Re: [gmx-users] Regarding calculation of Spatial Distribution Function

[Dilip H N]

I want to calculate water SDF around C-alpha of glycine molecule. So here i
have followed the commands..
Step 2:- gmx trjconv -s nptmd.tpr -f nptmd.xtc -o abc.tng -boxcenter tric
-ur compact -pbc none
and it asks me
Select group for output
Group 0 ( System) has  1543 elements
Group 1 ( Protein) has10 elements
Group 2 ( Protein-H) has 5 elements
Group 3 ( C-alpha) has 1 elements
Group 4 ( Backbone) has 3 elements
Group 5 ( MainChain) has 3 elements
Group 6 ( MainChain+Cb) has 3 elements
Group 7 ( MainChain+H) has 6 elements
Group 8 ( SideChain) has 4 elements
Group 9 ( SideChain-H) has 2 elements
Group10 (Prot-Masses) has10 elements
Group11 (non-Protein) has  1533 elements
Group12 ( Water) has  1533 elements
Group13 ( SOL) has  1533 elements
Group14 ( non-Water) has10 elements
and i have selected Group 0 (System),
Step3:- gmx trjconv -s nptmd.tpr -f abc.tng -o def.tng -fit rot+trans
Select group for least squares fit Group 0 ( System) has 1543 elements
Group 1 ( Protein) has 10 elements Group 2 ( Protein-H) has 5 elements
Group 3 ( C-alpha) has 1 elements Group 4 ( Backbone) has 3 elements Group
5 ( MainChain) has 3 elements Group 6 ( MainChain+Cb) has 3 elements Group
7 ( MainChain+H) has 6 elements Group 8 ( SideChain) has 4 elements Group 9
( SideChain-H) has 2 elements Group 10 ( Prot-Masses) has 10 elements Group
11 ( non-Protein) has 1533 elements Group 12 ( Water) has 1533 elements
Group 13 ( SOL) has 1533 elements Group 14 ( non-Water) has 10 elements
If i give group 3 (since it has C-alpha atoms), but i am getting an error as
Fatal error: Need at least 2 atoms to fit!

So, how can i solve this issue..?? since C-alpha is only one atom..

Thank you.


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On Tue, Apr 3, 2018 at 2:25 PM, Dilip H N <cy16f01.di...@nitk.edu.in> wrote:

> Hello,
> I want to do the Spatial Distribution Function,
> I tried to follow the manual gmx spatial.
> I am following the five-step protocol which is given in gmx spatial
> manual..
> 1) I have an index file ndx_CaOw.ndx (which contains the C-alpha and all
> the Ow's of water molecules, Is this index good or should i have all the
> molecules..??)
> 2) in the second step-  "gmx trjconv -s a.tpr
> <http://manual.gromacs.org/online/tpr.html> -f a.tng
> <http://manual.gromacs.org/online/tng.html> -o b.tng
> <http://manual.gromacs.org/online/tng.html> -boxcenter tric -ur compact
> -pbc none" here we need to give the input file ie., -f a.tng from where
> does this .tng file i need to give the input..?? How do i create a .tng
> file.. what information does this tng file contain...??
>
> Any suggestions...
>
> Thank you.
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
> ‌
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[gmx-users] Regarding calculation of Spatial Distribution Function

[Dilip H N]

Hello,
I want to do the Spatial Distribution Function,
I tried to follow the manual gmx spatial.
I am following the five-step protocol which is given in gmx spatial manual..
1) I have an index file ndx_CaOw.ndx (which contains the C-alpha and all
the Ow's of water molecules, Is this index good or should i have all the
molecules..??)
2) in the second step-  "gmx trjconv -s a.tpr
 -f a.tng
 -o b.tng
 -boxcenter tric -ur compact
-pbc none" here we need to give the input file ie., -f a.tng from where
does this .tng file i need to give the input..?? How do i create a .tng
file.. what information does this tng file contain...??

Any suggestions...

Thank you.
-- 
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DILIP.H.N
Ph.D Student
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[gmx-users] Regarding time steps for calculation of Hydrogen Bond Dynamics

[Dilip H N]

Hello all,

I have run a simulation for 10 ns (0.001 * 1000 = 1 ps) and have
saved the data for every 0.5 ps (nstxout= 500etc.,...) (which comes to
2 frames...).
Since if i extract the trajectory in .gro format for the full simulation,it
will be such a huge file, so i intended to extract the trajectories having
500 frames since it will be relatively less file size. The command is:

gmx trjconv -f nptmd.xtc -s nptmd.tpr -pbc mol -o nptmdtrj500.gro -dt 20

which gives the full trajectory, but has 500 frames in total (ie., from
t=0ns to t=10ns, the frames are 500 with an interval of 20 ns).

So, my question is that, is this trajectory sufficient/good to analyze the
hydrogen bond dynamics (intermittent and continuous)...??
I have the trajectories extracted in .gro file for time t=0, t=20, t=40 and
so on... So the interactions/bonding is taken for t=20 ns... Is this affect
the dynamics study..??

Can anybody suggest the best possible way of trajectories (like how many
time frames/intervals etc.,) to be taken for HB Dynamics..??

Any suggestions are highly appreciated.

Thank you.
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DILIP.H.N
PhD Student



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Re: [gmx-users] Regarding calculation of Hydrogen-Bond

[Dilip H N]

1) I tried with the Nitrogen atom of glycine and the oxygen atom of water
also using the command

gmx hbond -f nptmd.trr -s nptmd.tpr -n NgOw.ndx -num abc.xvg

but still, i am getting the same error as:-
Specify 2 groups to analyze:
Group 0 (  N) has 1 elements
Group 1 ( OW) has   511 elements
Select a group: 0
Selected 0: 'N'
Select a group: 1
Selected 1: 'OW'
Checking for overlap in atoms between N and OW
Calculating hydrogen bonds between N (1 atoms) and OW (511 atoms)
Found 0 donors and 512 acceptors
No Donors found
---
Program: gmx hbond, version 2016.2
Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
Fatal error:
Nothing to be done

2) I tried to find out the distance between Calpha(Ca) and Ow from the
command
gmx hbond -f nptmd.trr -s nptmd.tpr -n NgOw.ndx -dist abc.xvg

but still, i am getting the same error as above one.

Any suggestions...

Thank you.

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On Tue, Mar 13, 2018 at 7:34 PM, Erik Marklund <erik.markl...@kemi.uu.se>
wrote:

> A shortcut would be to only look at the C-O distance, which can be done
> with gmx hbond without modification.
>
> Kind regards,
> Erik
>
> > On 13 Mar 2018, at 15:01, Jeremy T First <jeremy_fi...@utexas.edu>
> wrote:
> >
> > Hi Dilip,
> >
> > There is quite a bit of literature, especially recently, that considers
> the
> > alpha carbon as a hydrogen bond donor. How well this is represented in
> your
> > simulation will depend on your force field.
> >
> > You will likely need to develop your own gromacs tool to calculate this,
> > but it should be quite easy. We recently wrote a tool that does something
> > very similar, but you would need to edit it for your own purposes. If you
> > are interested in using our code as a template, feel free to contact me
> off
> > list.
> >
> > Good luck!
> > Jeremy
> >
> >
> >
> >
> > Jeremy Todd First
> > Webb Research Group
> > University of Texas at Austin
> > jeremy_fi...@utexas.edu
> > (443) 243-1187
> >
> > On Tue, Mar 13, 2018 at 7:25 AM, Erik Marklund <erik.markl...@kemi.uu.se
> >
> > wrote:
> >
> >> The point is that Calpha don’t form hydrogen bonds.
> >>
> >> Erik
> >> ______
> >> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> >> Department of Chemistry – BMC, Uppsala University
> >> +46 (0)18 471 4539
> >> erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>
> >>
> >> On 13 Mar 2018, at 13:20, Dilip H N <cy16f01.di...@nitk.edu.in >> cy16f01.di...@nitk.edu.in>> wrote:
> >>
> >> Then how can i calculate the hydrogen bonding between C-alpha and Oxygen
> >> atom of water molecules..??
> >> What are the other possible ways..??
> >>
> >>
> >>
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> >>
> >> On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund <
> erik.markl...@kemi.uu.se<
> >> mailto:erik.markl...@kemi.uu.se>>
> >> wrote:
> >>
> >> Dear Dilip,
> >>
> >> The Calpha is not considered a hbond donor.
> >>
> >> Kind regards,
> >> Erik
> >> __
> >> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> >> Department of Chemistry – BMC, Uppsala University
> >> +46 (0)18 471 4539
> >> erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> >> erik.markl...@kemi.uu.se>
> >>
> >> On 13 Mar 2018, at 11:03, Dilip H N <cy16f01.di...@nitk.edu.in >> cy16f01.di...@nitk.edu.in> >> cy16f01.di...@nitk.edu.in<mailto:cy16f01.di...@nitk.edu.in>>> wrote:
> >>
> >> Hello,
> >> I want to calculate Hydrogen bonding between C-alpha of glycine and the
> >> oxygen atom of water molecules.
> >> So, i gave the command as:-
> >>
> >> gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg
> >>
> >> but i got the error as:
> >> Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
> >> Found 0 donors and 511 acceptors
> >> 

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

[Dilip H N]

Then how can i calculate the hydrogen bonding between C-alpha and Oxygen
atom of water molecules..??
What are the other possible ways..??



