Any numbers should do. Make sure you use different random number seeds for
different trajectories if you intend to produce different trajectories.
This is particularly important if you start from the same coordinates.
yong
On Thu, 22 Jan 2004, L Jin wrote:
> Yong,
>
> Thank you for reply. Is there a good scale for the random number of the seeds?
> Or just any number I choose randomly. Thanks
>
> Lan
>
>
>
>
> Quoting "Dr. Yong Duan" <yduan.albert.chem.udel.edu>:
>
> >
> > The trajectory in mdcrd only contains coordinates. If you need the
> > velocities, you need to save them by setting ntvel(?)=(e.g.)500. This will
> > trigger saving of velocities to mdvel everything 500 steps. You then need
> > to combine the velocities and coordinates to restrt.
> >
> > HOWEVER, if you start the simulations from the restrt files combined this
> > way you will produce really the same trajectory delayed by (e.g.) 500
> > steps (they will eventually diverge if the simulations are done on
> > parallel machines).
> >
> > Alternatively, you may consider reassigning velocities by chosing
> > different random number seeds (from the restrt files you already created).
> >
> > good luck.
> >
> > yong
> >
> > On Thu, 22 Jan 2004, L Jin wrote:
> >
> > > Dear all,
> > >
> > > I am trying to run the MD by using a certain frame's coordinate and
> > velocity
> > > which within the mdcrd file. So I need to pick it out and get the restrt
> > file
> > > for this frame. e.g. I got 500 frames in the mdcrd and I want the 385 frame
> > to
> > > run a new MD. I tried to use carnal and ptraj to get this restrt but I can
> > just
> > > get the coordinate without velocity in the restrt output file like the
> > > followings. Please anybody can give me some suggestion how can I get the
> > restrt
> > > completely?
> > >
> > > restrt file generated by ptraj
> > > 51
> > > 2.0590000 1.8020000 0.1660000 3.0230000 2.6819999 0.7610000
> > > 2.5130000 3.4100001 1.9090000 3.8599999 3.3820000 -0.1530000
> > > 4.2100000 1.6600000 1.1760000 4.4899998 1.8730000 0.2290000
> > > 5.1469998 2.3640001 2.1240001 4.7519999 3.2920001 2.5390000
> > > 5.3990002 1.4920000 3.3920000 4.5170002 1.5039999 4.0320001
> > > 5.7389998 0.1350000 3.0050001 5.2249999 -0.1240000 2.2360001
> > > 6.4359999 2.0070000 4.2110000 7.7700000 2.0920000 3.6320000
> > > 8.1059999 1.1370000 3.2290001 8.7279997 2.6229999 4.6989999
> > > 9.6490002 3.0860000 4.3449998 8.2100000 3.4540000 5.1780000
> > > 9.1680002 1.7280000 5.6450000 9.8739996 0.2450000 5.3429999
> > > 8.8760004 -0.6690000 4.8649998 10.8629999 0.5040000 4.3350000
> > > 10.4540005 -0.0850000 6.5990000 6.5229998 2.6970000 1.4970000
> > > 6.9419999 1.8190000 1.0050000 6.3720002 3.7969999 0.6110000
> > > 5.5009999 3.8260000 0.2090000 7.5960002 3.1340001 2.5000000
> > > 7.2750001 4.0840001 2.9270000 8.8310003 3.2070000 1.7650000
> > > 9.3649998 4.5229998 1.6020000 9.4919996 5.1279998 2.8740001
> > > 9.9709997 6.2709999 3.0250001 10.7299995 6.8769999 2.0380001
> > > 10.9289999 7.9380002 2.0690000 11.0670004 6.1149998 0.7540000
> > > 12.0959997 6.2810001 0.4380000 10.2869997 6.7789998 -0.1770000
> > > 10.5810003 6.3509998 -0.9850000 9.7040005 6.9660001 4.2919998
> > > 9.0319996 6.5070000 5.2199998 10.1309996 8.2510004 4.4640002
> > > 9.7220001 8.5629997 5.2740002 8.6590004 5.0910001 0.9960000
> > > 10.7080002 4.5650001 0.8440000 11.4709997 4.0879998 1.4590000
> > > 10.5850000 3.9070001 -0.4270000 11.7819996 4.0250001 -1.4730000
> > > 11.6269999 2.8529999 -2.2630000 12.9379997 3.9670000 -0.6300000
> > > 11.4569998 5.2820001 -2.1229999
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000
> > > 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> > >
> > >
> > > CARNAL temporary title
> > > 51
> > > 2.0590000 1.8020000 0.1660000 3.0230000 2.6820000 0.7610000
> > > 2.5130000 3.4100000 1.9090000 3.8600000 3.3820000 -0.1530000
> > > 4.2100000 1.6600000 1.1760000 4.4900000 1.8730000 0.2290000
> > > 5.1470000 2.3640000 2.1240000 4.7520000 3.2920000 2.5390000
> > > 5.3990000 1.4920000 3.3920000 4.5170000 1.5040000 4.0320000
> > > 5.7390000 0.1350000 3.0050000 5.2250000 -0.1240000 2.2360000
> > > 6.4360000 2.0070000 4.2110000 7.7700000 2.0920000 3.6320000
> > > 8.1060000 1.1370000 3.2290000 8.7280000 2.6230000 4.6990000
> > > 9.6490000 3.0860000 4.3450000 8.2100000 3.4540000 5.1780000
> > > 9.1680000 1.7280000 5.6450000 9.8740000 0.2450000 5.3430000
> > > 8.8760000 -0.6690000 4.8650000 10.8630000 0.5040000 4.3350000
> > > 10.4540000 -0.0850000 6.5990000 6.5230000 2.6970000 1.4970000
> > > 6.9420000 1.8190000 1.0050000 6.3720000 3.7970000 0.6110000
> > > 5.5010000 3.8260000 0.2090000 7.5960000 3.1340000 2.5000000
> > > 7.2750000 4.0840000 2.9270000 8.8310000 3.2070000 1.7650000
> > > 9.3650000 4.5230000 1.6020000 9.4920000 5.1280000 2.8740000
> > > 9.9710000 6.2710000 3.0250000 10.7300000 6.8770000 2.0380000
> > > 10.9290000 7.9380000 2.0690000 11.0670000 6.1150000 0.7540000
> > > 12.0960000 6.2810000 0.4380000 10.2870000 6.7790000 -0.1770000
> > > 10.5810000 6.3510000 -0.9850000 9.7040000 6.9660000 4.2920000
> > > 9.0320000 6.5070000 5.2200000 10.1310000 8.2510000 4.4640000
> > > 9.7220000 8.5630000 5.2740000 8.6590000 5.0910000 0.9960000
> > > 10.7080000 4.5650000 0.8440000 11.4710000 4.0880000 1.4590000
> > > 10.5850000 3.9070000 -0.4270000 11.7820000 4.0250000 -1.4730000
> > > 11.6270000 2.8530000 -2.2630000 12.9380000 3.9670000 -0.6300000
> > > 11.4570000 5.2820000 -2.1230000
> > >
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>
>
>
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Received on Fri Jan 23 2004 - 01:53:01 PST
