<div class="gmail_quote"><br>Hello Justin,<br><br>Thanks a lot for your reply.<br>I am using the option "freezegrps" in my .mdp file, given below:<br>-----------------------------------------------------------------------------------------------------------------------------------------<br>
<br>;define = -DSTRONG_POSRES<br>define = -DPOSRES ; position restrain the protein<div class="im"><br>; Run parameters<br>integrator = md ; leap-frog integrator<br></div>nsteps = 10000 ; 2 * 50000 = 100 ps<div class="im">
<br>
dt = 0.002 ; 2 fs<br></div>; Output control<br>nstxout = 100 ; save coordinates every 0.2 ps<br>nstvout = 100 ; save velocities every 0.2 ps<br>nstenergy = 100 ; save energies every 0.2 ps<br>
nstlog = 100 ; update log file every 0.2 ps<br>; Bond parameters<br>continuation = no ; first dynamics run<br>constraint_algorithm = lincs ; holonomic constraints<br>constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained<br>
lincs_iter = 1 ; accuracy of LINCS<br>lincs_order = 4 ; also related to accuracy<br>; Neighborsearching<br>ns_type = grid ; search neighboring grid cels<br>nstlist = 5 ; 10 fs<br>
rlist = 1.0 ; short-range neighborlist cutoff (in nm)<br>rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)<br>rvdw = 1.0 ; short-range van der Waals cutoff (in nm)<br>
; Electrostatics<br>coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics<br>pme_order = 4 ; cubic interpolation<br>fourierspacing = 0.16 ; grid spacing for FFT<br>
; Temperature coupling is on<br>tcoupl = V-rescale ; modified Berendsen thermostat<br>tc-grps = Protein Non-Protein ; two coupling groups - more accurate<br>tau_t = 0.1 0.1 ; time constant, in ps<br>
ref_t = 300 300 ; reference temperature, one for each group, in K<br>; Pressure coupling is off<br>pcoupl = no ; no pressure coupling in NVT<br>; Periodic boundary conditions<br>pbc = xyz ; 3-D PBC<br>
; Dispersion correction<br>DispCorr = EnerPres ; account for cut-off vdW scheme<br>; Velocity generation<br>gen_vel = yes ; assign velocities from Maxwell distribution<br>gen_temp = 300 ; temperature for Maxwell distribution<br>
gen_seed = -1 ; generate a random seed<br><br>freezegrps = Fixed<br>freezedim = Y Y Y<br>--------------------------------------------------------------------------------------------------------------------------------------------<br>
<br>I was just wondering how to give the "energygrp_excl" parameters with it. Can you please guide me regarding this and also please go through the other parameters in the .mdp file.<br><br>Regards,<br><font color="#888888"><br>
Anirban</font><div><div></div><div class="h5"><a name="12848176b461c478_egexcl"><br>
</a>
<h4><a name="12848176b461c478_egexcl"><br></a></h4><br><br><br><br><div class="gmail_quote">On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><br>
<br>
Anirban Ghosh wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello Justin,<br>
<br>
In my topology file I am declaring:<br>
---------------------------------------------------------------------------------------------------------------<br>
; Include Position restraint file<br>
#ifdef POSRES<br>
#include "posre.itp"<br>
#endif<br>
<br>
; Strong position restraints on rest of B2AR<br>
#ifdef STRONG_POSRES<br>
#include "strong_posre.itp"<br>
#endif<br>
<br>
</blockquote>
<br></div>
What is in strong_posre.itp? Presumably you're only restraining certain residues, right? Did you create this with genrestr and an appropriate index group?<div><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
; Include water topology<br>
#include "spc.itp"<br>
-----------------------------------------------------------------------------------------------------------------<br>
And in my .mdp file I am giving:<br>
-----------------------------------------------------------------------------------------------------------------<br>
define = -DSTRONG_POSRES ; Run parameters<br>
integrator = md ; leap-frog integrator<br>
nsteps = 5000 ; 2 * 50000 = 100 ps<br>
dt = 0.002 ; 2 fs<br>
-------------------------------------------------------------------------------------------------------------------<br>
</blockquote>
<br></div>
If this is the entirety of your .mdp file, you're asking for trouble. Allowing all other parameters to be taken as default is very dangerous, and probably inappropriate (most notably cutoff electrostatics).<div>
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
But now what I am getting is that if I run MD using these restraints on the helical portion of the protein, then I am getting LINCS errors. However, if I allow the entire protein to move during MD, then it is running fine. What mistake am I making? And how can I freeze properly the helical portions and simulate only the loop? Thanks a lot in advance.<br>
<br>
</blockquote>
<br></div>
Recognize that there is a difference between "freezing" and "restraining." Read in the manual about what freezing is versus position restraints. Either way, you should be able to get things up and running, but position restraints are a bit easier to implement.<br>
<br>
If an unrestrained simulation runs fine (using that fragmented .mdp file?) then there are probably just bad clashes in the system that the restraints are not allowing to relax.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Regards,<br>
<br>
Anirban<div><div></div><div><br>
<br>
On Fri, Apr 23, 2010 at 5:37 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Anirban Ghosh wrote:<br>
<br>
Hi ALL,<br>
<br>
I want to do a MD simulation by restraining (freezing) the<br>
helical portions and allowing only the loop regions to move. I<br>
tried doing this by applying heavy restrain on the helical<br>
residues by generating a .itp file with the "genrestr" command<br>
with an index file containing the desired residue numbers.<br>
However during the simulation I am finding that the entire<br>
protein is moving. Am I doing anything wrong? Or is there any<br>
other way to freeze a portion of a protein? Any suggestion is<br>
welcome. thanks a lot in advance.<br>
<br>
<br>
If your protein is still moving, then you aren't correctly applying<br>
your position restraints. Without seeing your topology and .mdp<br>
file, there's no way to know what you're doing wrong.<br>
<br>
You can also use the freezegrps option in the .mdp file, but then<br>
you also have to make sure you're using the appropriate<br>
energygrp_excl, etc. It is generally much easier to apply position<br>
restraints.<br>
<br>
-Justin<br>
<br>
<br>
Regards,<br>
<br>
Anirban<br>
<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></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div><br>
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========================================<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]<a href="http://vt.edu" target="_blank">vt.edu</a> | (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>
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