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On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund <erik.markl...@kemi.uu.se>
wrote:

> Dear Dilip,
>
> The Calpha is not considered a hbond donor.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>
>
> On 13 Mar 2018, at 11:03, Dilip H N <cy16f01.di...@nitk.edu.in cy16f01.di...@nitk.edu.in>> wrote:
>
> Hello,
> I want to calculate Hydrogen bonding between C-alpha of glycine and the
> oxygen atom of water molecules.
> So, i gave the command as:-
>
> gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg
>
> but i got the error as:
> Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
> Found 0 donors and 511 acceptors
> No Donors found
> ---
> Program: gmx hbond, version 2016.2
> Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
> Fatal error:
> Nothing to be done
>
> So, how can i solve this issue..?? Is there no any Hydrogen bonding between
> this..?? (I think there is some hydrogen bonding present ...)
>
> Any suggestions are appreciated.
>
> Thank you.
>
> --
> With Best Regards,
>
> DILIP.H.N
> PhD Student
>
>
>
> ‌
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Ph.D Student
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[gmx-users] Regarding calculation of Hydrogen-Bond

[Dilip H N]

Hello,
I want to calculate Hydrogen bonding between C-alpha of glycine and the
oxygen atom of water molecules.
So, i gave the command as:-

gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg

but i got the error as:
Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
Found 0 donors and 511 acceptors
No Donors found
---
Program: gmx hbond, version 2016.2
Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
Fatal error:
Nothing to be done

So, how can i solve this issue..?? Is there no any Hydrogen bonding between
this..?? (I think there is some hydrogen bonding present ...)

Any suggestions are appreciated.

Thank you.

-- 
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DILIP.H.N
PhD Student



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Re: [gmx-users] Calculate RDF within a certain distance from atom

[Dilip H N]

I have the RDF between Calpha-Ow, and it is showing a slight hump/peak
around 0.47nm. So, i am further interested in studying how water molecules
are oriented towards it closely...what is happening around within 0.7nm
distance of Calpha w.r.t Ow...

Any suggestions...??

Thank you.




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On Tue, Feb 20, 2018 at 10:58 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 2/20/18 11:53 AM, Dilip H N wrote:
>
>> Hello,
>> How to get RDF within a certain distance..??
>>
>> Say for eg., i have glycine amino-acid and i want the RDF of Oxygen water
>> atoms within 0.7nm of C-alpha (Calpha-Ow).
>>
>> how can i get it from in-house gmx rdf command...??
>>
>
> What do you hope to achieve from such a metric? RDF has to be normalized
> against bulk occupancy, which will of course not be achieved at a 0.7-nm
> distance. If you are interested in certain properties within given
> solvation shells, distances, etc. compute the normal RDF so that it is
> properly normalized and interpret the outcome of that calculation.
>
> -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
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[gmx-users] Calculate RDF within a certain distance from atom

[Dilip H N]

Hello,
How to get RDF within a certain distance..??

Say for eg., i have glycine amino-acid and i want the RDF of Oxygen water
atoms within 0.7nm of C-alpha (Calpha-Ow).

how can i get it from in-house gmx rdf command...??

Any suggestions are appreciated...

Thank you.


-- 
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Ph.D. Student



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Re: [gmx-users] Regarding No more replaceable solvent!

[Dilip H N]

I have a system of 1aminoacid+511 water molecules (total is 512
molecules).and the box length is 2.52nm.

So, even if i replace by 45 Na+ and 45 Cl- ions (total is 90 ions) and
still i have 511-90 = 421 water molecules. and i think this is well within
the solubility...

How many water molecules are being removed for each ion..?? (when i
replaced 10Na+ and 10Cl- ions ie., 511-20=491 water molecules were there
and this system was being well, but now with 45 ions each, i am getting the
error...)

Then how do i solve this issue..??

Any suggestions.

Thank you.




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On Mon, Feb 19, 2018 at 11:49 AM, Alex <nedoma...@gmail.com> wrote:

> How about you actually open your 'glywi.gro' prior to adding more ions and
> count the number of water molecules, and then compare it with the number of
> ions you want to add? With concentration known and the knowledge of your
> box volume, this comparison shouldn't be a problem.
>
> Alex
>
>
> On 2/18/2018 11:14 PM, Dilip H N wrote:
>
>> Hello,
>> I added 10 Na+ and Cl- ions to the aminoacid-water system containing 512
>> molecules through the command
>> gmx genion -s em.tpr -o abc.gro -p topol.top -pname NA -nname CL -np 10
>> -nn
>> 10
>>
>> but now, i want to increase the concentration, so i want to add 45 Na+ and
>> Cl- ions (from calculation, the concentration for 45 ions is 5M...), but
>> when i give the commands:
>> gmx genion -s em.tpr -o glywi.gro -p topol.top -pname NA -nname CL -np 45
>> -nn 45
>>   (or)
>> gmx genion -s em.tpr -o glywi.gro -p topol.top -pname NA -nname CL -conc 5
>>
>> I am getting the error as:
>>
>> No more replaceable solvent!
>>
>> So, Is there any limit here..?? The maximum concentration that i can get
>> is
>> 2M (through -conc 2 command), and after that, if i change from -conc2 to
>> -conc3 etc., i am getting the same error as "No more replaceable
>> solvent!".
>>
>> Any suggestions are appreciated...
>>
>> Thank you
>>
>>
>>
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Re: [gmx-users] Regarding No more replaceable solvent!

[Dilip H N]

Thank you sir...
Yes, I will post it in the group...




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On Mon, Feb 19, 2018 at 12:17 PM, Alex <nedoma...@gmail.com> wrote:

> Please be kind to respond to the list and not to my email. I believe that
> 3-4 water molecules get removed per ion, depending on the insertion cutoff,
> so with 90 x 4, you're left in a situation where there's pretty much no
> water left. Gromacs is actually doing you a huge favor with this error,
> because it could manage to insert all the ions and you would end up
> simulating something nonsensical.
>
> Increase your box size appropriately.
>
> Alex
>
>
> On 2/18/2018 11:30 PM, Dilip H N wrote:
>
>> Sir,
>> In connection with the above-mentioned title...
>>
>> I have a system of 1glycine+511 water molecules (total is 512
>> molecules).and the box length is 2.51nm.
>>
>> So, even if i replace by 45 Na+ and 45 Cl- ions (total is 90 ions) and
>> still i have 511-90 = 421 water molecules. and i think this is well within
>> the solubility...
>>
>> Then how do i solve this issue..??
>>
>> Any suggestions sir.
>>
>> Thank you.
>>
>>
>>
>>
>>
>> --
>> With Best Regards,
>>
>> DILIP.H.N
>> Ph.D. Student
>>
>>
>>
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[gmx-users] Regarding No more replaceable solvent!

[Dilip H N]

Hello,
I added 10 Na+ and Cl- ions to the aminoacid-water system containing 512
molecules through the command
gmx genion -s em.tpr -o abc.gro -p topol.top -pname NA -nname CL -np 10 -nn
10

but now, i want to increase the concentration, so i want to add 45 Na+ and
Cl- ions (from calculation, the concentration for 45 ions is 5M...), but
when i give the commands:
gmx genion -s em.tpr -o glywi.gro -p topol.top -pname NA -nname CL -np 45
-nn 45
 (or)
gmx genion -s em.tpr -o glywi.gro -p topol.top -pname NA -nname CL -conc 5

I am getting the error as:

No more replaceable solvent!

So, Is there any limit here..?? The maximum concentration that i can get is
2M (through -conc 2 command), and after that, if i change from -conc2 to
-conc3 etc., i am getting the same error as "No more replaceable solvent!".

Any suggestions are appreciated...

Thank you


-- 
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DILIP.H.N
Ph.D. Student



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[gmx-users] Cannot find position restraint file restraint.gro (option -r).

[Dilip H N]

Hello,

1] I have installed the latest version of gromacs (gromacs 2018), and when
i give the command,
gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr

I am getting the error as:
Program: gmx grompp, version 2018
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2008)
Fatal error:
Cannot find position restraint file restraint.gro (option -r).
>From GROMACS-2018, you need to specify the position restraint coordinate
files
explicitly to avoid mistakes, although you can still use the same file as
you
specify for the -c option.

