AMBER Archive (2004)

Subject: Re: AMBER: Implicit 4r md

From: Stefano.Pieraccini_at_unimi.it
Date: Wed Dec 01 2004 - 02:52:27 CST

I notice, on the attached output, that you haven't neutralized the sistem. A neutral sistem is required for ewald sum, and it is artificially neutralized with uniform plasma (see your output). Maybe this can cause a problem. You problem could also depend on the initial structure. If it is a PDB file or a part of a pdb file, there should be no problems, but if it was drawn by hand, some artifacts may be present that make the energy high and that can't be solved by minimization.

Stefano Pieraccini
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hello amber,
I am performing Implicit solvent md on small proteins using 4r dielectric, restraing the helices ans sheets. The input file for the initial minimization step is:
&cntrl
        imin=1,
        ntx=1,ntb=0,
        ntr=1,dielc=4,cut=300.0,
        maxcyc=1000, ncyc=500,
 &end
 &ewald
        eedmeth=5,
 &end
restraint 1
 25.0
RES 10 19
RES 25 37
RES 42 55
END
END
My problem is that the total energy at the start of the minimization is positive and after the minimization (1000 steps) is positive. Is there someting which i am doing wrong, because of which total energy is positive. I am attaching the output file.
Thanks.

                
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<DIV>
<DIV>hello amber,</DIV>
<DIV>I am performing Implicit solvent md on small proteins using 4r dielectric, restraing the helices ans sheets. The input file for the initial minimization step is:</DIV>
<DIV>&amp;cntrl<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; imin=1,<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ntx=1,ntb=0,<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ntr=1,dielc=4,cut=300.0,<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; maxcyc=1000, ncyc=500,<BR>&nbsp;&amp;end<BR>&nbsp;&amp;ewald<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; eedmeth=5,<BR>&nbsp;&amp;end<BR>restraint 1<BR>&nbsp;25.0<BR>RES 10 19<BR>RES 25 37<BR>RES 42 55<BR>END<BR>END</DIV>
<DIV>My problem is that the total energy at the start of the minimization is positive and after the minimization (1000 steps) is positive. Is there someting which i am doing wrong, because of which total energy is positive. I am attaching the output file.</DIV>
<DIV>Thanks.</DIV></DIV><p>
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