gen_vel = no<BR>
gen-temp = 300<BR>
gen-seed = 173529<BR>
; OPTIONS FOR BONDS<BR>
constraints = all-bonds<BR>
constraint_algorithm = shake<BR>
shake_tol = 0.0001<BR>
morse = no<BR>
<BR>
<BR>
rgds,<BR>
Jes<BR>
<BR>
<BR>
<BR>
On Fri, 28 Mar 2008 David van der Spoel wrote :<BR>
>JMandumpal wrote:<BR>
>>Dear list,<BR>
>><BR>
>> 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).<BR>
>><BR>
>><BR>
>it is difficult to run NVE.<BR>
>what constraint settings etc. do you use and what cutoffs.<BR>
><BR>
>> 100.000000 -15887.623027<BR>
>> 101.500000 -15887.961065<BR>
>> 103.000000 -15894.289055<BR>
>> 104.500000 -15898.915859<BR>
>> 106.000000 -15903.562196<BR>
>> 107.500000 -15906.540627<BR>
>> 109.000000 -15912.662455<BR>
>> 110.500000 -15915.571468<BR>
>> 112.000000 -15917.889520<BR>
>> 113.500000 -15923.955612<BR>
>> 115.000000 -15929.135491<BR>
>> 116.500000 -15932.507824<BR>
>> 118.000000 -15937.882055<BR>
>> 119.500000 -15941.562218<BR>
>> 121.000000 -15945.644608<BR>
>> 122.500000 -15949.063632<BR>
>> 124.000000 -15953.389791<BR>
>> 125.500000 -15957.524802<BR>
>> 127.000000 -15962.299775<BR>
>> 128.500000 -15967.579640<BR>
>> 130.000000 -15972.576889<BR>
>> 131.500000 -15975.427574<BR>
>> 133.000000 -15980.852975<BR>
>> 134.500000 -15985.584201<BR>
>> 136.000000 -15988.488715<BR>
>> 137.500000 -15993.295989<BR>
>> 139.000000 -15997.867767<BR>
>> 140.500000 -16000.630051<BR>
>> 142.000000 -16005.100451<BR>
>> 143.500000 -16009.649201<BR>
>> 145.000000 -16014.842764<BR>
>> 146.500000 -16019.498233<BR>
>> 148.000000 -16022.975477<BR>
>> 149.500000 -16027.677441<BR>
>> 151.000000 -16032.965475<BR>
>> 152.500000 -16036.043976<BR>
>> 154.000000 -16039.844112<BR>
>> 155.500000 -16044.836132<BR>
>> 157.000000 -16047.992186<BR>
>> 158.500000 -16052.196926<BR>
>> 160.000000 -16056.946593<BR>
>><BR>
>><BR>
>>-----------------------<BR>
>>I corrected these variables to:<BR>
>>tinit = 100<BR>
>><BR>
>>init_step = 0<BR>
>><BR>
>>Where could be the problem, then? Or should I run for even longer?<BR>
>><BR>
>>regards,<BR>
>>Jes<BR>
</P>
<br><br>
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