2] But if i give the same command (gmx grompp -f nvt.mdp -c em.gro -p topol.top
-o nvt.tpr) in gromacs 2016.2, the compilation is working fine without any
errors.

So, how should i define position restrains coordinates explicitly..??
how do i solve this issue..??

Any suggestions are appreciated.
-- 
With Best Regards,

DILIP.H.N
Ph.D. Student
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Re: [gmx-users] Regarding Beta-alanine structure

[Dilip H N]

Hello,
I have got the zwitterion structure of beta-alanine from ChEBI website, and
the ChEBI Id is *CHEBI:57966.*
I downloaded in mol2 format and tried with the CGenFF and swissparam servers
to get the charmm FF. but i have got two different charges for each of the
case.

In case of CGenFF the charges i got by uploading the zwitterionic
beta-alanine.mol2:

ESI *0.000 ! param penalty=   4.000 ; charge penalty=  12.737
GROUP! CHARGE   CH_PENALTY
ATOM N  NG3P3  -0.299 !2.500
ATOM C1 CG324   0.127 !   10.269
ATOM C2 CG321  -0.245 !   12.737
ATOM O1 OG2D2  -0.760 !0.850
ATOM C3 CG2O3   0.587 !   12.403
ATOM O2 OG2D2  -0.760 !0.850
ATOM H1 HGP20.330 !0.000
ATOM H2 HGP20.330 !0.000
ATOM H3 HGP20.330 !0.000
ATOM H4 HGA20.090 !2.500
ATOM H5 HGA20.090 !2.500
ATOM H6 HGA20.090 !0.000
ATOM H7 HGA20.090 !0.000

In case of SwissParam the charges i got by uploading the zwitterionic
beta-alanine.mol2:
[ atoms ]
; nr type resnr resid atom cgnr charge mass
   1 NRP  1  LIG N1   1 -0.8530  14.0067
   2 CR1  LIG C1   2  0.5030  12.0110
   3 CR1  LIG C2   3 -0.1060  12.0110
   4 O2CM   1  LIG O1   4 -0.9000  15.9994
   5 CO2M   1  LIG C3   5  0.9060  12.0110
   6 O2CM   1  LIG O2   6 -0.9000  15.9994
   7 HNRP   1  LIG H1   7  0.4500   1.0079
   8 HNRP   1  LIG H2   8  0.4500   1.0079
   9 HNRP   1  LIG H3   9  0.4500   1.0079
  10 HCMM 1  LIG H4 10  0.   1.0079
  11 HCMM 1  LIG H5 11  0.   1.0079
  12 HCMM 1  LIG H6 12  0.   1.0079
  13 HCMM 1  LIG H7 13 -0.   1.0079

So, how can i validate that which charges for the molecule, is correct..??
Which one is correct one to run the simulation in gromacs (using charmm36
FF)..??

Any suggestions are appreciated.
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On Thu, Feb 8, 2018 at 1:37 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> You should start with the original literature and/or CHARMM forcefield
> distribution for its documentation. That wasn't ported to the force field
> files one can use with GROMACS.
>
> Mark
>
> On Thu, Feb 8, 2018 at 7:19 AM Dilip H N <cy16f01.di...@nitk.edu.in>
> wrote:
>
> > Hello,
> > I want to simulate beta-alanine amino-acid. But in charmm36 FF there are
> > four different names (three/four letter code) for ALA, ie., ALA, DALA,
> > ALAI, ALAO.
> > Out of this, i wanted to know which one corresponds to beta-alanine
> > structure..??
> >
> > I tried in Avogadro software and i could build only alanine structure,
> and
> > not beta-alanine. How can i get the pdb file of beta-alanine..?? any
> other
> > ways..?
> > So, can anybody help me regarding this..??
> >
> > Thank you.
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D. Student
> >
> >
> >
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[gmx-users] Regarding Beta-alanine structure

[Dilip H N]

Hello,
I want to simulate beta-alanine amino-acid. But in charmm36 FF there are
four different names (three/four letter code) for ALA, ie., ALA, DALA,
ALAI, ALAO.
Out of this, i wanted to know which one corresponds to beta-alanine
structure..??

I tried in Avogadro software and i could build only alanine structure, and
not beta-alanine. How can i get the pdb file of beta-alanine..?? any other
ways..?
So, can anybody help me regarding this..??

Thank you.

-- 
With Best Regards,

DILIP.H.N
Ph.D. Student



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[gmx-users] Regarding simulation of ions-water system

[Dilip H N]

Hello,
I want to simulate Ca2+, CO32- ions in the water system. So these were the
following commands i followed:
gmx editconf -f abc.gro -box xxx -o def.gro
gmx insert-molecules -f def.gro -ci ghi.gro -nmol x -o jkl.gro
gmx solvate -cp jkl.gro -cs scp216.gro -o mno.gro
gmx pdb2gmx -f mno.gro -o mno.pdb (to generate topology)
gmx grompp -f ions.tpr -c mno.gro -p topol.top -o ions.tpr
gmx genion -s ions.tpr -o pqr.gro -p topol.top -pname CAL -np xx
I hope these are the proper ways to generate topology and add ions and to
set up the system...(Any modifications are appreciated.)

And when i gave the energy minimization command (gmx grompp -f em.mdp -c
pqr.gro -p topol.top -o em.tpr), i am getting the following error:

Excluding 3 bonded neighbours molecule type 'Other'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Ion2'
turning H bonds into constraints...
Removing all charge groups because cutoff-scheme=Verlet

Atom 1 'CAL' in moleculetype 'Ion2' is not bound by a potential or
constraint to any other atom in the same moleculetype.

Atom 2 'CAL' in moleculetype 'Ion2' is not bound by a potential or
constraint to any other atom in the same moleculetype.

how to resolve this error..?? (Is this because of the cutoff scheme..?? )

Any suggestions are highly appreciated.

-- 
With Best Regards,

DILIP.H.N
Ph.D. Student



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Re: [gmx-users] Regarding finding a ion/molecule in forecefield

[Dilip H N]

1] I wanted carbonate ion with -2 ion charge. (i checked in atomtypes.atp
where, carbonate  is mentioned as "CG2O6 12.01100 ; carbonyl C: urea,
carbonate",  "OG2D2  15.99940 ; carbonyl O: negative groups: carboxylates,
carbonate").
And i also checked with ions.itp (in which the ions are represented), but i
could find only calcium with +2 charge and not carbonate ion. (hope while
converting from gmx pdb2gmx is it converted into an ion ..??)

2] In general how can i find/search for the required molecule and in which
forcefield is it present in...?

Thank you.




‌

On Fri, Dec 29, 2017 at 6:19 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 12/29/17 7:43 AM, Dilip H N wrote:
>
>> Hello all,
>> How to find out/search a specific molecule or ion is present in which
>> forcefield (say for eg., Ca 2+ or carbonate ion CO32-, or any other
>> molecule), and hence can generate .pdb file corresponding to that residue
>> naming in the FF and generate its topology.
>>
>> In this case, i needed Ca2+ (calcium ion), CO32- (carbonate ion) and in
>> which forcefield is it present.
>>
>> Any suggestions...
>>
>
> Both are in CHARMM36. Ca2+ is CAL and carbonate is CO3.
>
> -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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Ph.D Student
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[gmx-users] Regarding finding a ion/molecule in forecefield

[Dilip H N]

Hello all,
How to find out/search a specific molecule or ion is present in which
forcefield (say for eg., Ca 2+ or carbonate ion CO32-, or any other
molecule), and hence can generate .pdb file corresponding to that residue
naming in the FF and generate its topology.

In this case, i needed Ca2+ (calcium ion), CO32- (carbonate ion) and in
which forcefield is it present.

Any suggestions...

Thank you.


-- 
With Best Regards,

DILIP.H.N
Ph.D. Student



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Re: [gmx-users] my minimization structure looks like a messy box?

[Dilip H N]

Hello,
You need to use -pbc mol in your command for viewing the trajectory, then
this issue will be solved.



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On Wed, Dec 13, 2017 at 11:23 PM, MD  wrote:

> ah, that explains. thanks Justin!
> Ming
>
> On Wed, Dec 13, 2017 at 11:42 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 12/13/17 11:41 AM, MD wrote:
> >
> >> It looks like this
> >> https://drive.google.com/open?id=1DMy1otIYQZD8uxF6sZaZzZK4qN1z_qyD
> >>
> >
> > That's classic PBC.
> >
> > -Justin
> >
> >
> > On Wed, Dec 13, 2017 at 11:04 AM, Justin Lemkul  wrote:
> >>
> >>
> >>> On 12/13/17 11:02 AM, MD wrote:
> >>>
> >>> Hi Gromacs folks,
>  Any of you have experienced having a messy box looking gro file after
>  em.mdp?
> 
>  Probably http://www.gromacs.org/Documentation/Terminology/Periodic_
> >>> Boundary_Conditions but you'll have to define "messy" if that's not
> >>> what's going on.
> >>>
> >>> -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
> >>>
> >>> ==
> >>>
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at http://www.gromacs.org/Support
> >>> /Mailing_Lists/GMX-Users_List before posting!
> >>>
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>> * For (un)subscribe requests visit
> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>> send a mail to gmx-users-requ...@gromacs.org.
> >>>
> >>>
> > --
> > ==
> >
> > 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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Ph.D Student
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Re: [gmx-users] Regarding calculating the water orientation profile

[Dilip H N]

So what exactly does this Orientation Profile means.??
I am really confused with the exact approach towards it...


