AMBER Archive (2005)

Subject: Re: AMBER: Problem with restart file

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Thu Jan 13 2005 - 09:40:14 CST

Hi,

For your first problem, you can try to superimpose your trajectory to a
reference frame and then do the averaging. If your molecule of interest
is migrating or rotating, averaging without removing these motions might
give your some "strange" values.
For your second question, try to set ntwr to a negative number. This
tells sander to write a second set of restrt files every ntwr steps.
This can be quite a lifesaver, thanks to Tom ...

Cheers,

Guanglei

Azira Muhamad wrote:
> Dear AMBER users,
> I run a 300ps MD simulation on AMBER8 (Beowulf cluster 4 nodes, gigabit
> ethernet connection, HP Proliant ML150 server). The trajectory file
> looks ok, can be viewed by VMD. However when I tried to take some
> snapshots from the trajectory using ptraj, it produced corrupted restart
> file. This is the input file for ptraj:
>
> trajin sub1comp_md.crd 350 350
> average sub1comp_md350.xyz rest
>
> the restart file produced strange values,as shown below (apart of the
> .xyz file) from line 4 to 10:
>
> 28.0300007 25.3099995 19.5300007 28.7900009 27.1900005 20.2700005
> 29.7600002 26.4699993 21.1299992 29.8400002 26.9300003 22.4099998
> 30.6900005 25.6299992 20.7000008 3.2300000 27.1599998 18.9500008
> -1018.0000000-915.6400146-677.5300293 788.15997311166.75000001177.6600342
> -308.3599854-888.1199951 161.2500000 849.9099731-238.67999271442.6899414
> -331.1499939 772.55999761087.2500000-945.71002201156.0200195 5.5799999
> -456.7500000 77.3300018 679.0800171-472.9500122 167.7500000-151.5899963
> 196.7400055-874.6900024 870.9199829 926.6599731 709.2199707-344.5199890
> 566.9600220-294.3900146 737.4000244 14.2399998-699.9799805-336.4599915
> -912.9299927 522.0300293 3.0699999 29.5100002 41.6500015 9.4300003
> 29.0799999 41.0000000 8.8800001 29.1100006 41.5400009 10.2900000
> 19.0599995 41.2799988 29.1499996 19.5000000 41.2599983 28.2900009
> 18.4400005 40.5499992 29.1100006 32.0999985 38.6199989 4.8800001
> 31.4200001 38.0099983 4.5900002 32.0999985 38.5499992 5.8299999
>
>
> That's the first problem. Secondly, the restart file produced every 500
> steps was corrupted eventhough the trajectory file was ok. So I couldn't
> use the restart file when my simulation was interrupted. How can I solve
> this problem? Any suggestions?
>
> Azira Muhamad
> Universiti Putra Malaysia
>
>
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