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On 15/11/2011 6:06 PM, Harpreet Basra wrote:
<blockquote
cite="mid:CAEAiM5uDe=UrfEWLuB7CGpm+P_K6cZX1KpbGTQz3TRv4En6bnw@mail.gmail.com"
type="cite">
<div>Hi</div>
<div> </div>
<div> </div>
<div>I am still stuck with same problem of obtaining positive
potential energy. </div>
<div> </div>
<div>>>On 11/11/2011 5:07 PM, Harpreet Basra wrote:</div>
<div>>> Hi</div>
<div>>></div>
<div>>> I am trying to generate an equilibrated box of 216
TFE molecules.To</div>
<div>>> generate the 216 TFE molecule box i performed
following steps:</div>
<div>> </div>
<div>>A suggested workflow can be found here</div>
<div>><a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation"
target="_blank">http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation</a></div>
<div> </div>
<div>I have been following this link only. </div>
<div> </div>
<div>> </div>
<div>></div>
<div>>> 1) I got the tfe.gro file and created a cubic box of
edge length =</div>
<div>>> 0.516 nm containing 1 TFE molecule (at its center),
using the</div>
<div>>> following command:</div>
<div>>></div>
<div>>>>> editconf -f tfe.gro -c -o tfe_box.gro -bt
cubic -box 0.516</div>
<div>>> I chose this length because in the tfe.gro file
dimensions of the TFE</div>
<div>>> molecule are 0.516 0.516 0.516.</div>
<div>> </div>
<div>>That's not a good reason. Choose a volume and shape that
makes sense for</div>
<div>>your target density. Cubic probably doesn't make sense
when a</div>
<div>>rectangular shape is possible. Then you'll probably want
to choose -nbox</div>
<div>>differently later.</div>
<div> </div>
<div>I chose a rectangular box too. still i get a positive value
for PE and moreover all the molecules move towards two opposite
walls of the box. I am not sure that the way I am using the
genconf command is the correct way. because I have tried every
other possibility for not getting a positive potential, with no
success. So here are my .gro file and the topology file for TFE.
</div>
<div> </div>
<div>*****tfe.gro file*****</div>
<div> </div>
<div> <span lang="EN">7
<p>1TFE F1T 1 0.444 0.344 0.246</p>
<p>1TFE CT 2 0.334 0.245 0.246</p>
<p>1TFE F2T 3 0.350 0.160 0.364</p>
<p>1TFE F3T 4 0.350 0.160 0.127</p>
<p>1TFE CH2T 5 0.187 0.326 0.246</p>
<p>1TFE OT 6 0.075 0.220 0.246</p>
<p>1TFE HT 7 -0.019 0.266 0.246</p>
<p>0.49174 0.49174 0.49174</p>
<p> </p>
<p>****topology file****</p>
<span lang="EN">
<p>[ moleculetype ]</p>
<p>; Name nrexcl</p>
<p>TFE 3</p>
<p>[ atoms ]</p>
<p>; nr type resnr resid atom cgnr charge mass</p>
<p>1 FTFE 1 TFE F1T 1 -0.170 18.9984 </p>
<p>2 CTFE 1 TFE CT 1 0.452 12.0110 </p>
<p>3 FTFE 1 TFE F2T 1 -0.170 18.9984 </p>
<p>4 FTFE 1 TFE F3T 1 -0.170 18.9984 </p>
<p>5 CHTFE 1 TFE CH2T 1 0.273 14.0270 </p>
<p>6 OTFE 1 TFE OT 1 -0.625 15.9994 </p>
<p>7 H 1 TFE HT 1 0.410 1.0080 </p>
<p>[ bonds ]</p>
<p>; ai aj fu c0, c1, ...</p>
<p>2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1 </p>
<p>2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2 </p>
<p>2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3 </p>
<p>2 5 2 0.153 7150000.0 0.153 7150000.0 ; C1 C2 </p>
<p>5 6 2 0.143 8180000.0 0.143 8180000.0 ; C2 O </p>
<p>6 7 2 0.100 15700000.0 0.100 15700000.0 ; O H </p>
<p>[ pairs ]</p>
<p>; ai aj fu c0, c1, ...</p>
<p>1 6 1 ; F1 O </p>
<p>2 7 1 ; C1 H </p>
<p>3 6 1 ; F2 O </p>
<p>4 6 1 ; F3 O </p>
<p>[ angles ]</p>
<p>; ai aj ak fu c0, c1, ...</p>
<p>1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2 </p>
<p>1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3 </p>
<p>1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2 </p>
<p>3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3 </p>
<p>3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2 </p>
<p>4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2 </p>