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On Fri, Nov 24, 2017 at 12:47 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> "Coming closer" implies you care about distance, but your original question
> was about orientation. So it's unclear what you want.
>
> Mark
>
> On Thu, 23 Nov 2017 16:50 Dilip H N <cy16f01.di...@nitk.edu.in> wrote:
>
> > I want to calculate whether the water molecules are coming closer towards
> > the N-terminal or towards the C-terminal of the amino-acid throughout
> the
> > simualtion.
> > And hence it can shed some light on the Hydrogen bond
> > dynamicshopefully...
> >
> > Thank you
> >
> >
> >
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> > >
> >
> > On Thu, Nov 23, 2017 at 6:05 PM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > It sounds like to need to be more clear about what you want to
> calculate
> > > before you can sensibly find a tool to do it. You should be able to
> write
> > > down the equation for what you want to compute as your observation long
> > > before you run a simulation, or how will you know what data to collect?
> > >
> > > Mark
> > >
> > > On Thu, 23 Nov 2017 07:26 Dilip H N <cy16f01.di...@nitk.edu.in> wrote:
> > >
> > > > Hello Sir,
> > > > I have run a simulation of amino-acid (glycine) with water molecules
> > for
> > > 10
> > > > ns. Now i need to find out/analyze that whether the water molecules
> are
> > > > getting/more oriented towards N-terminal of glycine or towards the
> > > > C-terminal of glycine. (i hope this is what water orientation profile
> > > means
> > > > ie., the preferential orientation of water towards particular
> > > > moeity/group...).
> > > > So, which is the exact module/command to find this..?? wether gmx
> > sorient
> > > > or gmx gangle or gmx angle ..??
> > > >
> > > > How to resolve this issue...
> > > >
> > > > Thank you
> > > >
> > > >
> > > > --
> > > > With Best Regards,
> > > >
> > > > DILIP.H.N
> > > > Ph.D Student
> > > >
> > > >
> > > >
> > > > ‌
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> >
> >
> >
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> > --
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With Best Regards,

DILIP.H.N
Ph.D Student
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Re: [gmx-users] Regarding calculating the water orientation profile

[Dilip H N]

Hi Joao Sir,
Yes, that was me, who had asked the questions some time ago, but i had no
success in this.



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On Fri, Nov 24, 2017 at 12:11 AM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> Wait, now I remember, you even approached me in a private message and we
> exchanged quite a few emails. Did you try any of my suggestions? No
> success?
>
> J
>
> On Thu, Nov 23, 2017 at 7:36 PM, João Henriques <
> joao.m.a.henriq...@gmail.com> wrote:
>
> > Hi,
> >
> > I clearly remember replying to something similar sometime ago, and I'm
> > almost sure the post was yours. It may be a good idea to rummage through
> > the mailing list, because I'm pretty sure this type of analysis has been
> > discussed here more than once.
> >
> > Cheers,
> > J
> >
> > On Thu, Nov 23, 2017 at 4:41 PM, Dilip H N <cy16f01.di...@nitk.edu.in>
> > wrote:
> >
> >> I want to calculate whether the water molecules are coming closer
> towards
> >> the N-terminal or towards the C-terminal of the amino-acid throughout
> the
> >> simualtion.
> >> And hence it can shed some light on the Hydrogen bond
> >> dynamicshopefully...
> >>
> >> Thank you
> >>
> >>
> >>
> >> <https://mailtrack.io/> Sent with Mailtrack
> >> <https://chrome.google.com/webstore/detail/mailtrack-for-gma
> >> il-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&
> >> utm_medium=signature_campaign=signaturevirality>
> >>
> >> On Thu, Nov 23, 2017 at 6:05 PM, Mark Abraham <mark.j.abra...@gmail.com
> >
> >> wrote:
> >>
> >> > Hi,
> >> >
> >> > It sounds like to need to be more clear about what you want to
> calculate
> >> > before you can sensibly find a tool to do it. You should be able to
> >> write
> >> > down the equation for what you want to compute as your observation
> long
> >> > before you run a simulation, or how will you know what data to
> collect?
> >> >
> >> > Mark
> >> >
> >> > On Thu, 23 Nov 2017 07:26 Dilip H N <cy16f01.di...@nitk.edu.in>
> wrote:
> >> >
> >> > > Hello Sir,
> >> > > I have run a simulation of amino-acid (glycine) with water molecules
> >> for
> >> > 10
> >> > > ns. Now i need to find out/analyze that whether the water molecules
> >> are
> >> > > getting/more oriented towards N-terminal of glycine or towards the
> >> > > C-terminal of glycine. (i hope this is what water orientation
> profile
> >> > means
> >> > > ie., the preferential orientation of water towards particular
> >> > > moeity/group...).
> >> > > So, which is the exact module/command to find this..?? wether gmx
> >> sorient
> >> > > or gmx gangle or gmx angle ..??
> >> > >
> >> > > How to resolve this issue...
> >> > >
> >> > > Thank you
> >> > >
> >> > >
> >> > > --
> >> > > With Best Regards,
> >> > >
> >> > > DILIP.H.N
> >> > > Ph.D Student
> >> > >
> >> > >
> >> > >
> >> > > ‌
> >> > > <https://mailtrack.io/> Sent with Mailtrack
> >> > > <
> >> > > https://chrome.google.com/webstore/detail/mailtrack-for-
> gmail-inbox/
> >> > ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail_
> >> > medium=signature_campaign=signaturevirality
> >> > > >
> >> > > --
> >> > > Gromacs Users mailing list
> >> > >
> >> > > * Please search the archive at
> >> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> > > posting!
> >> > >
> >> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> > >
> >> > > * For (un)subscribe requests visit
> >> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> >> > > send a mail to gmx-users-requ...@gromacs.org.
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Ple

Re: [gmx-users] Regarding calculating the water orientation profile

[Dilip H N]

I want to calculate whether the water molecules are coming closer towards
the N-terminal or towards the C-terminal of the amino-acid throughout  the
simualtion.
And hence it can shed some light on the Hydrogen bond
dynamicshopefully...

Thank you



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On Thu, Nov 23, 2017 at 6:05 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> It sounds like to need to be more clear about what you want to calculate
> before you can sensibly find a tool to do it. You should be able to write
> down the equation for what you want to compute as your observation long
> before you run a simulation, or how will you know what data to collect?
>
> Mark
>
> On Thu, 23 Nov 2017 07:26 Dilip H N <cy16f01.di...@nitk.edu.in> wrote:
>
> > Hello Sir,
> > I have run a simulation of amino-acid (glycine) with water molecules for
> 10
> > ns. Now i need to find out/analyze that whether the water molecules are
> > getting/more oriented towards N-terminal of glycine or towards the
> > C-terminal of glycine. (i hope this is what water orientation profile
> means
> > ie., the preferential orientation of water towards particular
> > moeity/group...).
> > So, which is the exact module/command to find this..?? wether gmx sorient
> > or gmx gangle or gmx angle ..??
> >
> > How to resolve this issue...
> >
> > Thank you
> >
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> >
> >
> >
> > ‌
> > <https://mailtrack.io/> Sent with Mailtrack
> > <
> > https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/
> ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail_
> medium=signature_campaign=signaturevirality
> > >
> > --
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> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
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-- 
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DILIP.H.N
Ph.D Student
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[gmx-users] Regarding calculating the water orientation profile

[Dilip H N]

Hello Sir,
I have run a simulation of amino-acid (glycine) with water molecules for 10
ns. Now i need to find out/analyze that whether the water molecules are
getting/more oriented towards N-terminal of glycine or towards the
C-terminal of glycine. (i hope this is what water orientation profile means
ie., the preferential orientation of water towards particular
moeity/group...).
So, which is the exact module/command to find this..?? wether gmx sorient
or gmx gangle or gmx angle ..??

How to resolve this issue...

