<div dir="ltr"><div class="gmail_quote"><div dir="ltr"><p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-family:"Times New Roman",serif;font-size:10pt;direction:ltr;color:rgb(0,0,0)"><font color="#222222"><font face="arial, sans-serif"><font size="3" style="font-size:12pt">Dear
gmx-developers</font></font></font></p>
<p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-family:"Times New Roman",serif;font-size:10pt;direction:ltr;color:rgb(0,0,0)"><span style="font-size:12pt;font-family:arial,sans-serif;color:rgb(34,34,34)">I
know these issues must be addressed at gmx-users but please pardon my
insistence/stubbornness on putting it on gmx-developers.</span><br></p>
<p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-family:"Times New Roman",serif;font-size:10pt;direction:ltr;color:rgb(0,0,0)"><span style="font-size:12pt;font-family:arial,sans-serif;color:rgb(34,34,34)">I
was trying to do free energy calculations (V 5.1.2 ).</span><br></p>
<p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-family:"Times New Roman",serif;font-size:10pt;direction:ltr;color:rgb(0,0,0)"><span style="font-size:12pt;font-family:arial,sans-serif;color:rgb(34,34,34)">It
is a simple molecule such as ethanol which is being decoupled from
water. In the first step I try to decouple charges from the system.
So in this setup VDW parameters are never modified; only
electrostatics are turned off. OPLS forcefield + tip4p water model.</span><br></p>
<p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-family:"Times New Roman",serif;font-size:10pt;direction:ltr;color:rgb(0,0,0)">
<font color="#222222"><font face="arial, sans-serif"><font size="3" style="font-size:12pt">I
am using thermodynamic integration rather than gmx-bar. In order to
do the same I am making use of the dual topology (type B directive)
.</font></font></font></p>
<p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-family:"Times New Roman",serif;font-size:10pt;direction:ltr;color:rgb(0,0,0)"><span style="font-size:12pt;font-family:arial,sans-serif;color:rgb(34,34,34)">In
the .mdp file for production run I have tried two setups</span><br></p>
<p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-family:"Times New Roman",serif;font-size:10pt;direction:ltr;color:rgb(0,0,0)"><span style="font-size:12pt;font-family:arial,sans-serif;color:rgb(34,34,34)">1)
I have persisted with sc-alpha directive (which is applicable with
gmx-bar and couple-moltype setup) and added -maxwarn option to my gmx
command.</span><br></p>
<p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-family:"Times New Roman",serif;font-size:10pt;direction:ltr;color:rgb(0,0,0)"><span style="font-size:12pt;font-family:arial,sans-serif;color:rgb(34,34,34)">2)
In the second set I removed sc-alpha directive.</span><br></p>
<p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-family:"Times New Roman",serif;font-size:10pt;direction:ltr;color:rgb(0,0,0)"><span style="font-size:12pt;font-family:arial,sans-serif;color:rgb(34,34,34)">But
sc-coul in both the cases is set to default value which happens to be
no.</span><br></p>
<p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-family:"Times New Roman",serif;font-size:10pt;direction:ltr;color:rgb(0,0,0)"><span style="font-size:12pt;font-family:arial,sans-serif;color:rgb(34,34,34)">I
have observed that dh/dl values in both the cases differ
significantly.</span><br></p>
<p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-family:"Times New Roman",serif;font-size:10pt;direction:ltr;color:rgb(0,0,0)">
<font color="#222222"><font face="arial, sans-serif"><font size="3" style="font-size:12pt">~
511 kJ/mol and ~ 92 kJ/mol</font></font></font></p>
<p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-family:"Times New Roman",serif;font-size:10pt;direction:ltr;color:rgb(0,0,0)">
<font color="#222222"><font face="arial, sans-serif"><font size="3" style="font-size:12pt">Since
while turning off elctrostaics VDW don't change I expected both set
of simulations to give similar values.</font></font></font></p>
<p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-family:"Times New Roman",serif;font-size:10pt;direction:ltr;color:rgb(0,0,0)">
<font color="#222222"><font face="arial, sans-serif"><font size="3" style="font-size:12pt">I
have attached my working setup for both set of simulations along with
output of .xvg files as well. </font></font></font>
</p><p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;direction:ltr"><font color="#222222"><font face="arial, sans-serif"><font><span style="font-size:16px"><a href="https://drive.google.com/file/d/1P6gP2KYx3MYy_jL5OkJ6UUsZeMNI811F/view?usp=sharing" target="_blank">https://drive.google.com/file/d/1P6gP2KYx3MYy_jL5OkJ6UUsZeMNI811F/view?usp=sharing</a></span><br></font></font></font></p><p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-family:"Times New Roman",serif;font-size:10pt;direction:ltr;color:rgb(0,0,0)"><span style="font-size:12pt;font-family:arial,sans-serif;color:rgb(34,34,34)">I
am using customized work flow so atom name nomenclature may not
necessarily match with the one used by gromacs.</span><br></p>
<p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-family:"Times New Roman",serif;font-size:10pt;direction:ltr;color:rgb(0,0,0)">
<font color="#222222"><font face="arial, sans-serif"><font size="3" style="font-size:12pt">I
kindly request you guys to look at the same. If I have blundered
please don't hesitate put all of this in trash! :) </font></font></font>
</p>
<p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-family:"Times New Roman",serif;font-size:10pt;direction:ltr;color:rgb(0,0,0)"><span style="font-size:12pt;font-family:arial,sans-serif;color:rgb(34,34,34)">Regards</span><br></p>
<p lang="en-US" class="m_-6872877582002082935gmail-western" align="justify" style="margin-bottom:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-family:"Times New Roman",serif;font-size:10pt;direction:ltr;color:rgb(0,0,0)"><span style="font-size:12pt;font-family:arial,sans-serif;color:rgb(34,34,34)">Deepak</span><br></p>
<br></div>
</div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Deepak U. Bapat<div><br></div></div></div></div>