Re: [AMBER] heat further an equilibrated system

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 22 Jan 2010 12:52:02 -0500

This is still unreadable... is there no option for "plain text" or
"ascii" or something for your email program/account?

On Fri, Jan 22, 2010 at 12:40 PM, Jayalakshmi Sridhar <jsridhar.xula.edu> wrote:
>
>   <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;    ________________________   _______________________<br
>   />&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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-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Jan 22 2010 - 10:00:04 PST
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