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On 24/10/2011 6:56 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopzeZBScCoj1bu6_sF39mh-jZjmbE_CzMuNb6QtRL3XbCg@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
These are particular to the force field involved, not the software.
Please consult the appropriate literature, and see what others have
used for similar work.<br>
<br>
<blockquote
cite="mid:CAALQopzeZBScCoj1bu6_sF39mh-jZjmbE_CzMuNb6QtRL3XbCg@mail.gmail.com"
type="cite">
<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>
</blockquote>
<br>
Smaller EM steps might do something.<br>
<br>
<blockquote
cite="mid:CAALQopzeZBScCoj1bu6_sF39mh-jZjmbE_CzMuNb6QtRL3XbCg@mail.gmail.com"
type="cite">
<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>
</blockquote>
<br>
We can't tell from this information.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopzeZBScCoj1bu6_sF39mh-jZjmbE_CzMuNb6QtRL3XbCg@mail.gmail.com"
type="cite"><br>
<br>
Thanks,<br>
James<br>
<br>
<br>
<div class="gmail_quote">
2011/10/23 James Starlight <span dir="ltr"><<a
moz-do-not-send="true" 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 moz-do-not-send="true"
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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