<p>2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O </p>
<p>5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H </p>
<p>[ dihedrals ]</p>
<p>; ai aj ak al fu c0, c1, m, ...</p>
<p>6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1 </p>
<p>2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H </p>
</span></span></div>
<div> </div>
<div>and to construct a box of TFE solvent i took the tfe.gro file
and replicated the TFE molecule by using </div>
<div> </div>
<div> </div>
<div>genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6</div>
<div> </div>
<div> </div>
<div>can u plz suggest is it that I am using genconf in a wrong
way that it is causing this problem? I am not sure how many
molecules (-nbox option in genconf) should i keep in the box in
order to get a mass density of 1383g/L for TFE. </div>
</blockquote>
<br>
That link says "<span class="Apple-style-span" style="color: rgb(79,
107, 114); font-family: arial, verdana, helvetica; font-size:
12px; font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: 15px; orphans: 2;
text-align: -webkit-auto; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); display: inline !important;
float: none; ">Work out how much volume a single molecule would
have in the box of your chosen density and size. Use<span
class="Apple-converted-space"> </span></span><a title="editconf"
rel="internal" href="http://www.gromacs.org/editconf" class="new "
style="color: rgb(175, 102, 102); text-decoration: none;
border-bottom-width: 1px; border-bottom-style: dotted;
border-bottom-color: rgb(175, 102, 102); font-family: arial,
verdana, helvetica; font-size: 12px; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing: normal;
line-height: 15px; orphans: 2; text-align: -webkit-auto;
text-indent: 0px; text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); ">editconf</a><span class="Apple-style-span" style="color:
rgb(79, 107, 114); font-family: arial, verdana, helvetica;
font-size: 12px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height: 15px;
orphans: 2; text-align: -webkit-auto; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); display: inline !important; float: none; "><span
class="Apple-converted-space"> </span>to place a box of that
size around your single molecule.</span>" It does not seem to me
that you have done this.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAEAiM5uDe=UrfEWLuB7CGpm+P_K6cZX1KpbGTQz3TRv4En6bnw@mail.gmail.com"
type="cite">
<div> </div>
<div>thanks</div>
<div> </div>
<div>Harpreet</div>
<div> </div>
<div>> </div>
<div>>> 2) Then using genconf command i replicated the box
to get a bigger box</div>
<div>>> with 216 TFE molecules using the following command:</div>
<div>>></div>
<div>>>>> genconf -f tfe_box.gro -o out.gro -rot
-nbox 6</div>
<div>>> 3) Energy minimization was done using STEEPEST
descent</div>
<div>>></div>
<div>>> 4) Then I performed 5ns NVT (300K) equilibration and
followed by 5ns</div>
<div>>> NPT (300K, 1atm) equilibration.</div>
<div>>></div>
<div>>> After doing all these steps still I obtain a
positive a potentail</div>
<div>>> energy. I get positive potential energy of the
system (2.45+E04</div>
<div>>> kJ/mol) and kinetic energy as 4.03+E03 kJ/mol, thus
giving a positive</div>
<div>>> total energy of the system. My question is whether
obtaining positive</div>
<div>>> potential energy indicate some error in my TFE
solvent box ? Is it</div>
<div>>> because of large Fluorine atoms of TFE ? Does it
mean its not properly</div>
<div>>> equilibrated ? What can I do to equilibrate it?</div>
<div>> </div>
<div>>You probably have atomic overlaps from your choice of
cubic 0.516 box</div>
<div>>earlier. Did you look at the results of genconf before
computing with them?</div>
<div>> </div>
<div>>Mark</div>
<div> </div>
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