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On 22/12/2010 5:44 PM, Qin Qiao wrote:
<blockquote
cite="mid:AANLkTimm-OLMD_i+SJWVYuYxA5zrguoKVMVBRXx_cy9T@mail.gmail.com"
type="cite">Dear all,<br>
<br>
I posted yesterday but didn't get answer..I guess it's due to my
wrong approach to ask. I would like to explain more and hope I
would get your help.<br>
<br>
I'm doing an REMD, and want to have a strong temperature coupling
to make sure every replica is at its target temperature. I guess I
could do it by setting tau_t small in the Nose-hoover T coupling,
but there will come the warning in Gromacs. <br>
<br>
I maxwarned the warning to proceed, and find the temperature is
ok, but I am not sure whether it will introduce some artifacts in
the simulation and what kind of artifacts. Could you tell me?
Thanks a lot.<br>
</blockquote>
<br>
The temperature coupling algorithms are discussed in the literature,
when they were derived (citations in GROMACS manual) and
subsequently. I suggest you do your own homework there. The use of
REMD is more or less irrelevant to the trade-offs when deciding what
temperature coupling scheme to use.<br>
<br>
Mark <br>
<br>
<blockquote
cite="mid:AANLkTimm-OLMD_i+SJWVYuYxA5zrguoKVMVBRXx_cy9T@mail.gmail.com"
type="cite"><br>
Best,<br>
<br>
Qin<br>
<br>
<div class="gmail_quote">2010/12/21 Qin Qiao <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:qiaoqin47@gmail.com">qiaoqin47@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">Dear all,<br>
<br>
I wonder what will happen in Nose-hoover coupling when tau_t =
dt * nsttcouple, while nsttcouple = nstlist. (I used -maxwarn
1 to ignore the Gromacs warning)<br>
<br>
I tried this setting, to find the temperature is OK, but I am
not sure whether it will introduce some artifacts in the
simulation and what kind of artifacts. Could you tell me?
Thanks in advance.<br>
<br>
Best,<br>
<font color="#888888"><br>
Qin<br>
<br>
<br>
</font></blockquote>
</div>
<br>
</blockquote>
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