AMBER Archive (2004)

Subject: Re: AMBER: restrt

From: Dr. Yong Duan (yduan_at_albert.chem.udel.edu)
Date: Thu Jan 22 2004 - 07:24:40 CST

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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