Thank you


-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding water orientation profile

[Dilip H N]

Hello,
I want to do the water orientation profile for the amino-acid which is
surrounded by water molecules as in my case amino-acid+water mixture.
ie., i want to find out whether the water is orientation is more towards
the N-terminal or towards the C-terminal of the amino acid and hence the
orientation profile. I want to know throught the simulation around which
terminal water molecules are more oriented as a function of time or etc.,

I have a simulation done in GROMACS with one amino-acid in presence
of cosolvents which is solvated with water for 10 ns. So I want to have the
water orientation profile.But i tried with gmx sorient command, but i am
unable to understand it.. and also through gmx h2order which
calculates the orientation
of water molecules with respect to the normal of the box, but i need to
calculate with respect to N-terminal or through C-terminal.
What is the best way to solve this..??

Any suggestions are highly appreciated.

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Running MD simulations at a particular temperature

[Dilip H N]

Sir,
As u have mentioned in the link http://www.gromacs.org/Documen
tation/Terminology/Force_Fields/CHARMM the cutoffs are described here for
CHARMM FF.
So similarly, how can i get the cutoffs for OPLSAA, Amber, GROMOS etc.,
forcefields in gromacs..?? Is there any source, or only through literature
survey the cutoffs need to be fixed..??

Thank you..



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<#>

On Wed, Oct 18, 2017 at 7:13 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 10/18/17 9:41 AM, Dilip H N wrote:
>
>> Justin Sir,
>> Even i am also using Charmm 36FF. So as u have mentioned in previois
>> message, can u kindly suggest then what ate the correct cutoffs..??
>> And what would be the other modifications that needs to be done in order
>> to
>> incorporate the Charmm FF
>>
>
> I think I post this link to the mailing list weekly...
>
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>
> -Justin
>
> Thank you
>>
>>
>>
>> <https://mailtrack.io/> Sent with Mailtrack
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>> utm_medium=signature_campaign=signaturevirality>
>>
>>
>> On Wed, Oct 18, 2017 at 6:46 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>> On 10/18/17 9:14 AM, Pandya, Akash wrote:
>>>
>>> So I equilibrated my system at 338.15 K , do I still need to use the
>>>> simulated annealing option to maintain that temperature? My NPT mdp
>>>> file is
>>>> shown below.
>>>>
>>>> Simply maintaining a temperature is done by employing a thermostat and
>>> reference temperature. Annealing is used to change temperature over time,
>>> so you don't need that here.
>>>
>>> title   = CHARMM27 A33FabGLY NPT equilibration
>>>
>>>> define  = -DPOSRES  ; position restrain the protein
>>>> ; Run parameters
>>>> integrator  = md; leap-frog integrator
>>>> nsteps  = 5 ; 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= yes   ; Restarting after NVT
>>>> 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 cells
>>>> 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)
>>>>
>>>> Your title says CHARMM, but these aren't the correct cutoffs for using
>>> the
>>> CHARMM force field.
>>>
>>> -Justin
>>>
>>>
>>> ; 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  = Nose-Hoover   ; Nose-Hoover thermostat
>>>> tc-grps = Protein Non-Protein   ; two coupling groups - more
>>>> accurate
>>>> tau_t   = 0.5   0.5 ; time constant, in ps
>>>> ref_t   = 338.15338.15  ; reference temperature, one for
>>>> each group, in K
>>>> ; Pressure coupling is on
>>>> pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
>>>> pcoupltype  = isotropic  

[gmx-users] Regarding topology generation by using topologen_1.1.pl script

[Dilip H N]

Hello,
I want to create a topology file for ammonia molecule and run using oplsaa
FF. since ammonia molecule is not there in oplsaa FF, i created the
molecule in Avogadro software and saved it as .pdb format. Then using the
topolgen_1.1.pl pearl script (script by Justin Lemkul), i generated the
topology. But the net charge on the molecule is 0.18 (for one molecule of
ammonia).

1] So how do i neutralize the net charge (because it is difficult to add a
non-integer charge), and hence carry out the simulation as neutral
system..??

2] Or is it possible to run by other scripts like mktop, acpype etc..??

Any suggestions are appreciated.

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding box size and the rlist values

[Dilip H N]

Hello,
I am running a simulation of my system of box length 2.1 nm (since i have
less number of molecules and small molecular size), and i am using
charmm 36 FF, hence i am using rlist = 1.2 (since these are the parameters
for charmm FF in the link
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM).
But if i do the compilation for energy minimization (by gmx
grompp command), i get the following error as:-

"ERROR: The cut-off length is longer than half the shortest box vector or
longer than the smallest box diagonal element. Increase the box size or
decrease rlist."

So which is the correct method to solve this..?
1] can i change/decrease the rlist (this would violate the charmm FF
parameters) or

2] if i increase the box length, it runs fine.
But after this, if i do nvt followed by npt equilibration, hereafter in
the npt simulation, the box size decreases, and here, the box size is less
than rlist, which again gives the same error ("ERROR: The cut-off length is
longer than half the shortest box vector or longer than the smallest box
diagonal element. Increase the box size or decrease rlist.")  during
compilation of production md run.

So what is the correct method/way to overcome this issue...??

Any suggestions are appreciated

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Running MD simulations at a particular temperature

[Dilip H N]

Justin Sir,
Even i am also using Charmm 36FF. So as u have mentioned in previois
message, can u kindly suggest then what ate the correct cutoffs..??
And what would be the other modifications that needs to be done in order to
incorporate the Charmm FF

Thank you



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On Wed, Oct 18, 2017 at 6:46 PM, Justin Lemkul  wrote:

>
>
> On 10/18/17 9:14 AM, Pandya, Akash wrote:
>
>> So I equilibrated my system at 338.15 K , do I still need to use the
>> simulated annealing option to maintain that temperature? My NPT mdp file is
>> shown below.
>>
>
> Simply maintaining a temperature is done by employing a thermostat and
> reference temperature. Annealing is used to change temperature over time,
> so you don't need that here.
>
> title   = CHARMM27 A33FabGLY NPT equilibration
>> define  = -DPOSRES  ; position restrain the protein
>> ; Run parameters
>> integrator  = md; leap-frog integrator
>> nsteps  = 5 ; 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= yes   ; Restarting after NVT
>> 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 cells
>> 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)
>>
>
> Your title says CHARMM, but these aren't the correct cutoffs for using the
> CHARMM force field.
>
> -Justin
>
>
> ; 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  = Nose-Hoover   ; Nose-Hoover thermostat
>> tc-grps = Protein Non-Protein   ; two coupling groups - more
>> accurate
>> tau_t   = 0.5   0.5 ; time constant, in ps
>> ref_t   = 338.15338.15  ; reference temperature, one for
>> each group, in K
>> ; Pressure coupling is on
>> pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
>> pcoupltype  = isotropic ; uniform scaling of box vectors
>> tau_p   = 2.0   ; time constant, in ps
>> ref_p   = 1.0   ; reference pressure, in bar
>> compressibility = 4.5e-5; isothermal compressibility of water,
>> bar^-1
>> refcoord_scaling = com
>> ; Periodic boundary conditions
>> pbc = xyz   ; 3-D PBC
>> ; Dispersion correction
>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = no; Velocity generation is off
>>
>>
>> Akash
>> -Original Message-
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
>> Abraham
>> Sent: 17 October 2017 10:28
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Running MD simulations at a particular
>> temperature
>>
>> Hi,
>>
>> That's your question as part of your experimental design. Why do you want
>> to do simulated annealing?
>>
>> Mark
>>
>> On Tue, Oct 17, 2017 at 10:57 AM Pandya, Akash > >
>> wrote:
>>
>> Is simulated annealing carried out during NPT or in the production run?
>>>
>>> Akash
>>>
>>> -Original Message-
>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
>>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
>>> Lemkul
>>> Sent: 20 September 2017 03:20
>>> To: gmx-us...@gromacs.org
>>> Subject: Re: [gmx-users] Running MD simulations at a particular
>>> temperature
>>>
>>>
>>>
>>> On 9/19/17 4:25 PM, Pandya, Akash wrote:
>>>
 Hi all,

 I want to run my MD simulation at 65 degrees Celsius. The mdp file
 has a

>>> field as shown below:
>>>
 ref_t= 338.15  338.15 ; reference

>>> temperature, one for each group, in K
>>>
 I am wondering whether the simulation has already reached the
 desired

>>> 

[gmx-users] Regarding ATB/PRODRG server for charmm 36 FF

[Dilip H N]

Hello,
1] I want to run simulations using charmm 36 FF in gromacs, will it be
compatible with charmm 36 FF ..??

2] How does it asses the molecule naming since in each force field the
atoms of the molecules may be named differently...

Any suggestions...

Thank you.



-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Regarding Residue in chain has different type (Other) from starting residue

[Dilip H N]

Thank you Justin Sir,

1] But how do i solve this issue..?? and make sure that pdb2gmx is not
interpreting my input as being a single chain and it's finding dissimilar
residue types..?? even i tried with gmx pdb2gmx with -ter command, but
still, i am getting the same results

2] If i view the structure in VMD and type protein in Graphical
representations->selected atoms, I am viewing only Glycine, and if i type
resname TMAO then i am viewing the tmao molecules ..., any inference here
can i have here..??

