date:20110117

[gmx-users] g_covar

2011-01-17 Thread shahrbanoo karbalaee

Thank you justin and  his colleagues and you  Mr Tsjerk.

-- 
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Re: [gmx-users] eNERGY mINIMIZATION

2011-01-17 Thread Mark Abraham


On 18/01/2011 3:12 PM, bharat gupta wrote:

Sir,
That's what  I want to know how u found out that the P.E. is ok and 
then what about the PE graph ??


A value of large magnitude and negative sign is probably OK. Exactly how 
large varies widely with system composition, force field, etc. So nobody 
worries much about this.


Does it has to be some what parallel to x-axis in case of every 
minimized structure as in my case its not parallel to x-axis , rather 
its getting down towards the x-axis.. ... generally for a miminized 
structure how it should be ??


Like I said last time, the apparent gradient is not physical, so don't 
stress about it. The physical things are the magnitude of the energy, 
and the magnitude of the force.


... I again carried out the minimzation with emtol = 1000 and the 
values of PE and max force are


Steepest Descents converged to Fmax < 1000 in 826 steps

Potential Energy = -7.1715738e+05



OK, so this is a bit lower. Maybe you could go further. Maybe it's 
enough already. That depends on your purpose, but for simulation 
preparation, see my previous email.



Maximum force = 9.6300812e+02 on atom 1669

Norm of force = 2.0939770e+01

--

Correct me if I am wrong ... If the Fmax < Emtol , it means that the 
structure is minimized ??




Check out manual section 7.3.5.

One more thing I want to know .. since we are changing the topol file 
also while minimzation then the repitition of minimization again would 
lead to any drastic changes to the topology or not .. as in my case I 
first did with emtol = 2000 and then with emtol = 1000 ??




EM is fast, so you may as well just start from your original structure 
each time, so you have a simple workflow.


Mark
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Re: [gmx-users] eNERGY mINIMIZATION

2011-01-17 Thread bharat gupta

Sir,

That's what  I want to know how u found out that the P.E. is ok and then
what about the PE graph ?? Does it has to be some what parallel to x-axis in
case of every minimized structure as in my case its not parallel to x-axis
, rather its getting down towards the x-axis.. ... generally for a miminized
structure how it should be ?? ... I again carried out the minimzation with
emtol = 1000 and the values of PE and max force are


Steepest Descents converged to Fmax < 1000 in 826 steps

Potential Energy = -7.1715738e+05

Maximum force = 9.6300812e+02 on atom 1669

Norm of force = 2.0939770e+01

--

Correct me if I am wrong ... If the Fmax < Emtol , it means that the
structure is minimized ??

One more thing I want to know .. since we are changing the topol file also
while minimzation then the repitition of minimization again would lead to
any drastic changes to the topology or not .. as in my case I first did with
emtol = 2000 and then with emtol = 1000 ??




---
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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Re: [gmx-users] eNERGY mINIMIZATION

2011-01-17 Thread Mark Abraham


On 18/01/2011 2:50 PM, bharat gupta wrote:

Hi,
I did the energy minimization of my protein (230 amino acids) after 
adding ions .. and after checking the potential energy of the system I 
was getting thee graph which is different from the one given  in the 
lysozyme tutorial i.e. the the potential line in graph is not parallel 
to the x axix..


You're comparing apples and oranges... maybe lysozyme is already pretty 
close to the minimum. Consider the axis scales, also. Note that the 
energy change per EM step doesn't have any physical meaning.



Here is are conditions that I used for minimization :

define = -DFLEX_SPC

constraints = none

integrator = steep

nsteps = 5

;

; Energy minimizing stuff

;

emtol = 2000

emstep = 0.01

nstcomm = 1

ns_type = grid

rlist = 1

coulombtype = PME

rcoulomb = 1.0

rvdw = 1.0

Tcoupl = no

Pcoupl = no

gen_vel = no


I got the following result :-
Steepest Descents converged to Fmax < 2000 in 296 steps

Potential Energy = -6.9540075e+05

Maximum force = 1.9863752e+03 on atom 1669

Norm of force = 3.7864201e+01

--

I want to know which parameters are important  to get a correct 
minimized structure and what value do I have to take for emtol and 
nsteps to minimize the structure properly.. Also how would I know that 
at what value of emtol my protein will be minimized..




How long should a piece of string be? Your PE is OK, so if you reduce 
emtol then you can reduce the maximum force. This will prolong the EM if 
you think you need to do that.


I checked the manual to get some details but there only the basic 
theory of minimzation is written.. A detailed explanation will be more 
helpful...




