<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><pre><br>you mean that i should have it as protein and Ions but no water<br><br>tc-grps = Protein ions <br>tau_t = 0.1 0.1 <br>ref_t = 300 300 <br></pre><div><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Arial" size="2"><hr size="1"><b><span style="font-weight: bold;">De :</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span style="font-weight: bold;">À :</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Envoyé le :</span></b> Mercredi 13 Juillet 2011 14h42<br><b><span style="font-weight: bold;">Objet :</span></b> Re: Re : [gmx-users] Re: Adding Ions<br></font><br><br><br>errabah fatima ezzahra
wrote:<br>> <br>> *I am trying to do a Short position restrained simulation so i wrote * grompp -f pr.mdp -c system.gro -p file.top -o file.tpr , i added the NA+ to the pr.mdp file<br>> here the pr.mdp<br>> tc-grps = Protein W NA+<br><br>First of all, you should never do this.<br><br><a href="http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do" target="_blank">http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do</a><br><br>> tau_t = 0.1 0.1 0.1<br>> ref_t = 300 300 300<br>> ; Energy monitoring<br>> energygrps = Protein W NA+<br>> <br>> but it gave me an error :<br>> Fatal error:<br>> Group
NA+ not found in indexfile.<br>> Maybe you have non-default goups in your .mdp file, while not using the '-n' option of grompp.<br>> In that case use the '-n' option.<br>> <br>> i dont have an indexfile ? <br><br>The error message is a bit misleading. I have changed it for the upcoming release. The group name "NA+" is incorrect in some way. The names you can specify in the .mdp file without creating an index group are called "default groups," a listing of which (for version 4.5) can be found at:<br><br><a href="http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups" target="_blank">http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups</a><br><br>All [moleculetype] names are available by default. In your case you should probably just use "Protein Non-protein" as your tc-grps.<br><br>-Justin<br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D.
Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org"
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br><br></div></div></div></body></html>