Thank you...


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<#>

On Mon, Oct 16, 2017 at 1:30 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 10/15/17 2:42 AM, Dilip H N wrote:
>
>> Hello,
>> I have a simulations system and by gmx pdb2gmx i am generating the
>> topology, but i am getting the warnings as:-
>> Identified residue GLY1 as a starting terminus.
>> Warning: Residue TMAO12 in chain has different type (Other) from starting
>> residue GLY1 (Protein).
>> Warning: Residue TMAO13 in chain has different type (Other) from starting
>> residue GLY1 (Protein).
>> Warning: Residue TMAO14 in chain has different type (Other) from starting
>> residue GLY1 (Protein).
>> Warning: Residue TMAO15 in chain has different type (Other) from starting
>> residue GLY1 (Protein).
>> Warning: Residue TMAO16 in chain has different type (Other) from starting
>> residue GLY1 (Protein).
>> More than 5 unidentified residues at end of chain - disabling further
>> warnings.
>> Identified residue GLY1 as a ending terminus
>>
>> Topology is generated, but why am i getting this..?? all the parameters
>> for
>> tmao, glycine molecules are already prescribed in the .rtp, .atp
>> files etc., in forcefield...
>>
>> Any suggestions are appreciated...
>>
>>
>>
> It means pdb2gmx is interpreting your input as being a single chain and
> it's finding dissimilar residue types (something that's protein and other
> things that are not). There probably isn't any functional consequence to
> this, but pdb2gmx warns users about such cases because there are times when
> this can cause problems or unintended outcomes.
>
> -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] Regarding Residue in chain has different type (Other) from starting residue

[Dilip H N]

Hello,
I have a simulations system and by gmx pdb2gmx i am generating the
topology, but i am getting the warnings as:-
Identified residue GLY1 as a starting terminus.
Warning: Residue TMAO12 in chain has different type (Other) from starting
residue GLY1 (Protein).
Warning: Residue TMAO13 in chain has different type (Other) from starting
residue GLY1 (Protein).
Warning: Residue TMAO14 in chain has different type (Other) from starting
residue GLY1 (Protein).
Warning: Residue TMAO15 in chain has different type (Other) from starting
residue GLY1 (Protein).
Warning: Residue TMAO16 in chain has different type (Other) from starting
residue GLY1 (Protein).
More than 5 unidentified residues at end of chain - disabling further
warnings.
Identified residue GLY1 as a ending terminus

Topology is generated, but why am i getting this..?? all the parameters for
tmao, glycine molecules are already prescribed in the .rtp, .atp
files etc., in forcefield...

Any suggestions are appreciated...


-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding beta-alanine amino acid molecule in charmm 36 FF

[Dilip H N]

Hello,
1] I wanted to simulate beta-alanine amino acid. Since i am using charmm 36
FF for simulation of other molecules too, so prefer using the same
Forcefield.
But i tried searching in the .rtp file, but only alanine  [ALA] amino-acid
is there...but not beta-alanine. So i am not able to find it in charmm 36
FF ...
So can anybody help/suggest on how to solve this issue..

2] How can i find the required molecule in the .rtp file..?? since its full
name is not written in the file.for eg., what is [ 11BPO ]..?? which
molecule does it represent..?? etc...

Thank you...
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding charges for atoms in a molecule

[Dilip H N]

Hello,
I have an amino-acid (eg. glycine) and water mixture, and by using charmm36
ff forcefield, I got the topology file through gmx pdb2gmx -f abc.pdb -o
abc.gro command.
1] In the topology file, the charges for each atom are assigned. from where
are these charges assigned..?? is it from the .rtp file, itp file..??

2] If so, I compared the charges in the generated topology file and in the
merged.rtp file, but the charges are different in both the files...

3] I even checked in the ffnonbonded.itp file, but here for all the atom
types the charges are 0.00 only...(why is this so...??)

So, from where (or) where are the charges specified..in which file

Any suggestions are appreciated...


-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Regarding wired RDF of TMAO and Aminoacid

[Dilip H N]

1*]Regarding the shrinking of the box length:-*

(a)In the npt.mdp file, i am keeping the line [define = -DPOSRES; position
restrain the protein], and running the simulation and after this for npt
production md run (nptmd.mdp, where there is no position restrain). And
after this, if i compare the two files (npt.gro and nptmd.gro), the box
length is further decreased in the nptmd.gro file.
(b) But, if in the npt.mdp file if i remove the position restrain
(-DPOSRES), and then run the simulation, followed by npt proproduction md
run, and then compare the two files (npt.gro and nptmd.gro), the box length
is decreased very slightly (ie., the values are changed in the second/third
decimal point, which is i hope acceptable.)


2]*Regarding the commands:-*

(a)  creating/generating the box with aminoacid:- gmx editconf -f
aminoacid.gro -o aminoacidbox.gro -c -b 2 2 2 (where 2 is the box length)
(b)  inserting the TMAO molecules to the box:- gmx insert-molecules -f
aminoacidbox.gro -ci tmao.gro -nmol 26 -o aminoacidtmao.gro
(c) Solvating the mixture with water :- gmx solvate -cp aminoacidtmao.gro
-cs spc216.gro -o aminoacidtmaowater.gro -maxsol 229
Here I am adding water molecules to the previously added aminoacidtmao
mixture.
I am keeping the number of aminoacid constant, and varying the numbers
of tmao and water molecules to get different concentrations [in this case,
26 molecules of tmao (-nmol 26) and 229 molecules of water (-maxsol 229),
and in other mixtures the tmao and water molecules are changed ].
So, Ideally, in the RDF's, the peak positions must be same but only change
in the heights of the solvation shells, since due to the varying
concentrations. But in my case, i am getting different peaks, for varying
the concentrations, hence i am not getting the analogy...

3] I am running the simulations again and after plotting the RDF's and
i will post the RDF's in the link mentioned...

Thank you...


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<#>

On Sat, Oct 7, 2017 at 2:54 AM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> 1) take one of your systems, repeat the setup with different random seeds,
> run another 20 ns and make the RDF
>
>
> 2) post the two RDFs of different runs with the same concentrations here:
> http://photobucket.com/
>
> 3) reply to this list with a link to your image and explain what it is
> about your results that don't make sense to you.
>
> Beyond that, the only thing that I can suggest is that it looks bizarre
> that you use the -maxsol option when you add water. You mention that your
> box "keeps shrinking" so perhaps you do have an issue. Normally one would
> add water at full density after adding a variable number of TMAO to get
> different TMAO concentrations (i.e., vary the initial concentration of TMAO
> not the initial concentration of water).
>
> And if you want to send commands, then the XX placeholders are really
> making it hard to know what you are doing. Actual commands are better.
>
> I'm going to leave this thread at this point. Feel free to PM me to let me
> know that you have posted your images to photobucked and put a link on the
> gmx list and I will take a look and reply on list.
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Dilip H N
> <cy16f01.di...@nitk.edu.in>
> Sent: 06 October 2017 02:39:49
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Regarding wired RDF of TMAO and Aminoacid
>
> 1] My simulations in the production MD are for 10 ns. I am first doing
> energy minimization, followed by NPT run of 2ns (100; 0.002 * 100 =
> 2000 ps[2ns]), and then followed by NPT Production MD run for 10 ns
> (1000; 0.001 * 1000 = 1 ps [10 ns]). During the npt simulation,
> the box length is reducing, and further during the nptmd ie., production
> md too the box length is getting reduced still further. I am not getting
> any idea over this... Is the time duration enough or still i need to do it
> for more timestep..??
>
> 2] Regarding the commands i use to get the mixtures into the simulation box
> are:-
> (a)  creating the box:- gmx editconf -f abc.gro -o abcbox.gro -c -b X X X
> (b)  inserting the molecules:- gmx insert-molecules -f abcbox.gro -ci
> def.gro -nmol X -o ghi.gro
> (c) Solvating the mixture with water :- gmx solvate -cp ghi.gro -cs
> spc216.gro -o jkl.gro -maxsol XXX
> So these are the commands which i give in order to generate my Simulation
> box containing Amino acid, TMAO and Water mixture.
> Hope these are the right set of commands... and then i start
> simulation...EM followed by NPT followed by NPTMD...
>
> Th

Re: [gmx-users] Regarding wired RDF of TMAO and Aminoacid

[Dilip H N]

1] My simulations in the production MD are for 10 ns. I am first doing
energy minimization, followed by NPT run of 2ns (100; 0.002 * 100 =
2000 ps[2ns]), and then followed by NPT Production MD run for 10 ns
(1000; 0.001 * 1000 = 1 ps [10 ns]). During the npt simulation,
the box length is reducing, and further during the nptmd ie., production
md too the box length is getting reduced still further. I am not getting
any idea over this... Is the time duration enough or still i need to do it
for more timestep..??