The purpose of EM is normally to relieve bad contacts, fill solvent 
voids, etc. Do something plausible (like you've done) and then try the 
next step. If you get problems there, go back and do EM harder (among 
other strategies)


Mark
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[gmx-users] eNERGY mINIMIZATION

2011-01-17 Thread bharat gupta

Hi,

I did the energy minimization of my protein (230 amino acids) after adding
ions .. and after checking the potential energy of the system I was getting
thee graph which is different from the one given  in the lysozyme tutorial
i.e. the the potential line in graph is not parallel to the x axix.. Here is
are conditions that I used for minimization :


define = -DFLEX_SPC

constraints = none

integrator = steep

nsteps = 5

;

; Energy minimizing stuff

;

emtol = 2000

emstep = 0.01

nstcomm = 1

ns_type = grid

rlist = 1

coulombtype = PME

rcoulomb = 1.0

rvdw = 1.0

Tcoupl = no

Pcoupl = no

gen_vel = no

I got the following result :-

Steepest Descents converged to Fmax < 2000 in 296 steps

Potential Energy = -6.9540075e+05

Maximum force = 1.9863752e+03 on atom 1669

Norm of force = 3.7864201e+01

--

I want to know which parameters are important  to get a correct minimized
structure and what value do I have to take for emtol and nsteps to minimize
the structure properly.. Also how would I know that at what value of emtol
my protein will be minimized.. I checked the manual to get some details but
there only the basic theory of minimzation is written.. A detailed
explanation will be more helpful...

-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
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Re: [gmx-users] spurious forces while doing pulling simulation

2011-01-17 Thread Amit Choubey

It seems that i cannot figure out a way to change the absolute reference
point (Its the origin by default).

Amit

On Mon, Jan 17, 2011 at 5:52 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> Yes Justin i understand that. Heres what i think is going on
>>
>> I dont have any reference group. Now the COM distance is calculated wrt
>> the origin and whenever the COM is more than half of the box its causing
>> problem.
>>
>>
> Correct.
>
>
>  I think changing the absolute reference to the initial COM of the pull
>> group (using pull_init1) should fix this issue but i am not confident.
>>
>>
> Using a defined reference group is the better method.  That way, the pull
> distance is calculated with respect to this reference, and it sounds like
> that will allow you to use the box you have already set up.
>
> -Justin
>
>  Thanks for looking into this.
>>
>> On Mon, Jan 17, 2011 at 5:36 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Amit Choubey wrote:
>>
>>Hi,
>>
>>I am still not able to see the reason for the periodic distances
>>coming into picture.
>>
>>
>>I guess I don't fully understand your procedure.  If you only want
>>to pull to a COM separation of 15 nm, there should be no problem,
>>but yet you're achieving a COM separation of 18.5 nm?  That's
>>exactly the problem.  If your box is 37 nm, 18.5 nm corresponds to
>>the transition at which the code utilizes either the unit cell
>>distance or the periodic distance as the restraint distance.  So it
>>is as this point that your forces go haywire.
>>
>>-Justin
>>
>>Also, why pull_geometry = direction_periodic cannot be used with
>>P-coupling; although it seems to do what i want.
>>
>>Amit
>>
>>On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey
>>mailto:kgp.a...@gmail.com>
>>>> wrote:
>>
>>   Hi,
>>
>>   Initially, the pull group center of mass is at 8.16 nm and i
>>want to
>>   pull 15 nm. I started with a box size of 37 nm in the pull
>>direction.
>>   The problem occurs when the COM is at 18.5 nm (ie at half the
>> box
>>   length).
>>
>>   Thanks for the attention.
>>
>>   Amit
>>
>>   On Mon, Jan 17, 2011 at 11:40 AM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>   >> wrote:
>>
>>
>>
>>   Amit Choubey wrote:
>>
>>   Hi all,
>>
>>   I am trying to do pulling simulation. Following are
>>the pull
>>   parameters
>>
>>   pull = umbrella
>>   pull_geometry = direction
>>   pull_vec1 = 0 0 1
>>   pull_group1 = RNA
>>   pull_rate1 = 0.01
>>   pull_k1 = 1000
>>   pull_start = yes
>>
>>   Everything works fine until the pull group COM
>>reaches half
>>   the box length. The COM position changes by the box
>>length
>>   and that causes huge force on the group. What should
>>i do to
>>   fix this ? Also i am using NPT coupling.
>>
>>
>>   You have to use a sufficiently large box, otherwise the
>>periodic
>>   distance becomes the reference distance when this
>>happens.  This
>>   has been discussed numerous times on the list (hint:
>>there is an
>>   archive for a reason!) and in the tutorial linked here:
>>
>>
>> http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling
>>
>>   -Justin
>>
>>   Amit
>>
>>
>>   -- 
>>
>>   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 list
>> gmx-users@gromacs.org 
>>   > >>
>>
>>
>>   http://lists.gromacs.org/mailman/listinfo/gmx-users
>>   Please search the archive at
>>   http://www.gromacs.org/Support/Mailing_Lists/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
>>
>>

