subject:"\[gmx\-users\] Freezing a portion of a protein during simulation"

Re: [gmx-users] Freezing a portion of a protein during simulation

2010-04-29 Thread Justin A. Lemkul




Anirban Ghosh wrote:

Hello Justin,

Thanks a lot for your reply.
I am using the option "freezegrps" in my .mdp file, given below:
-

;define  = -DSTRONG_POSRES
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 0.2 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) 
constrained

lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics

pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more 
accurate

tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 300   300 ; reference temperature, one for each 
group, in K

; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell 
distribution

gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed

freezegrps  = Fixed
freezedim   = Y Y Y


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.




If you're using freezegrps, I see no need to define position restraints.

As for the exclusions, your group "Fixed" has to be listed in energygrps, and 
exclusions within this group are established with "energygrp_excl = Fixed 
Fixed."  There are a whole host of errors that can come up, based on what 
exactly "Fixed" comprises, but there are some good threads in the archives on 
how to fix these.  I still think using position restraints is far easier...


-Justin


Regards,

Anirban







On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul > wrote:




Anirban Ghosh wrote:

Hello Justin,

In my topology file I am declaring:

---
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Strong position restraints on rest of B2AR
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif


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?


; Include water topology
#include "spc.itp"

-
And in my .mdp file I am giving:

-
define   = -DSTRONG_POSRES; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5000  ; 2 * 5 = 100 ps
dt = 0.002 ; 2 fs

---


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).

[gmx-users] Freezing a portion of a protein during simulation

2010-04-29 Thread Anirban Ghosh

Hello Justin,

Thanks a lot for your reply.
I am using the option "freezegrps" in my .mdp file, given below:
-

;define  = -DSTRONG_POSRES
define  = -DPOSRES  ; position restrain the protein

; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1 ; 2 * 5 = 100 ps

dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 0.2 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more
accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 300   300 ; reference temperature, one for each group,
in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed

freezegrps  = Fixed
freezedim   = Y Y Y


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.

Regards,

Anirban






On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul  wrote:

>
>
> Anirban Ghosh wrote:
>
>> Hello Justin,
>>
>> In my topology file I am declaring:
>>
>> ---
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre.itp"
>> #endif
>>
>> ; Strong position restraints on rest of B2AR
>> #ifdef STRONG_POSRES
>> #include "strong_posre.itp"
>> #endif
>>
>>
> 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?
>
>
>  ; Include water topology
>> #include "spc.itp"
>>
>> -
>> And in my .mdp file I am giving:
>>
>> -
>> define   = -DSTRONG_POSRES; Run parameters
>> integrator  = md; leap-frog integrator
>> nsteps  = 5000  ; 2 * 5 = 100 ps
>> dt = 0.002 ; 2 fs
>>
>> ---
>>
>
> 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).
>
>
>  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.
>>
>>
> 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 easie

[gmx-users] Freezing a portion of a protein during simulation

2010-04-28 Thread Anirban Ghosh

Hello Justin,

Thanks a lot for your reply.
I am using the option "freezegrps" in my .mdp file, given below:
-

;define  = -DSTRONG_POSRES
define  = -DPOSRES  ; position restrain the protein

; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1 ; 2 * 5 = 100 ps

dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 0.2 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more
accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 300   300 ; reference temperature, one for each group,
in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed

freezegrps  = Fixed
freezedim   = Y Y Y


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.

Regards,

Anirban






On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul  wrote:

>
>
> Anirban Ghosh wrote:
>
>> Hello Justin,
>>
>> In my topology file I am declaring:
>>
>> ---
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre.itp"
>> #endif
>>
>> ; Strong position restraints on rest of B2AR
>> #ifdef STRONG_POSRES
>> #include "strong_posre.itp"
>> #endif
>>
>>
> 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?
>
>
>  ; Include water topology
>> #include "spc.itp"
>>
>> -
>> And in my .mdp file I am giving:
>>
>> -
>> define   = -DSTRONG_POSRES; Run parameters
>> integrator  = md; leap-frog integrator
>> nsteps  = 5000  ; 2 * 5 = 100 ps
>> dt = 0.002 ; 2 fs
>>
>> ---
>>
>
> 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).
>
>
>  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.
>>
>>
> 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 easie

Re: [gmx-users] Freezing a portion of a protein during simulation

2010-04-28 Thread Anirban Ghosh

Hello Justin,

Thanks a lot for your reply.
I am using the option "freezegrps" in my .mdp file, given below:
-

;define  = -DSTRONG_POSRES
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 0.2 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more
accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 300   300 ; reference temperature, one for each group,
in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed

freezegrps  = Fixed
freezedim   = Y Y Y


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.

