problems in sander

From: devi rvel <>
Date: Sun 07 May 2000 07:53:52 GMT

Problem 1:-dynamics
     I got some problem while doing dynamics for my 14mer dna molecule(
using PME ) . During my production run I heated the molecule to 300K for
20 ps and for rest of the cycles I wanted to maintain the temperature at
300k itself. This I split it into two parts as follows:
1) heating from 10k to 300k for 20ps
2) maintaining the temperature at 300k for 700ps.
When I started my second part of the dynamics, using the output
co-ordinates of the first step, I got intially 426K ,eventhough it is
heated upto 300k in the previous step.Immediately after 0.004ps (ie
20.004ps) it is coming to 300k and stays there itself for the rest of the
cycles. I am not able to find out the reason for this. If there is any
other way to rectify this problem, please let me know about it.

Problem 2:-minimization
     I had problems in fixing ions for my dna molecule using the “edit”.
Initially I fixed the ions at the bisector of O1P-P-O2P angle and 5A
distance away from the phosphate and I used box option to add water
molecules. There I got few ion-ion short contacts and I carried out my free
minimization(with PME) using the same co-ordinates itself. After 23141
cycles the molecule reaches the RMS gradient of 0.01kcal/mol/A . But few
ions are moving close to the phosphate and anionic oxygens to a distance of
3.5A and 2.3A respecitvely.Some ion-ion contact is also there.

Please , help me to solve these problems .


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Received on Sun May 07 2000 - 00:53:52 PDT
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