Re: [gmx-users] spurious forces while doing pulling simulation

2011-01-17 Thread Justin A. Lemkul

Amit Choubey wrote:

Yes Justin i understand that. Heres what i think is going on

I dont have any reference group. Now the COM distance is calculated wrt 
the origin and whenever the COM is more than half of the box its causing 
problem.

Correct.

I think changing the absolute reference to the initial COM of the pull 
group (using pull_init1) should fix this issue but i am not confident.

Using a defined reference group is the better method.  That way, the pull 
distance is calculated with respect to this reference, and it sounds like that 
will allow you to use the box you have already set up.

-Justin

Thanks for looking into this.

On Mon, Jan 17, 2011 at 5:36 PM, Justin A. Lemkul > wrote:

Amit Choubey wrote:

Hi,
I am still not able to see the reason for the periodic distances
coming into picture.

I guess I don't fully understand your procedure.  If you only want
to pull to a COM separation of 15 nm, there should be no problem,
but yet you're achieving a COM separation of 18.5 nm?  That's
exactly the problem.  If your box is 37 nm, 18.5 nm corresponds to
the transition at which the code utilizes either the unit cell
distance or the periodic distance as the restraint distance.  So it
is as this point that your forces go haywire.

-Justin

Also, why pull_geometry = direction_periodic cannot be used with
P-coupling; although it seems to do what i want.

Amit

On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey
mailto:kgp.a...@gmail.com>
>> wrote:

   Hi,

   Initially, the pull group center of mass is at 8.16 nm and i
want to
   pull 15 nm. I started with a box size of 37 nm in the pull
direction.
   The problem occurs when the COM is at 18.5 nm (ie at half the box
   length).

   Thanks for the attention.

   Amit

   On Mon, Jan 17, 2011 at 11:40 AM, Justin A. Lemkul
mailto:jalem...@vt.edu>
   >> wrote:

   Amit Choubey wrote:

   Hi all,

   I am trying to do pulling simulation. Following are
the pull
   parameters

   pull = umbrella
   pull_geometry = direction
   pull_vec1 = 0 0 1
   pull_group1 = RNA
   pull_rate1 = 0.01
   pull_k1 = 1000
   pull_start = yes

   Everything works fine until the pull group COM
reaches half
   the box length. The COM position changes by the box
length
   and that causes huge force on the group. What should
i do to
   fix this ? Also i am using NPT coupling.

   You have to use a sufficiently large box, otherwise the
periodic
   distance becomes the reference distance when this
happens.  This
   has been discussed numerous times on the list (hint:
there is an
   archive for a reason!) and in the tutorial linked here:

 http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling

   -Justin

   Amit

   -- 

   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 list  
 gmx-users@gromacs.org 

   >

   http://lists.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive at
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before posting!
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   >.

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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  |

Re: [gmx-users] spurious forces while doing pulling simulation

2011-01-17 Thread Amit Choubey

Yes Justin i understand that. Heres what i think is going on

I dont have any reference group. Now the COM distance is calculated wrt the
origin and whenever the COM is more than half of the box its causing
problem.

I think changing the absolute reference to the initial COM of the pull group
(using pull_init1) should fix this issue but i am not confident.

Thanks for looking into this.

