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FYI I forgot to also say that the issue with demux.pl has been reported in published work too:<br>
<br>
<a class="moz-txt-link-freetext" href="https://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00981">https://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00981</a><br>
<br>
Cheers<br>
<br>
Tom<br>
<br>
<div class="moz-cite-prefix">On 07/07/2019 09:35, Piggot T. wrote:<br>
</div>
<blockquote type="cite" cite="mid:2B0A7FDA-EC80-4963-AF13-4B90FA39B35F@soton.ac.uk">
<div dir="ltr">Hi,</div>
<div dir="ltr"><br>
</div>
<div dir="ltr">This is a known problem, see:</div>
<div dir="ltr"><br>
</div>
<div dir="ltr"><a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgroups.google.com%2Fforum%2Fm%2F%23!topic%2Fplumed-users%2FXhB34MmSpjM&data=01%7C01%7Ct.piggot%40soton.ac.uk%7Ce60885b7a642493feb3008d702b623c5%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=wDSHOK8gRVVHHgINz%2FtaJug3QqUEGv2QWy%2B9Dag%2Fos8%3D&reserved=0" originalsrc="https://groups.google.com/forum/m/#!topic/plumed-users/XhB34MmSpjM" shash="opn7C7xjOuYBys0cbP/u6rFu7H8rrUv81Lc5RXHMtXiadRUHZwDTnlRhzDI+CoiUBa9RB2kTujdf3/S7e4aaMHUV7ua51GYuk1dPixrmYUCnULAATFoRtuGIQTC1baHautb7WZFS+qQt0dWjpgDbahYGqUNVOzWnffceU6QDmxg=" moz-do-not-send="true">https://groups.google.com/forum/m/#!topic/plumed-users/XhB34MmSpjM</a></div>
<div dir="ltr"><br>
</div>
<div dir="ltr">There’s also a modified script provided there too that I’ve used without problem for long trajectories.</div>
<div dir="ltr"><br>
</div>
<div dir="ltr">I guess the script provided by GROMACS should be updated. It is probably worth reporting it on redmine.</div>
<div dir="ltr"><br>
</div>
<div dir="ltr">Cheers </div>
<div dir="ltr"><br>
</div>
<div dir="ltr">Tom</div>
<div dir="ltr"><br>
On 7 Jul 2019, at 07:05, Yong Wang <<a href="mailto:wyongciac@gmail.com" moz-do-not-send="true">wyongciac@gmail.com</a>> wrote:<br>
<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">Hi,
<div><br>
</div>
<div>We are running a normal REMD with 10 replicas and an exchange frequency of 0.2ps, and tried to use
<a href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdemux.pl&data=01%7C01%7Ct.piggot%40soton.ac.uk%7Ce60885b7a642493feb3008d702b623c5%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=U4y9sZuuLMLGvDtLxeMXosz%2BhQYOPwqnuda6Lm8xGQY%3D&reserved=0" originalsrc="http://demux.pl" shash="yWdVREwmF0RvpvypbLibTttHf9Bm402lVqzeBZVC1VdzzWw03QC53kfh0Tu3995nCbONdZL5U1Z8RldtCsiqeU6dux3ZtlvmLVoUisuqrQVZAcu4b2i+zo3me/ZnzdO9jvBQ0O3FtIDUwr8kyTMEwil7wo5Xnq8nk0WrFGeSHVs=" moz-do-not-send="true">
demux.pl</a> to get continuous trajectories. But we found the demuxed trajectories always become discontinuous after 100ns. After some frustrating debugging, we found the replica index file (replica_index.xvg) was not corrected generated by
<a href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdemux.pl&data=01%7C01%7Ct.piggot%40soton.ac.uk%7Ce60885b7a642493feb3008d702b623c5%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=U4y9sZuuLMLGvDtLxeMXosz%2BhQYOPwqnuda6Lm8xGQY%3D&reserved=0" originalsrc="http://demux.pl" shash="yWdVREwmF0RvpvypbLibTttHf9Bm402lVqzeBZVC1VdzzWw03QC53kfh0Tu3995nCbONdZL5U1Z8RldtCsiqeU6dux3ZtlvmLVoUisuqrQVZAcu4b2i+zo3me/ZnzdO9jvBQ0O3FtIDUwr8kyTMEwil7wo5Xnq8nk0WrFGeSHVs=" moz-do-not-send="true">
demux.pl</a>. For example, the output looks like this:</div>
<div><br>
</div>
<div>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">99998.8
<span class="gmail-Apple-converted-space"> </span>9<span class="gmail-Apple-converted-space">
</span>2<span class="gmail-Apple-converted-space"> </span>4<span class="gmail-Apple-converted-space">
</span>0<span class="gmail-Apple-converted-space"> </span>5<span class="gmail-Apple-converted-space">
</span>8<span class="gmail-Apple-converted-space"> </span>3<span class="gmail-Apple-converted-space">
</span>7<span class="gmail-Apple-converted-space"> </span>6<span class="gmail-Apple-converted-space">
</span>1</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">99999 <span class="gmail-Apple-converted-space">
