<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>I am trying to do energy minimization but <br></span></div><div><br><span></span></div><div>
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<ul><li><h5><font size="3"><span style="font-weight: normal;">grompp -f
em.mdp -c </span></font><font face="Bitstream Charter, serif"><font size="3"><span style="font-weight: normal;">waterbox_ions.gro</span></font></font><font size="3"><span style="font-weight: normal;">
-p </span></font><font face="Bitstream Charter, serif"><font size="3"><span style="font-weight: normal;">file.top
</span></font></font><font size="3"><span style="font-weight: normal;">-o
em.tpr</span></font></h5>
</li><li><h5><font size="3"><span style="font-weight: normal;">mdrun -v -s
em.tpr -c system</span></font><font face="Bitstream Charter, serif"><font size="3"><span style="font-weight: normal;">.gro</span></font></font></h5></li></ul>the <font><font><font face="Bitstream Charter, serif"><font size="3"><span style="font-weight: normal;">waterbox_ions.gro have the NA ions but when i check the system.gro it does not have the ions <br></span></font></font></font></font></div><div><br><font><font><font face="Bitstream Charter, serif"><font size="3"><span style="font-weight: normal;"></span></font></font></font></font></div><div><font><font><font face="Bitstream Charter, serif"><font size="3"><span style="font-weight: normal;">what am i doing wrong here??<br></span></font></font></font></font></div><div>
</div><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"
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