On Mon, Jan 17, 2011 at 5:36 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> Hi,
>> I am still not able to see the reason for the periodic distances coming
>> into picture.
>>
>>
> I guess I don't fully understand your procedure.  If you only want to pull
> to a COM separation of 15 nm, there should be no problem, but yet you're
> achieving a COM separation of 18.5 nm?  That's exactly the problem.  If your
> box is 37 nm, 18.5 nm corresponds to the transition at which the code
> utilizes either the unit cell distance or the periodic distance as the
> restraint distance.  So it is as this point that your forces go haywire.
>
> -Justin
>
>  Also, why pull_geometry = direction_periodic cannot be used with
>> P-coupling; although it seems to do what i want.
>>
>> Amit
>>
>> On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey > kgp.a...@gmail.com>> wrote:
>>
>>Hi,
>>
>>Initially, the pull group center of mass is at 8.16 nm and i want to
>>pull 15 nm. I started with a box size of 37 nm in the pull direction.
>>The problem occurs when the COM is at 18.5 nm (ie at half the box
>>length).
>>
>>Thanks for the attention.
>>
>>Amit
>>
>>On Mon, Jan 17, 2011 at 11:40 AM, Justin A. Lemkul >> wrote:
>>
>>
>>
>>Amit Choubey wrote:
>>
>>Hi all,
>>
>>I am trying to do pulling simulation. Following are the pull
>>parameters
>>
>>pull = umbrella
>>pull_geometry = direction
>>pull_vec1 = 0 0 1
>>pull_group1 = RNA
>>pull_rate1 = 0.01
>>pull_k1 = 1000
>>pull_start = yes
>>
>>Everything works fine until the pull group COM reaches half
>>the box length. The COM position changes by the box length
>>and that causes huge force on the group. What should i do to
>>fix this ? Also i am using NPT coupling.
>>
>>
>>You have to use a sufficiently large box, otherwise the periodic
>>distance becomes the reference distance when this happens.  This
>>has been discussed numerous times on the list (hint: there is an
>>archive for a reason!) and in the tutorial linked here:
>>
>>
>> http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling
>>
>>-Justin
>>
>>Amit
>>
>>
>>-- 
>>
>>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/Support/Mailing_Lists/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/Support/Mailing_Lists
>>
>>
>>
>>
> --
> 
>
> 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
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> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] spurious forces while doing pulling simulation

2011-01-17 Thread Justin A. Lemkul




Amit Choubey wrote:
Hi, 

I am still not able to see the reason for the periodic distances coming 
into picture.




I guess I don't fully understand your procedure.  If you only want to pull to a 
COM separation of 15 nm, there should be no problem, but yet you're achieving a 
COM separation of 18.5 nm?  That's exactly the problem.  If your box is 37 nm, 
18.5 nm corresponds to the transition at which the code utilizes either the unit 
cell distance or the periodic distance as the restraint distance.  So it is as 
this point that your forces go haywire.


-Justin

Also, why pull_geometry = direction_periodic cannot be used with 
P-coupling; although it seems to do what i want.


Amit

On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey > wrote:


Hi,

Initially, the pull group center of mass is at 8.16 nm and i want to
pull 15 nm. I started with a box size of 37 nm in the pull direction. 


The problem occurs when the COM is at 18.5 nm (ie at half the box
length).

Thanks for the attention.

Amit

On Mon, Jan 17, 2011 at 11:40 AM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



Amit Choubey wrote:

Hi all,

I am trying to do pulling simulation. Following are the pull
parameters

pull = umbrella
pull_geometry = direction
pull_vec1 = 0 0 1
pull_group1 = RNA
pull_rate1 = 0.01
pull_k1 = 1000
pull_start = yes

Everything works fine until the pull group COM reaches half
the box length. The COM position changes by the box length
and that causes huge force on the group. What should i do to
fix this ? Also i am using NPT coupling.


You have to use a sufficiently large box, otherwise the periodic
distance becomes the reference distance when this happens.  This
has been discussed numerous times on the list (hint: there is an
archive for a reason!) and in the tutorial linked here:


http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling

-Justin

Amit


-- 



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


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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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Re: [gmx-users] table-extension in mdp ?!

2011-01-17 Thread TJ Mustard

On January 17, 2011 at 4:32 PM jojo J wrote:

Dear users,

Please help me with the following problem. My simulation is crashing for an unstability reason I guess. Can you please help me what wrong is exaclty. I had done the simulation with exactly the same input files but with version 4.0.7 and never got this error. Thanks for your comments.

Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'solute'
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 8685.00

NOTE 1 [file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy

NOTE 2 [file md.mdp]:
The sum of the two largest charge group radii (0.204120) is larger than
rlist (1.10) - rvdw (1.00)

Analysing residue names:
There are: 240 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Largest charge group radii for Van der Waals: 0.102, 0.102 nm
This run will generate roughly 343 Mb of data

output.mdrun

step 7200, will finish Tue Jan 18 03:51:24 2011imb F 9%
step 7300, will finish Tue Jan 18 03:44:57 2011Warning: 1-4 interaction between 2121 and 2128 at distance 12.290 which is larger than the 1-4 table size 2.100 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

I seem to have a similar problem but you are having many more than I. If I were you I would fix the two "NOTES" first. Once those go away the 1-4 interaction warning might disappear as well.

TJ Mustard
Email: musta...@onid.orst.edu

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