<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div><span class="Apple-style-span" style="font-family: times, serif; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Yes. I did check the tau_t issue. I used tau_t=2ps as recommended in the manual.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Again here, the simulation with 0.002 ps step gives rise to 303K. But, from now on, as per your( and Justin's) recommendation, I am going to use the tau_t=2ps and rvdw<rlist in conjunction with 0.001 ps time step when using sd integrator from my production/equilibration run for all lambda.</div></span></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:times new roman, new york, times,
serif;font-size:12pt"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Wed, August 3, 2011 11:00:30 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP<br></font><br>
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On 4/08/2011 1:51 AM, Sanku M wrote:
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<div>Hi Mark and Justin,</div>
<div> I did investigate on the rvdw=rlist issue. But, I found
even if I make rvdw < rlist and still keep time step 0.002,
the average temperature goes to 303 K.</div>
<div>Only reducing the time step does help ( even if rvdw=rlist)
to get average temperature to 300K.</div>
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<br>
... and the tau_t issue I mentioned?<br>
<br>
Mark<br>
<br>
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