</span>9<span class="gmail-Apple-converted-space"> </span>2<span class="gmail-Apple-converted-space">
</span>4<span class="gmail-Apple-converted-space"> </span>0<span class="gmail-Apple-converted-space">
</span>8<span class="gmail-Apple-converted-space"> </span>5<span class="gmail-Apple-converted-space">
</span>7<span class="gmail-Apple-converted-space"> </span>3<span class="gmail-Apple-converted-space">
</span>6<span class="gmail-Apple-converted-space"> </span>1</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">99999.2
<span class="gmail-Apple-converted-space"> </span>9<span class="gmail-Apple-converted-space">
</span>2<span class="gmail-Apple-converted-space"> </span>4<span class="gmail-Apple-converted-space">
</span>8<span class="gmail-Apple-converted-space"> </span>0<span class="gmail-Apple-converted-space">
</span>5<span class="gmail-Apple-converted-space"> </span>7<span class="gmail-Apple-converted-space">
</span>3<span class="gmail-Apple-converted-space"> </span>6<span class="gmail-Apple-converted-space">
</span>1</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">99999.4
<span class="gmail-Apple-converted-space"> </span>9<span class="gmail-Apple-converted-space">
</span>2<span class="gmail-Apple-converted-space"> </span>8<span class="gmail-Apple-converted-space">
</span>4<span class="gmail-Apple-converted-space"> </span>5<span class="gmail-Apple-converted-space">
</span>0<span class="gmail-Apple-converted-space"> </span>7<span class="gmail-Apple-converted-space">
</span>3<span class="gmail-Apple-converted-space"> </span>1<span class="gmail-Apple-converted-space">
</span>6</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">99999.6
<span class="gmail-Apple-converted-space"> </span>9<span class="gmail-Apple-converted-space">
</span>2<span class="gmail-Apple-converted-space"> </span>8<span class="gmail-Apple-converted-space">
</span>5<span class="gmail-Apple-converted-space"> </span>4<span class="gmail-Apple-converted-space">
</span>0<span class="gmail-Apple-converted-space"> </span>7<span class="gmail-Apple-converted-space">
</span>3<span class="gmail-Apple-converted-space"> </span>1<span class="gmail-Apple-converted-space">
</span>6</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">99999.8
<span class="gmail-Apple-converted-space"> </span>9<span class="gmail-Apple-converted-space">
</span>2<span class="gmail-Apple-converted-space"> </span>8<span class="gmail-Apple-converted-space">
</span>5<span class="gmail-Apple-converted-space"> </span>4<span class="gmail-Apple-converted-space">
</span>0<span class="gmail-Apple-converted-space"> </span>7<span class="gmail-Apple-converted-space">
</span>3<span class="gmail-Apple-converted-space"> </span>6<span class="gmail-Apple-converted-space">
</span>1</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">100000<span class="gmail-Apple-converted-space">
</span>9<span class="gmail-Apple-converted-space"> </span>2<span class="gmail-Apple-converted-space">
</span>8<span class="gmail-Apple-converted-space"> </span>4<span class="gmail-Apple-converted-space">
</span>5<span class="gmail-Apple-converted-space"> </span>0<span class="gmail-Apple-converted-space">
</span>7<span class="gmail-Apple-converted-space"> </span>3<span class="gmail-Apple-converted-space">
</span>6<span class="gmail-Apple-converted-space"> </span>1</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">100000<span class="gmail-Apple-converted-space">
</span>2<span class="gmail-Apple-converted-space"> </span>9<span class="gmail-Apple-converted-space">
</span>8<span class="gmail-Apple-converted-space"> </span>4<span class="gmail-Apple-converted-space">
</span>0<span class="gmail-Apple-converted-space"> </span>5<span class="gmail-Apple-converted-space">
</span>7<span class="gmail-Apple-converted-space"> </span>3<span class="gmail-Apple-converted-space">
</span>6<span class="gmail-Apple-converted-space"> </span>1</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">100000<span class="gmail-Apple-converted-space">
