<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">It sounds like there is something wrong with the 'B' topology. Have you tried the 'decoupling' .mdp parameters? They're there specifically for your type of calculations.<div><br></div><div>Sander<br><div><br></div><div><br><div><div>On Sep 2, 2010, at 04:58 , Emanuel Birru wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div lang="EN-AU" link="blue" vlink="purple"><div class="WordSection1" style="page: WordSection1; "><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US">Hi,<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US"><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US">I am doing a partition coefficient of solute between 1-Octanol and water using gromacs ffG53a6 force field. Actually I am trying to reproduce Garrido et al’ s paper (J. Chem Theory Comput. 2009). The first thing I have done is to predict the Gibbs free energy of salvation of pentane (my solute) in 1-Octanol by thermodynamics integration method using 16<span class="Apple-converted-space"> </span></span><span lang="EN-US" style="font-family: 'Times New Roman', serif; ">λ</span><span lang="EN-US"><span class="Apple-converted-space"> </span>(lambda) values. It works well for<span style="color: rgb(31, 73, 125); "><span class="Apple-converted-space"> </span></span></span><span lang="EN-US" style="font-family: 'Times New Roman', serif; ">λ</span><span lang="EN-US">=0. 0.05, 0.1, 0.2, 0.3, 0.4 and 0.5. The problem ha<span style="color: rgb(31, 73, 125); ">s</span><span class="Apple-converted-space"> </span>stated<span class="Apple-converted-space"> </span><span style="color: rgb(31, 73, 125); ">at</span><span class="Apple-converted-space"> </span></span><span lang="EN-US" style="font-family: 'Times New Roman', serif; ">λ=0.6 and it is LINCS error which says as follows:</span><span lang="EN-US"><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: 36pt; "><span lang="EN-US">Fatal error:<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 72pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US">Too many LINCS warnings (1001)<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 72pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US">If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US">The atoms that make the problem are pentane atoms.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US"><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US">I have put the parameter file that I am using on this link<span class="Apple-converted-space"> </span><a href="http://hydra.pharm.monash.edu.au/md_project/production.txt" style="color: blue; text-decoration: underline; ">http://hydra.pharm.monash.edu.au/md_project/production.txt</a><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US"><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US">Before I run the production simulation I minimized the system well as exactly stated on the paper.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US" style="color: rgb(31, 73, 125); "> <o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US">After I got the error I have tried to run it again by changing the time step and the soft core value i.e sc_alpha and run three jobs independently<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 54pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt; "><span lang="EN-US"><span>1.<span style="font: normal normal normal 7pt/normal 'Times New Roman'; "> <span class="Apple-converted-space"> </span></span></span></span><span lang="EN-US">With 1fs time step and sc_alpha = 1.51<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 54pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt; "><span lang="EN-US"><span>2.<span style="font: normal normal normal 7pt/normal 'Times New Roman'; "> <span class="Apple-converted-space"> </span></span></span></span><span lang="EN-US">With 2fs time step changing sc_alpha to 0.5 and<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 54pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt; "><span lang="EN-US"><span>3.<span style="font: normal normal normal 7pt/normal 'Times New Roman'; "> <span class="Apple-converted-space"> </span></span></span></span><span lang="EN-US">With 1fs time step and 0.5 sc_alpha<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US">The same problem happened for 2 and 3 but 1 works well, but the average dVpot/d</span><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><span class="Apple-converted-space"> </span>λ is not what I expected, its >+7. I could not figure it out where exactly the problem is.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US" style="font-family: 'Times New Roman', serif; ">Thanks in advance for your advise.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US" style="font-family: 'Times New Roman', serif; ">Cheers,<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-US" style="font-family: 'Times New Roman', serif; ">Emanuel</span><span lang="EN-US"><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div></div>--<span class="Apple-converted-space"> </span><br>gmx-developers mailing list<br><a href="mailto:gmx-developers@gromacs.org" style="color: blue; text-decoration: underline; ">gmx-developers@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" style="color: blue; text-decoration: underline; ">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>Please don't post (un)subscribe requests to the list. Use the<span class="Apple-converted-space"> </span><br>www interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-developers-request@gromacs.org" style="color: blue; text-decoration: underline; ">gmx-developers-request@gromacs.org</a>.</div></span></blockquote></div><br></div></div></body></html>