2] Regarding the commands i use to get the mixtures into the simulation box
are:-
(a)  creating the box:- gmx editconf -f abc.gro -o abcbox.gro -c -b X X X
(b)  inserting the molecules:- gmx insert-molecules -f abcbox.gro -ci
def.gro -nmol X -o ghi.gro
(c) Solvating the mixture with water :- gmx solvate -cp ghi.gro -cs
spc216.gro -o jkl.gro -maxsol XXX
So these are the commands which i give in order to generate my Simulation
box containing Amino acid, TMAO and Water mixture.
Hope these are the right set of commands... and then i start
simulation...EM followed by NPT followed by NPTMD...

Thank you...

With Best Regards,

DILIP.H.N
Ph.D Student


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With Best Regards,

DILIP.H.N
Ph.D Student
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[gmx-users] Regarding wired RDF of TMAO and Aminoacid

[Dilip H N]

Hello,
I have run an NPT MD simulation of an amino acid with TMAO (as a cosolvent)
and water for different concentration (by varying composition of cosolvent:
water). I have used Charmm36 FF for TMAO.
Now if i am plotting the RDF for Amino acid v/s Water in the presence of
different concentrations TMAO, I am getting wired RDF's for each
composition of TMAO present, the peaks are absurd.
Why is this happening..?? i have looked into the final structure of my
simulation in VMD which is correct
I am confused...
Any Suggestions are appreciated...


-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding box length variation after npt and production md run

[Dilip H N]

Hello,
I have ran an NPT simulation followed by NPT Production MD for different
concentrations, and after that, if i check the final .gro files of npt.gro
and  nptmd.gro (the production md .gro file), the box length of nptmd.gro
is still fluctuating, for some concentrations the nptmd.gro box length is
larger than npt.gro (which i am feeling as not correct) and in some
concentrations the nptmd.gro box length is shorter than npt.gro.
Still, the box length is fluctuating...
1] How can the box length increase after NPT simulation..??
2] So, how can i fix the box length, here??
Do i need to run for some more no of steps or time..?? [ i ran the NPT
simulation for 2 ns and NPT Production MD for 10 ns]

Any suggestions are appreciated

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding TMAO model in gromacs

[Dilip H N]

Hello,
1] I want to know which is the model of TMAO molecule that is present in
charmm36 FF ..??
2] How can i use the Kast, Netz, Garcia, etc models in gromacs .. (when i
referred the literature i came across the different models of TMAO and the
charges, sigma, epsilon values are different from the above-mentioned
models with respect to .rtp, ffnonbonded.itp files in charmm36 FF. )
Do i need to make changes in the .rtp files to incorporate the other models
?? or any other way..??
So how can i solve this issue...

Any suggestions are appreciated

Thank you

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding calculation of Lennard-Jones potential

[Dilip H N]

Hello,
I have a simulation mixture of aminoacid (eg., glycine) with water and
cosolvent. I want to calculate Lennard-Jones Parameters of the all atom
types. How can i calculate it...??

Can it be done with commands, or any other method..??
Any suggestions are appreciated...

Thank you..

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding position restraining in nvt.mdp and npt.mdp files

[Dilip H N]

Hello,
I am running a peptide simulation, i have done an energy minimization , now
going to do nvt/npt simulation...
My doubts are:-
1] Why is the position restrained (-DPORSE)in the nvt/npt mdp files..??
2] If i remove the -DPORSE than i can see the molecules moving , but with
option -DPORSE, the molecules have restricted movement...
So, Doesn't it affect the Dynamics of the system..?? Is there any
consequences of it..??
What is the significance of keeping the -DPORSE option..??

Any suggestions..?? or references from where i can get knowledge about it...

Thank you...


-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Regarding NPT simulation and box length variation

[Dilip H N]

Sir,
There is no any solvent that is protruding outside the box...all the
molecules are within the box itself, and still i am able to view the
gaps/empty area at some regions in the box...(which is indicating that the
box length is slightly bigger)
So how can i make sure that there are no any gaps in my box system and
hence proceed or further compress the box ..

These gaps can affect the analysis part like during calculating rdf, cn,
hydrogen bond dynamics, etc...i hope so... Or doen't it affect... any
ideas..??

Thank you...



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On Fri, Sep 1, 2017 at 12:21 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> These "gaps" are probably just what you expect with
> http://www.gromacs.org/Documentation/Terminology/
> Periodic_Boundary_Conditions
> for
> the configuration you are viewing. For example, if the solute protrudes out
> one side of the box, then there will be a matching gap on the other side of
> the box, because that's what PBC means. If you want to view a space-filled
> box, then you need to e.g. use trjconv to make it so.
>
> NPT isn't going to tolerate a region of vacuum ;-)
>
> Mark
>
> On Fri, Sep 1, 2017 at 8:32 AM Dilip H N <cy16f01.di...@nitk.edu.in>
> wrote:
>
> > Hello,
> > I am having a peptide and  water mixture in a cubic box of say 2.5 2.5
> 2.5
> > nm. and if i view in vmd i am able to see there are empty spaces/gaps at
> > some areas/regions (or in other words the box length is slightly bigger),
> > so i ran the energy minimization(with em.mdp) and followed by npt
> > simulation (with npt.mdp), to know the box length by allowing it to
> > fluctuate...
> > But after npt simulation if i view the final structure/full trajectory in
> > vmd, the box length has decreased slightly, but still i am able to see
> > there are empty spaces/gaps within the box. Is it ok with the gaps at
> some
> > areas or the molecules should be compactly arranged within the box..??
> >
> > I am trying with the following commands:-
> > gmx insert-molecules -f abc.gro -ci def.gro -nmol xxx -o ghi.gro #
> > inserting molecules
> > gmx solvate -cp ghi.gro -cs spc216.gro -o jkl.gro -maxsol xxx#
> > solvating with water
> > gmx grompp -f em.mdp -c jkl.gro -p topol.top -o em.tpr  #
> > energy minimization
> > gmx mdrun -v -s em.tpr -deffnm em
> > gmx grompp -f npt.mdp -c em.gro -p topol.top -o npt.tpr#
> > npt simulation
> > gmx mdrun -v -s npt.tpr -deffnm npt
> >
> > The gmx solvate command solvates with the empty spaces... and still after
> > energy minimization and npt simulation i am able to see some gaps in the
> > box through vmd.
> > How to get rid of these spaces inside the box.. or get the box compressed
> > still further with whole mixture of molecules are within the box.
> > So how can i solve this issue..?? Do i need to modify anything in the
> .mdp
> > files..or any where else..??
> > Here are the em.mdp and npt.mdp files attached...
> >
> > Any suggestions are highly appreciated 
> >
> > Thank you...
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> >
> >
> >
> > <https://mailtrack.io/> Sent with Mailtrack
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> > https://mailtrack.io/install?source=signature=en;
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> > >
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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[gmx-users] Coordination vs cumulative number in gmx_rdf

[Dilip H N]

Hello,
In the command to calculate rdf,
gmx rdf -f md.trr -s md.tpr -n abc.ndx -o rdf_abc.xvg -cn cn_abc.xvg
Is the cumulative number obtained using the -cn flag with gmx_rdf same as
coordination number?
If not, then how can I calculate coordination number from cumulative
number? or how can i calculate the corresponding coordination number in
with gromacs tools ..??

Any suggestions are highly appreciated...

Thank you..
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding Atom in residue XXX was not found in rtp entry with xxx atoms while sorting atoms

[Dilip H N]

Hello,
I have a amino acid and i am using charmm 36 FF to create the topology by:-
 gmx pdb2gmx -f abc.pdb -o abc.grobut i am getting error as:-

Atom HO in residue XXX was not found in rtp entry with xxx atoms while
sorting atoms.
So  if i use the -ignh flag in the gmx pdb2gmx command, i am getting the
topology and the .gro file, but i  in the .gro file the  the hydrogen in
the OH ie., in C terminal, is getting attached to N terminal (which was NH2
initially but in the .gro file it getting converted into NH3). So how do i
avoid the hydrogen getting shifted from OH or C terminal side to N terminal
side..??

How can i solve this error..??

Thank you...