</span>2<span class="gmail-Apple-converted-space"> </span>9<span class="gmail-Apple-converted-space">
</span>8<span class="gmail-Apple-converted-space"> </span>0<span class="gmail-Apple-converted-space">
</span>4<span class="gmail-Apple-converted-space"> </span>5<span class="gmail-Apple-converted-space">
</span>7<span class="gmail-Apple-converted-space"> </span>6<span class="gmail-Apple-converted-space">
</span>3<span class="gmail-Apple-converted-space"> </span>1</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">100001<span class="gmail-Apple-converted-space">
</span>9<span class="gmail-Apple-converted-space"> </span>2<span class="gmail-Apple-converted-space">
</span>0<span class="gmail-Apple-converted-space"> </span>8<span class="gmail-Apple-converted-space">
</span>5<span class="gmail-Apple-converted-space"> </span>4<span class="gmail-Apple-converted-space">
</span>7<span class="gmail-Apple-converted-space"> </span>6<span class="gmail-Apple-converted-space">
</span>3<span class="gmail-Apple-converted-space"> </span>1</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">100001<span class="gmail-Apple-converted-space">
</span>9<span class="gmail-Apple-converted-space"> </span>2<span class="gmail-Apple-converted-space">
</span>0<span class="gmail-Apple-converted-space"> </span>8<span class="gmail-Apple-converted-space">
</span>5<span class="gmail-Apple-converted-space"> </span>4<span class="gmail-Apple-converted-space">
</span>7<span class="gmail-Apple-converted-space"> </span>3<span class="gmail-Apple-converted-space">
</span>6<span class="gmail-Apple-converted-space"> </span>1</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">100001<span class="gmail-Apple-converted-space">
</span>2<span class="gmail-Apple-converted-space"> </span>9<span class="gmail-Apple-converted-space">
</span>8<span class="gmail-Apple-converted-space"> </span>0<span class="gmail-Apple-converted-space">
</span>4<span class="gmail-Apple-converted-space"> </span>5<span class="gmail-Apple-converted-space">
</span>3<span class="gmail-Apple-converted-space"> </span>7<span class="gmail-Apple-converted-space">
</span>1<span class="gmail-Apple-converted-space"> </span>6</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">100001<span class="gmail-Apple-converted-space">
</span>2<span class="gmail-Apple-converted-space"> </span>9<span class="gmail-Apple-converted-space">
</span>8<span class="gmail-Apple-converted-space"> </span>4<span class="gmail-Apple-converted-space">
</span>0<span class="gmail-Apple-converted-space"> </span>5<span class="gmail-Apple-converted-space">
</span>3<span class="gmail-Apple-converted-space"> </span>7<span class="gmail-Apple-converted-space">
</span>1<span class="gmail-Apple-converted-space"> </span>6</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">100001<span class="gmail-Apple-converted-space">
</span>2<span class="gmail-Apple-converted-space"> </span>9<span class="gmail-Apple-converted-space">
</span>4<span class="gmail-Apple-converted-space"> </span>8<span class="gmail-Apple-converted-space">
</span>0<span class="gmail-Apple-converted-space"> </span>5<span class="gmail-Apple-converted-space">
</span>7<span class="gmail-Apple-converted-space"> </span>3<span class="gmail-Apple-converted-space">
</span>1<span class="gmail-Apple-converted-space"> </span>6</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">100002<span class="gmail-Apple-converted-space">
</span>2<span class="gmail-Apple-converted-space"> </span>9<span class="gmail-Apple-converted-space">
</span>4<span class="gmail-Apple-converted-space"> </span>0<span class="gmail-Apple-converted-space">
</span>8<span class="gmail-Apple-converted-space"> </span>5<span class="gmail-Apple-converted-space">
</span>7<span class="gmail-Apple-converted-space"> </span>3<span class="gmail-Apple-converted-space">
</span>1<span class="gmail-Apple-converted-space"> </span>6</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">100002<span class="gmail-Apple-converted-space">
</span>2<span class="gmail-Apple-converted-space"> </span>9<span class="gmail-Apple-converted-space">
