As the consequence I've done my NMA calculations without of any constraints :)<br><br>integrator = nm ; Normal Mode Analysis<br>constraints = none<br><br><br>but I'm not sure if this could be valid because I didnt found any literature of such NMA in Gromacs. Could someone provide me with the appropriate cut-offs for the NMA in gromacs?<br>
<br>By the way before this NMA I've done 2 energy minimization calculations<br>first by Steepest algorithm (emtool= 1000) and then by CG ( emtool=10)<br>but resulting force was still not small enought (8.92766e+02). How I can futher minimize my structurere?<br>
<br>Finally I've forced with the diffuculty of the analysing of my data by the g_anaeig<br>E,g I want to obtain fluctuations of some atoms from my eigenvectors<br>g_anaeig -s fornma22.tpr -v eigenvec.trr -eig eigenval2.xvg -rmsf -first -1<br>
1 0<br><br>I've obtained a .xvg file fith the fluctuations along 1st mode but during opening that file by xgrace I've obtain some input error. Whats I've done wrong ?<br><br><br>Thanks,<br>James<br><br><br><div class="gmail_quote">
2011/10/23 James Starlight <span dir="ltr"><<a href="mailto:jmsstarlight@gmail.com">jmsstarlight@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
I want to come back to the question of the NMA in the Gromacs :)<br><br>I've found in manual possible algorithms of this analysis- I must calculate Hessian matrix via Md-run and then calculate modes with g_nmens program<br>
<br><br>1- I've performed CG minimization of my initianl structure<br><br>2- I've loadet to the gromp .tpr file of my minimized structure<br><br>3- I've used mdrun and obtain error <br>Fatal error:<br>Constraints present with Normal Mode Analysis, this combination is not supported<br>
<br>So I suppose that the problem with my .mdp file wich consist of the parametres for the NMA of Lyzosyme in water :)<br><br>integrator = nm ; Normal Mode Analysis<br><br>; Parameters describing how to find the neighbors of each atom and how to calculate the interactions<br>
nstlist = 1 ; Frequency to update the neighbor list and long range forces<br>ns_type = grid ; Method to determine neighbor list (simple, grid)<br>rlist = 1.0 ; Cut-off for making neighbor list (short range forces)<br>
coulombtype = PME ; Treatment of long range electrostatic interactions<br>rcoulomb = 1.0 ; Short-range electrostatic cut-off<br>rvdw = 1.0 ; Short-range Van der Waals cut-off<br>pbc = xyz ; Periodic Boundary Conditions (yes/no)<br>
<br><br>How I should edit this configure file for my NMA? <br>If I edit the above parametries for rvdw etc in accardance to the <a href="http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis?highlight=nm" target="_blank">http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis?highlight=nm</a> I've obtained error that<br>
<br>ERROR 1 [file nma.mdp]:<br> With coulombtype = PME, rcoulomb must be equal to rlist<br> If you want optimal energy conservation or exact integration use PME-Switch<br><br><br>ERROR 2 [file nma.mdp]:<br> With vdwtype = Cut-off, rvdw must be >= rlist<br>
<br>What are the most suitable coulombtype for the NMA and combination of the other options?<br><font color="#888888"><br><br>James<br><br> <br>
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