AMBER Archive (2004)

Subject: Re: AMBER: restrt

From: L Jin (s0344557_at_sms.ed.ac.uk)
Date: Thu Jan 22 2004 - 08:05:03 CST

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_at_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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