Regards,

Anirban





On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul  wrote:

>
>
> Anirban Ghosh wrote:
>
>> Hello Justin,
>>
>> In my topology file I am declaring:
>>
>> ---
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre.itp"
>> #endif
>>
>> ; Strong position restraints on rest of B2AR
>> #ifdef STRONG_POSRES
>> #include "strong_posre.itp"
>> #endif
>>
>>
> 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?
>
>
>  ; Include water topology
>> #include "spc.itp"
>>
>> -
>> And in my .mdp file I am giving:
>>
>> -
>> define   = -DSTRONG_POSRES; Run parameters
>> integrator  = md; leap-frog integrator
>> nsteps  = 5000  ; 2 * 5 = 100 ps
>> dt = 0.002 ; 2 fs
>>
>> ---
>>
>
> 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).
>
>
>  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.
>>
>>
> 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 t

Re: [gmx-users] Freezing a portion of a protein during simulation

2010-04-28 Thread Justin A. Lemkul




Anirban Ghosh wrote:

Hello Justin,

In my topology file I am declaring:
---
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Strong position restraints on rest of B2AR
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif



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?



; Include water topology
#include "spc.itp"
-
And in my .mdp file I am giving:
-
define   = -DSTRONG_POSRES
; Run parameters

integrator  = md; leap-frog integrator
nsteps  = 5000  ; 2 * 5 = 100 ps
dt = 0.002 ; 2 fs
---


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).


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.




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.


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.


-Justin


Regards,

Anirban

On Fri, Apr 23, 2010 at 5:37 PM, Justin A. Lemkul > wrote:




Anirban Ghosh wrote:

Hi ALL,

I want to do a MD simulation by restraining (freezing) the
helical portions and allowing only the loop regions to move. I
tried doing this by applying heavy restrain on the helical
residues by generating a .itp file with the "genrestr" command
with an index file containing the desired residue numbers.
However during the simulation I am finding that the entire
protein is moving. Am I doing anything wrong? Or is there any
other way to freeze a portion of a protein? Any suggestion is
welcome. thanks a lot in advance.


If your protein is still moving, then you aren't correctly applying
your position restraints.  Without seeing your topology and .mdp
file, there's no way to know what you're doing wrong.

You can also use the freezegrps option in the .mdp file, but then
you also have to make sure you're using the appropriate
energygrp_excl, etc.  It is generally much easier to apply position
restraints.

-Justin


Regards,

Anirban


-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


-- 
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] Freezing a portion of a protein during simulation

2010-04-28 Thread Anirban Ghosh

Hello Justin,

In my topology file I am declaring:
---
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Strong position restraints on rest of B2AR
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif

; Include water topology
#include "spc.itp"
-
And in my .mdp file I am giving:
-
define   = -DSTRONG_POSRES
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5000  ; 2 * 5 = 100 ps
dt = 0.002 ; 2 fs
---
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.

Regards,

Anirban


On Fri, Apr 23, 2010 at 5:37 PM, Justin A. Lemkul  wrote:

