Re: [AMBER] heat further an equilibrated system

From: Jayalakshmi Sridhar <jsridhar.xula.edu>
Date: Fri, 22 Jan 2010 11:40:28 -0600

   <div style="font-family: 'Times New Roman'; font-size: 1 6px;"><br />I was able to solve this problem. But am encount ering a new problem. When reading the reference coordinates it says- < br _moz_dirty="" />rfree: End of file on unit 5.<br _ moz_dirty="" />I have specified irest = 1 and ntx = 5 as I= am
   using a .rst file for reference. Should I change anything else? Thanks for the help.<br _moz_dirty="" />Jaya.<br /> <span>On 01/22/10, <b class="name">Jason Swails </b> &lt;jason.swails.gmail.com&gt;wrote:</span><bloc kquotecite="mid:64de6d71001220858t3181c11fx523bf8dd974d23f.mail .gmail.com" class="iwcQuote" style="border-left: 1px s olid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt; " type="cite"><div class="mimepart text plain">Could you please copy your email over to plain text? With all of the<br / >markup it is impossible to read your email.<br /><br />Than ks!<br />Jason<br /><br />On Fri, Jan 22, 2010 at 11:5= 5
   AM, Jayalakshmi Sridhar &lt;jsridhar.xula.edu&gt; wrote: <br />&gt;<br />&gt;   &lt;div style=&quot;f ont-family: 'Times New Roman'; font-size: 1   6px;&quot; &gt;Dear Amber Users,&lt;br _moz_dirty=&quot;&quot ; /&gt;I have  a<br />&gt;   protein which I initially heated to 300K and equilibrated  for 4 ns.   Now I wish to heat t= he
   system further to 325 K. I am using the final  4ns<br />&gt= ;
     equilibrated  system as starting point. I am getting the fol= lowing
      error:&lt;br _moz_dirty=&quot;&quot; / &gt;&lt;br _moz_dirty=&quot;&quot;    /&gt; &lt;br _moz_dirty=&quot;&quot; /&gt;&gt;$AMB ERHOME/exe/sander -O -i<br />&gt;   2a6_md16.in -p 2a6.p rmtop -c 2a6_md15.rst -r 2a6_md16. rst -o<br />&gt;   2a6_md16.out  -x  2a6_md16.mdcrd  -ref  2a6_md15.rst &lt;br   _moz_dirty=&quot;&quot; /&gt;&gt;At line 189 of file _rgroup.f&lt; br<br />&gt;   _moz_ dirty=&quot;&quot; /&gt; Fortran runtime error: End of f ile&lt;br<br />&gt;   _moz_dirty=&quot;&quot; /&gt;&lt; br _moz_dirty=&quot;&quot; /&gt;The input is<br />&gt;   given  below:&lt;br _moz_ di rty=&quot;&quot;/&gt;&amp;cntrl&lt;br<br/>& gt;   _moz_dirty=&quot;&quot;    /&gt;     i   min     =   0,&lt;br<br />&gt;   _m oz_dirty=&quot;&quot;    /&gt;     irest     =    1,   &lt;br<br />&gt;   _moz_dirty= &quot;&quot;  /&gt;  ntx    = 7,&lt;br _ moz_   dirty=&quot;&quot; /&gt;  ntb    = 1, &lt;br _moz_dirty=&quot;&quot;   /&gt;  cut     = 10,&lt;br _moz_dirty=&quot;&quot; /&gt;   ntr       = 1,&lt;br _moz_dirty=&quot;&q uot; /&gt;  ntc    =   2,&lt;br _moz_dirty= &quot;&quot; /&gt;  ntf    = 2,&lt;br _   moz_dirty=&quot;&quot; /&gt;  tempi  = 300.0, &lt;br _moz_dirty   =&quot;&quot; /&gt;  temp0   = 350.0,&lt;br _moz_dirty=&quot;&quot; /   &gt;  ntt    = 3,&lt;br _moz_dirty=&quot; &quot; /&gt;  gamma_   ln = 1.0,&lt;br _moz_ dirty=&quot;&quot; /&gt;  nstlim = 20000, dt<br /> &gt;   = 0.002&lt;br _moz_dirty=&quot;&quot; /&gt;  ntpr = 200, ntw x =<br />&gt;   200,   ntwr  = 2000&lt;br _moz_dirty=&quot;&quot; /&gt;  /&lt;br _   moz_dirty=&quot;&quot; /&gt;&lt ;br _moz_dirty=&quot;&quot; /&gt;Thank you for   t= he
   help.&lt;br _moz_dirty=&quot;&quot; /&gt;Jaya .&lt;br _moz_dirt   y=&quot;&quot; /&gt; &lt ;br /&gt;&lt;/div&gt;<br />&gt;<br />&gt; ________________________ _______________________<
   />&gt; AMBER mailing list<br />&gt; AMBER.ambermd.o rg<br />&gt; <a href="http://lists.ambermd.org/mailm an/listinfo/amber"target="_blank">http://lists.ambermd. org/mailman/listinfo/amber</a><br/>&gt;<br/>&gt;< br /><br /><br /><br />-- <br />---------------------- -----------------<br />Jason M. Swails<br />Quantum Theory Pro ject,<br />University of Florida<br />Ph.D. Graduate Stude nt<br />352-392-4032<br /><br />__________ ________________________ _____________<br />AMBER mailing list<br />AMBER.ambermd.org<br /><a href="http://lists.ambe rmd.org/mailman/listinfo/amber"target="_blank">http://l ists.ambermd.org/mailman/listinfo/amber</a><br/></div>< /blockquote></div>


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Received on Fri Jan 22 2010 - 10:00:03 PST
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