Re: [gmx-users] How to convert C6 from GROMOS54a7 to sigma for OPLSAA

2017-08-20 Thread Ming Tang 
Hi Justin, thanks for your guidance!

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Re: [gmx-users] Setting up SA

2017-08-20 Thread Nikhil Maroli 
Hi,
Why dont you run it and see for a shorter time.
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[gmx-users] Setting up SA

2017-08-20 Thread Seera Suryanarayana 
Dear gromacs users,

I have one peptide which has 25 residues. I have done simulation for 100ns.
When I presented my analysis in lab, I was suggested to do investigation of
my simulation by simulated annealing (SA). Then I have gone through the
simulated annealing notes which I found on gromacs website and I got some
idea to do simulated annealing. I added the annealing points and
temperatures in my .mdp file as follow.

;simulated annealing
annealing= single
annealing-points  = 7
annealing-time= 0 4000 8000 12000 16000 2 24000
annealing-temp   = 300 310 315 330 320 310 300

What I want to do here is that first try to increase the temperature
gradually for some time then get it down to the reference temperature i.e
300K and allowed it to end of the simulation (100ns). Kindly tell me
whether my simulated annealing set up is correct.
Surya
Graduate student
India.
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Re: [gmx-users] Average and bfactors.pdb

2017-08-20 Thread farial tavakoli 
 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear justin
Thank you for your replyIt means, there is no problem, i can ignore it ang go 
ahead? 

Sent from Yahoo Mail for iPhone


On Monday, August 21, 2017, 2:34 AM, Justin Lemkul  wrote:



On 8/20/17 11:51 AM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  Dear gmx users
> I removed jumps from my .xtc file before by using gmx trjconv and viewed my 
> complex in vmd, it was ok and rhere was no jump. Now i use gmx rmsf and the 
> same .xtc file which was created after using gmx trjconv, but when i view 
> average. Pdb and bfactors.pdb files in pymol, my protein is still brocken. 
> Would you please advice me how to solve this problem?

There is no physical significance to an average set of coordinates.  These may 
appear broken or distorted.

http://www.gromacs.org/Documentation/Terminology/Average_Structure

-Justin

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==

Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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[gmx-users] Doubt about hessian matrix in Normal mode analysis

2017-08-20 Thread Varvdekar Bhagyesh Rajendra 
Dear Justin,

I used the following command to print ascii format of the hessian matrix to a 
file from the default mtx format of gromacs obtained after normal mode analysis.

gmxdump_d -mtx nm.mtx > hessian_matrix.dat

I would like to confirm the way the hessian matrix is written in this new ascii 
file. Is the following way correct where the x, y, z coordinates of the first 
atom are considered, then second atom and so on and so forth in each row and 
column and the matrix elements are the second order derivatives of potential 
energy with respect to its corresponding row and column coordinates ?

Here x_i = x coordinate of the i_th atom, y_i = y coordinate of the i_th atom, 
z_i = z coordinate of the i_th atom.
And the matrix elements M are the second order of U (Potential energy) with 
respect to its corresponding row and column coordinate i.e. M = d^2 U / dx_i d_i

   | x1 | y1 | z1 | x2 | y2 | z2 | ... | x_n | y_n | z_n |
-|
x1 | M  |  M | M  |  M | M  | M  | ...
---
y1 | M  |  M | M  |  M | M  | M  | ...
--
z1 | M  |  M | M  |  M | M  | M  | ...
--
x2 | M  |  M | M  |  M | M  | M  | ...
---
y2 | M  |  M | M  |  M | M  | M  | ...
--
z2 | M  |  M | M  |  M | M  | M  | ...
--
.
.
.
x_N
y_N
z_N 
--


I got some hint from the following past thread but I would like to confirm the 
same.

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-June/098468.html

Thank you,

Bhagyesh
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Re: [gmx-users] Average and bfactors.pdb

2017-08-20 Thread Justin Lemkul 



On 8/20/17 11:51 AM, farial tavakoli wrote:

  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear gmx users
I removed jumps from my .xtc file before by using gmx trjconv and viewed my 
complex in vmd, it was ok and rhere was no jump. Now i use gmx rmsf and the 
same .xtc file which was created after using gmx trjconv, but when i view 
average. Pdb and bfactors.pdb files in pymol, my protein is still brocken. 
Would you please advice me how to solve this problem?


There is no physical significance to an average set of coordinates.  These may 
appear broken or distorted.


http://www.gromacs.org/Documentation/Terminology/Average_Structure

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Regarding naming dipeptide in charmm36 Forcefield

2017-08-20 Thread Justin Lemkul 



On 8/20/17 3:16 PM, Dilip H N wrote:

Have you run pdb2gmx to process a simple protein or polypeptide? This is
done for you.  Each amino acid is defined.  If you supply a coordinate file
with a GLY-GLY peptide, pdb2gmx does everything you need.
No Sir,  are thr any tutorials on polypeptide pdb generation and getting
the topology (pdb2gmx process).., which would be highly beneficial

Thank you...



It's the simplest GROMACS use case.  Look through any of the tutorials linked on 
gromacs.org.  You need to have the starting coordinates already; GROMACS does 
not have the ability to generate a PDB of any arbitrary polypeptide for you.