</span>0<span class="gmail-Apple-converted-space"> </span>4<span class="gmail-Apple-converted-space">
</span>8<span class="gmail-Apple-converted-space"> </span>5<span class="gmail-Apple-converted-space">
</span>3<span class="gmail-Apple-converted-space"> </span>7<span class="gmail-Apple-converted-space">
</span>6<span class="gmail-Apple-converted-space"> </span>1</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">100002<span class="gmail-Apple-converted-space">
</span>2<span class="gmail-Apple-converted-space"> </span>9<span class="gmail-Apple-converted-space">
</span>0<span class="gmail-Apple-converted-space"> </span>8<span class="gmail-Apple-converted-space">
</span>4<span class="gmail-Apple-converted-space"> </span>5<span class="gmail-Apple-converted-space">
</span>3<span class="gmail-Apple-converted-space"> </span>7<span class="gmail-Apple-converted-space">
</span>6<span class="gmail-Apple-converted-space"> </span>1</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">100002<span class="gmail-Apple-converted-space">
</span>2<span class="gmail-Apple-converted-space"> </span>9<span class="gmail-Apple-converted-space">
</span>8<span class="gmail-Apple-converted-space"> </span>0<span class="gmail-Apple-converted-space">
</span>4<span class="gmail-Apple-converted-space"> </span>5<span class="gmail-Apple-converted-space">
</span>3<span class="gmail-Apple-converted-space"> </span>7<span class="gmail-Apple-converted-space">
</span>6<span class="gmail-Apple-converted-space"> </span>1</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:17px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">
<span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">100002<span class="gmail-Apple-converted-space">
</span>2<span class="gmail-Apple-converted-space"> </span>8<span class="gmail-Apple-converted-space">
</span>9<span class="gmail-Apple-converted-space"> </span>4<span class="gmail-Apple-converted-space">
</span>0<span class="gmail-Apple-converted-space"> </span>5<span class="gmail-Apple-converted-space">
</span>3<span class="gmail-Apple-converted-space"> </span>7<span class="gmail-Apple-converted-space">
</span>6<span class="gmail-Apple-converted-space"> </span>1</span></p>
<div><br>
</div>
<div>As you can see, the time information in the first column was confused after 100000 (corresponding to 100ns). So we tried to correct the time information, and the problem seems solved. In our case, we made minor modifications on the
<a href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdemux.pl&data=01%7C01%7Ct.piggot%40soton.ac.uk%7Ce60885b7a642493feb3008d702b623c5%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=U4y9sZuuLMLGvDtLxeMXosz%2BhQYOPwqnuda6Lm8xGQY%3D&reserved=0" originalsrc="http://demux.pl" shash="yWdVREwmF0RvpvypbLibTttHf9Bm402lVqzeBZVC1VdzzWw03QC53kfh0Tu3995nCbONdZL5U1Z8RldtCsiqeU6dux3ZtlvmLVoUisuqrQVZAcu4b2i+zo3me/ZnzdO9jvBQ0O3FtIDUwr8kyTMEwil7wo5Xnq8nk0WrFGeSHVs=" moz-do-not-send="true">
demux.pl</a> script by simplify replacing "%-20g" by "%-20.1f". And it works for us! </div>
<div><br>
</div>
<div>I don't know if this is the best solution but I am reporting this and hope it is helpful to others. And the issue can only occur when we use an exchange frequency smaller than 1ps and run the simulation longer than 100ns. Could you identify if this is
a minor bug or just limited to our case? Thanks a lot!</div>
<div><br>
</div>
<div>Regards,</div>
<div>Yong</div>
<div><br>
</div>
-- <br>
<div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div dir="ltr">
<div dir="ltr"><br>
==========================<br>
<div dir="ltr" style="font-size:small">Yong Wang</div>
<div dir="ltr" style="font-size:small">Postdoc in Lindorff-Larsen Lab<br>
Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science
<div>Department of Biology, University of Copenhagen<br>
Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark<br>
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<pre class="moz-signature" cols="72">--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.
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