AMBER: 'vlimit exceeded'

From: Vikas Varshney <vikas_var.rediffmail.com>
Date: 14 Oct 2003 19:36:19 -0000

ear Amber Users, I am having a difficult time with "vlimit exceeded" problem and I do not know how to fix that out. I looked into forum mails regarding vlimit but couldn't get much out of it. That is why I am writing my problem below. I have tried both "ibelly=1" and "ntr = 1" options for constraining atoms on my system but nothing worked out. I will really appreciate if anybody can help me with this. Let me explain my system and my problem. My system is made up of an oligomer of PMMA, CCl4 which acts as a solvent, and AL2O3 surface. I build PMMA and CCl4 in xleap and got the charges from antechamber. For AL2O3, I got the .pdb file for the crystal coordinates and charges and LJ parameters for Al from literature which I added in gaff.dat. Initially, I equilibrated my system containing PMMA with CCl4 without Al203 with NVT and NPT runs. Then I combined the equilibrated system with the crystal in xleap and made a simulation box which now contained Al203 also. In the crystal, Al and O have valencies of 6 and 4 respectively. In this system I didn't connect Al and O atoms in the crystal as I thought these atoms are going to be fixed. Further, I was not able to connect these atoms because, xleap crashes when I try to connect Al with more than 3 oxygens, as it can take only 3 bonds from Al. When I tried to run minimization with 'NTR = 1' option, force constant being 1000 for restraining the crystal, I see after the minimization that the crystal has also been moved. This is probably true as I didn't connect the atoms inside the crystal. After that I tried 'ibelly=1' option for the minimization. In this case the crystal didn't move and I think minimization was successful. Then I tried to run NVT simulation with the restrt file of my minimization output wich 'ibelly=1' option, I start getting "vlimit exceeded" problem from the very first step.Further, when I see my mdcrd file, I see that crystal is fixed, ccl4 is not moving much and oligomer is vibrating very much. Further, the energies and temperatures are not realistic. I do not have any Idea how do I go about fixing vlimit exceeded problem. Any suggestion are highly welcomed. Many Regards Vikas


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Received on Tue Oct 14 2003 - 21:53:00 PDT
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