>
>
> Anirban Ghosh wrote:
>
>> Hi ALL,
>>
>> I want to do a MD simulation by restraining (freezing) the helical
>> portions and allowing only the loop regions to move. I tried doing this by
>> applying heavy restrain on the helical residues by generating a .itp file
>> with the "genrestr" command with an index file containing the desired
>> residue numbers. However during the simulation I am finding that the entire
>> protein is moving. Am I doing anything wrong? Or is there any other way to
>> freeze a portion of a protein? Any suggestion is welcome. thanks a lot in
>> advance.
>>
>
> If your protein is still moving, then you aren't correctly applying your
> position restraints.  Without seeing your topology and .mdp file, there's no
> way to know what you're doing wrong.
>
> You can also use the freezegrps option in the .mdp file, but then you also
> have to make sure you're using the appropriate energygrp_excl, etc.  It is
> generally much easier to apply position restraints.
>
> -Justin
>
>
>> Regards,
>>
>> Anirban
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
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Re: [gmx-users] Freezing a portion of a protein during simulation

2010-04-27 Thread Anirban Ghosh

Hello Justin,

In my topology file I am declaring:
---
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Strong position restraints on rest of B2AR
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif

; Include water topology
#include "spc.itp"
-
And in my .mdp file I am giving:
-
define   = -DSTRONG_POSRES
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5000  ; 2 * 5 = 100 ps
dt = 0.002 ; 2 fs
---
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.

Regards,

Anirban

On Fri, Apr 23, 2010 at 5:37 PM, Justin A. Lemkul  wrote:

>
>
> Anirban Ghosh wrote:
>
>> Hi ALL,
>>
>> I want to do a MD simulation by restraining (freezing) the helical
>> portions and allowing only the loop regions to move. I tried doing this by
>> applying heavy restrain on the helical residues by generating a .itp file
>> with the "genrestr" command with an index file containing the desired
>> residue numbers. However during the simulation I am finding that the entire
>> protein is moving. Am I doing anything wrong? Or is there any other way to
>> freeze a portion of a protein? Any suggestion is welcome. thanks a lot in
>> advance.
>>
>
> If your protein is still moving, then you aren't correctly applying your
> position restraints.  Without seeing your topology and .mdp file, there's no
> way to know what you're doing wrong.
>
> You can also use the freezegrps option in the .mdp file, but then you also
> have to make sure you're using the appropriate energygrp_excl, etc.  It is
> generally much easier to apply position restraints.
>
> -Justin
>
>
>> Regards,
>>
>> Anirban
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
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Re: [gmx-users] Freezing a portion of a protein during simulation

2010-04-23 Thread Justin A. Lemkul




Anirban Ghosh wrote:

Hi ALL,

I want to do a MD simulation by restraining (freezing) the helical 
portions and allowing only the loop regions to move. I tried doing this 
by applying heavy restrain on the helical residues by generating a .itp 
file with the "genrestr" command with an index file containing the 
desired residue numbers. However during the simulation I am finding that 
the entire protein is moving. Am I doing anything wrong? Or is there any 
other way to freeze a portion of a protein? Any suggestion is welcome. 
thanks a lot in advance.


If your protein is still moving, then you aren't correctly applying your 
position restraints.  Without seeing your topology and .mdp file, there's no way 
to know what you're doing wrong.


You can also use the freezegrps option in the .mdp file, but then you also have 
to make sure you're using the appropriate energygrp_excl, etc.  It is generally 
much easier to apply position restraints.


-Justin



Regards,

Anirban



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Freezing a portion of a protein during simulation

2010-04-23 Thread Anirban Ghosh

Hi ALL,

I want to do a MD simulation by restraining (freezing) the helical portions
and allowing only the loop regions to move. I tried doing this by applying
heavy restrain on the helical residues by generating a .itp file with the
"genrestr" command with an index file containing the desired residue
numbers. However during the simulation I am finding that the entire protein
is moving. Am I doing anything wrong? Or is there any other way to freeze a
portion of a protein? Any suggestion is welcome. thanks a lot in advance.

Regards,

Anirban
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Re: [gmx-users] Freezing a portion of a protein during simulation

[gmx-users] Freezing a portion of a protein during simulation

[gmx-users] Freezing a portion of a protein during simulation

Re: [gmx-users] Freezing a portion of a protein during simulation

Re: [gmx-users] Freezing a portion of a protein during simulation

[gmx-users] Freezing a portion of a protein during simulation

Re: [gmx-users] Freezing a portion of a protein during simulation

Re: [gmx-users] Freezing a portion of a protein during simulation

[gmx-users] Freezing a portion of a protein during simulation

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