-Justin

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==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Regarding naming dipeptide in charmm36 Forcefield

2017-08-20 Thread Dilip H N 
Have you run pdb2gmx to process a simple protein or polypeptide? This is
done for you.  Each amino acid is defined.  If you supply a coordinate file
with a GLY-GLY peptide, pdb2gmx does everything you need.
No Sir,  are thr any tutorials on polypeptide pdb generation and getting
the topology (pdb2gmx process).., which would be highly beneficial

Thank you...


 Sent with Mailtrack


On Fri, Aug 18, 2017 at 10:32 PM, Justin Lemkul  wrote:

>
>
> On 8/18/17 1:13 AM, Dilip H N wrote:
>
>> Thank you sir.,
>> 1] If so thn, is there any other possible way such that i can get a
>> peptide
>> (two aminoacids linked) and thn simulate it in CHARMM FF.. ?? (or) in
>> alanine dipeptide case which is the residue name in the .rtp file..?? and
>> how can i remove the n-methyl and  acetyl groups in order to get only
>> alanine dipeptide...
>>
>
> This doesn't make any sense to me.  The capping groups are what make
> alanine dipeptide (ALAD) what it is, not removing them.
>
> If you need to *generate* coordinates, then that's another matter. Plenty
> of software can do that (see links on gromacs.org).
>
> 2] Or should i modify modify any aminoacid (eg., glycine into diglycine)
>> into a peptide to run the simulation, and if so thn how can i take care of
>> charges in the peptide (since thee will be removal of H2O molecule between
>> them and diglycine case there will be some net charge resulting )..
>> I am running out of ideasSo any suggestions are welcome
>>
>
> Have you run pdb2gmx to process a simple protein or polypeptide? This is
> done for you.  Each amino acid is defined.  If you supply a coordinate file
> with a GLY-GLY peptide, pdb2gmx does everything you need.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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[gmx-users] Calculating the dielectric constant of a ligand

2017-08-20 Thread Sajad Ahrari 
Dear Users,
I am trying to calculate the dielectric constant of a ligand (5RC), so that I 
can use the output number in the binding free energy calculations by MM/PBSA 
method (by g_mmpbsa package). For this purpose, I used the "gmx_mpi dipoles -s 
5RC.tpr -f 5RC_last20ns.xtc -corr mol  -c dipcorr.xvg" command to produce the 
dipcorr.xvg and the used it as the input in "gmx_mpi dielecteric -f dipcorr.xvg 
-d deriv.xvg -o epsw.xvg -c cole.xvg" command. I suspect that the epsw.xvg 
should contain the desired information. However, I am not sure how to interpret 
it. Could you please give me a clue on how to proceed? The outputs are attached.
Thank you
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[gmx-users] Average and bfactors.pdb

2017-08-20 Thread farial tavakoli 
 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear gmx users
I removed jumps from my .xtc file before by using gmx trjconv and viewed my 
complex in vmd, it was ok and rhere was no jump. Now i use gmx rmsf and the 
same .xtc file which was created after using gmx trjconv, but when i view 
average. Pdb and bfactors.pdb files in pymol, my protein is still brocken. 
Would you please advice me how to solve this problem? 
Best Farial


Sent from Yahoo Mail for iPhone
 
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Re: [gmx-users] HSE in Charmm-gui membrane builder

2017-08-20 Thread Justin Lemkul 



On 8/20/17 12:17 AM, Мижээ Батсайхан wrote:

Dear gmx users,

I am sorry for asking about charmm-gui .
I would like to use HSE protonation state of HIS, and I am using Charmm-gui
membrane builder. But, Charmm-gui only produces HSD protonation state in my
initial system. How can I use HSE state?



Tell it to do so in step 2 in the "protonation state" selection.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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Re: [gmx-users] HSE in Charmm-gui membrane builder

2017-08-20 Thread Nikhil Maroli 
I guess there is a protonation option in charmm-gui. IF not you can do it
manually
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Re: [gmx-users] umbrella sample Question

2017-08-20 Thread yujie liu 

Thanks Justin,
 
You are right. Your script might not be compatible with my system or software, 
I tried to use another python script from other people  and showed a complete 
dat file. 

Thanks again

Yours, Liu
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Re: [gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation

2017-08-20 Thread Alex 

The error is actually telling you exactly what is wrong.

First relax your system with pressure coupling, then do pull in NVT. Or, 
possibly adjust the system in such a way that 'direction' pull could be 
used instead of 'direction-periodic'.


Alex


On 8/20/2017 1:53 AM, Alex Mathew wrote:

Dear Justin,

As per the manual i have changed parameters as

tcoupl  = berendsen
tc_grps = Protein   Non-Protein Chain_B
tau_t   = 1.01.01.0
ref_t   = 310   310   310
;
pcoupl  = berendsen
pcoupltype  = semiisotropic
tau_p   = 5.0
compressibility = 4.5e-5  4.5e-5
ref_p   = 1.0 1.0

but i'm getting the error as

Can not have dynamic box while using pull geometry 'direction-periodic' (dim
z)


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Re: [gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation

2017-08-20 Thread Alex Mathew 
Dear Justin,

As per the manual i have changed parameters as

tcoupl  = berendsen
tc_grps = Protein   Non-Protein Chain_B
tau_t   = 1.01.01.0
ref_t   = 310   310   310
;
pcoupl  = berendsen
pcoupltype  = semiisotropic
tau_p   = 5.0
compressibility = 4.5e-5  4.5e-5
ref_p   = 1.0 1.0

but i'm getting the error as

Can not have dynamic box while using pull geometry 'direction-periodic' (dim
z)
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