Re: [AMBER] About SMD simulation restart file

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Fri, 14 Oct 2011 17:06:54 -0700

Where would the velocities be read from in order to write them
out? The mdcrd files just have coordinates.

---
But if I use ptraj's trajout restart command to generate a new restart file from the last frame of my crd file, the velocity should be written out, shouldn't it?
----- Ursprüngliche Mail -----
| It holds for MD in general, not sure what SMD is or what degree of
| equilibration is required for it. Going from velocity = 0 to 300K
| without equilibration is like having your car pool ride drive through
| the house and scoop you out of bed without slowing down.
| 
| Bill
| 
| ---
| 
| does this hold only for SMD or for any kind of MD? I always thought a
| restart file is simply writing out coords and velocities in regular
| intervals. So what is the difference then from using the last
| snapshot saved in the crd file?
| 
| Antje
| 
| ----- Ursprüngliche Mail -----
| | > You can pick the last frame form the mdcrd and create your new
| | > restart.
| | 
| | Note that if you do this, you will have to re-equilibrate from
| | scratch.
| | 
| | Bill
| | 
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| | 
| 
| 
| 
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Received on Fri Oct 14 2011 - 17:30:02 PDT
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