[gmx-users] Normal Mode Analysis

[Mark Abraham]

On 24/10/2011 6:56 PM, James Starlight wrote:
> As the consequence I've done my NMA calculations without of any 
> constraints :)
>
> integrator    = nm        ; Normal Mode Analysis
> constraints         =  none
>
>
> 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?

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.

>
> By the way before this NMA I've done 2 energy minimization calculations
> first by Steepest algorithm (emtool= 1000) and then by CG ( emtool=10)
> but resulting force was still not small enought (8.92766e+02). How I 
> can futher minimize my structurere?

Smaller EM steps might do something.

>
> Finally I've forced with the diffuculty of the analysing of my data by 
> the  g_anaeig
> E,g I want to obtain fluctuations of some atoms from my eigenvectors
> g_anaeig -s fornma22.tpr -v eigenvec.trr -eig eigenval2.xvg -rmsf 
> -first -1
> 1 0
>
> 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 ?

We can't tell from this information.

Mark

>
>
> Thanks,
> James
>
>
> 2011/10/23 James Starlight <jmsstarlight at gmail.com 
> <mailto:jmsstarlight at gmail.com>>
>
>     I want to come back to the question of the NMA in the Gromacs :)
>
>     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
>
>
>     1- I've performed CG minimization of my initianl structure
>
>     2- I've loadet to the gromp .tpr file of my minimized structure
>
>     3-  I've used mdrun and obtain error
>     Fatal error:
>     Constraints present with Normal Mode Analysis, this combination is
>     not supported
>
>     So I suppose that the problem with my .mdp file wich consist of
>     the parametres for the NMA of Lyzosyme in water :)
>
>     integrator    = nm        ; Normal Mode Analysis
>
>     ; Parameters describing how to find the neighbors of each atom and
>     how to calculate the interactions
>     nstlist        = 1        ; Frequency to update the neighbor list
>     and long range forces
>     ns_type        = grid        ; Method to determine neighbor list
>     (simple, grid)
>     rlist        = 1.0        ; Cut-off for making neighbor list
>     (short range forces)
>     coulombtype    = PME        ; Treatment of long range
>     electrostatic interactions
>     rcoulomb    = 1.0        ; Short-range electrostatic cut-off
>     rvdw        = 1.0        ; Short-range Van der Waals cut-off
>     pbc        = xyz         ; Periodic Boundary Conditions (yes/no)
>
>
>     How I should edit this configure file for my NMA?
>     If I edit the above parametries for rvdw etc in accardance to the
>     http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis?highlight=nm
>     I've obtained error that
>
>     ERROR 1 [file nma.mdp]:
>       With coulombtype = PME, rcoulomb must be equal to rlist
>       If you want optimal energy conservation or exact integration use
>     PME-Switch
>
>
>     ERROR 2 [file nma.mdp]:
>       With vdwtype = Cut-off, rvdw must be >= rlist
>
>     What are the most suitable coulombtype for the NMA and combination
>     of the other options?
>
>
>     James
>
>
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111024/525dee1e/attachment.html>