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DILIP.H.N
Ph.D Student



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[gmx-users] Regarding indexing the atom labelled same in peptide

[Dilip H N]

Hello,
I have a Diglycine peptide in .gro file as:-
1GLY  N1   1.312   0.940   1.100  0.5173  0.1852  0.2665
1GLY H12   1.375   1.015   1.064  0.3308 -0.2009 -0.8897
1GLY H23   1.376   0.860   1.115  2.0625  0.7372 -2.9245
1GLY H34   1.242   0.907   1.031  0.2385  0.6317  0.3326
1GLY CA5   1.240   0.963   1.228  0.3801 -0.0854  0.2381
1GLYHA16   1.155   0.898   1.233  1.2980 -1.3807 -0.5280
1GLYHA27   1.321   0.963   1.300 -1.1296 -1.6137  1.9682
1GLY  C  8   1.185   1.101   1.232  0.0318 -0.2122 -0.1516
1GLY  O9   1.171   1.174   1.133  0.1199  0.2166  0.1513
2GLY  N   10   1.148   1.148   1.352 -1.0777 -0.3721 -0.4264
2GLY HN   11   1.142   1.091   1.434 -0.1054  0.0667 -0.0362
2GLY CA   12   1.092   1.277   1.377  0.5476  0.2162  0.2355
2GLYHA1   13   1.170   1.351   1.365  0.3836  0.3441 -0.0427
2GLYHA2   14   1.012   1.294   1.306 -0.5941  1.1037  1.7136
2GLY  C   15   1.031   1.298   1.514  0.2354 -0.4348  0.1971
2GLYOT1   16   0.923   1.238   1.541  0.2601 -0.2386  0.7420
2GLYOT2   17   1.091   1.369   1.598  0.1878 -0.0650 -0.0813

So now i want to index of the Nitrogen (N) of 1GLY only, but not N of
2GLY...

I tried the the following command as:-
gmx make_ndx -f abc.gro -o def.ndx
1 & a N

But it is giving  2 Protein_&_N  : 2 atoms
which is taking the N of 2GLY too into considerationwhich i don't
required, I need the N of ...1GLY only

So what is the correct command for this..??

Thank you...



With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Regarding Unknown cmap torsion between atoms

[Dilip H N]

Hello,
1] it is the solute+Diglycine which is the constituting the mixture...
2] the method to create the system for both were the same...
the commands are...
gmx editconf -f Diglycinechimera2.gro -o Diglybox.gro -c -box x y z
(generating the box)
gmx insert-molecules -f Diglybox.gro -ci abc.gro -nmol 10 -o Dglyabc.gro
and for other system, gmx insert-molecules -f Diglybox.gro -ci def.gro
-nmol 10 -o Dglydef.gro (adding the solute molecules and getting the final
system)...
here the two solute .gro files are abc.gro and def.groand i have
followed the same procedure...
and thn gmx pdb2gmx -f Dglyabc.gro (or) gmx pdb2gmx -f Dglydef.gro...there
is [cmap] option in one topology file and in other topology there is no
[cmap] option...

How is it different thn..??






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On Tue, Aug 22, 2017 at 11:49 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Your description is too confused to follow. Your use of the words solvent
> and solute is unclear. pdb2gmx will never make a cmap that goes outside a
> moleculetype.
>
> If one use of pdb2gmx made a cmap and the other did not, then they were
> fundamentally different. If you don't know what was different, then you
> aren't doing science because you don't know what your method was. If so,
> start again and keep a record in a shell script this time.
>
> Mark
>
> On Tue, Aug 22, 2017 at 8:05 AM Dilip H N <cy16f01.di...@nitk.edu.in>
> wrote:
>
> > 1] in the line 8231 [ Unknown cmap torsion between atoms 8 10 12 15 18]
> it
> > is the diglycine peptide molecule only, it is stating the atomic numbers
> of
> > the diglycine molecule (8,10,12,15) and solute molecule (18)
> > 2] but one more problem is the Diglycine nitrogen and the solute
> containing
> > nitrogen are labelled as same (as N only)...
> > ie., atoms 8,10,12,15 (here atom 10 is N, and other atoms are  C, CA)
> > belong to diglycine and atom 18 belong to solute molecule of atom N, and
> > hence i am getting the error...i hope so(But with other system tht i
> > ran had no [cmap] in topology and the atoms in the solute were labelled
> > differentlyand ran correctly..)
> > 3] So can  i remove/delete the [cmap] line  (i tried removing cmap
> line
> > in topology..and thn with gmx grompp option it is workin fine..) does
> that
> > cause any error/manipulating the topology..etc..?? can i proceed removing
> > [cmap] is thr any harm..?
> > 4] I tried also with removing the last coloumn in [cmap] ie., removing
> 18,1
> > of am,funct..since as i told above the atom 18 is of the solute nitrogen
> > molecule which is labelled as same in the .rtp file in charmmFF, which is
> > causing the problemssince the gmx grompp is trying to bond wiht the
> > atom 18 N  which is solute and not Diglycine (since both N's are labelled
> > same)
> > [ cmap ]
> > ;  aiajakalam funct
> > 810121518 1
> > and edited and got it as:-
> >
> > [ cmap ]
> > ;  aiajakal
> > 8101215
> > and thn now if i run gmx grompp -f min.mdp -c mixture.gro -p topol.top -o
> > min.tpr
> >  it is showing:-
> >  WARNING 1 [file topol.top, line 8231]:
> >   Too few parameters on line (source file
> >
> > /home/dilip/Downloads/gromacs-2016.2/src/gromacs/
> gmxpreprocess/toppush.cpp,
> > line 2198)
> > So i tried with gmx grompp -f min.mdp -c mixture.gro -p topol.top -o
> > min.tpr -maxwarn 2 , and now it is working fine...
> >
> > So i have tried with different options..and i have discussed what i have
> > got..but are they the correct way...to proceed..??
> >
> > Any suggestions are welcome...
> >
> > Thank you...
> >
> >
> > <https://mailtrack.io/> Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature=en;
> referral=cy16f01.di...@nitk.edu.in=22
> > >
> >
> > On Mon, Aug 21, 2017 at 11:14 PM, Mark Abraham <mark.j.abra...@gmail.com
> >
> > wrote:
> >
> > > Hi,
> > >
> > > If your procedure for the two systems was actually the same, then the
> > error
> > > does not come from your solute. Unfortunately only you know what is on
> > line
> > > 8231... Work out what you did differently, e.g. by doing it again and
> > > making sure you do it the same way.
> > >
> > > Mark
> > >
> > > On Mon, Aug 21, 2017 at 7:27 PM Dilip H N <cy16f01.di...@nitk.edu.in>
> > > wrote:
&g

Re: [gmx-users] Regarding Unknown cmap torsion between atoms

[Dilip H N]

1] in the line 8231 [ Unknown cmap torsion between atoms 8 10 12 15 18] it
is the diglycine peptide molecule only, it is stating the atomic numbers of
the diglycine molecule (8,10,12,15) and solute molecule (18)
2] but one more problem is the Diglycine nitrogen and the solute containing
nitrogen are labelled as same (as N only)...
ie., atoms 8,10,12,15 (here atom 10 is N, and other atoms are  C, CA)
belong to diglycine and atom 18 belong to solute molecule of atom N, and
hence i am getting the error...i hope so(But with other system tht i
ran had no [cmap] in topology and the atoms in the solute were labelled
differentlyand ran correctly..)
3] So can  i remove/delete the [cmap] line  (i tried removing cmap line
in topology..and thn with gmx grompp option it is workin fine..) does that
cause any error/manipulating the topology..etc..?? can i proceed removing
[cmap] is thr any harm..?
4] I tried also with removing the last coloumn in [cmap] ie., removing 18,1
of am,funct..since as i told above the atom 18 is of the solute nitrogen
molecule which is labelled as same in the .rtp file in charmmFF, which is
causing the problemssince the gmx grompp is trying to bond wiht the
atom 18 N  which is solute and not Diglycine (since both N's are labelled
same)
[ cmap ]
;  aiajakalam funct
810121518 1
and edited and got it as:-

[ cmap ]
;  aiajakal
8101215
and thn now if i run gmx grompp -f min.mdp -c mixture.gro -p topol.top -o
min.tpr
 it is showing:-
 WARNING 1 [file topol.top, line 8231]:
  Too few parameters on line (source file

/home/dilip/Downloads/gromacs-2016.2/src/gromacs/gmxpreprocess/toppush.cpp,
line 2198)
So i tried with gmx grompp -f min.mdp -c mixture.gro -p topol.top -o
min.tpr -maxwarn 2 , and now it is working fine...

So i have tried with different options..and i have discussed what i have
got..but are they the correct way...to proceed..??

Any suggestions are welcome...

Thank you...


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On Mon, Aug 21, 2017 at 11:14 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> If your procedure for the two systems was actually the same, then the error
> does not come from your solute. Unfortunately only you know what is on line
> 8231... Work out what you did differently, e.g. by doing it again and
> making sure you do it the same way.
>
> Mark
>
> On Mon, Aug 21, 2017 at 7:27 PM Dilip H N <cy16f01.di...@nitk.edu.in>
> wrote:
>
> > 1] I created Diglycine peptide from chimera software, and got the .pdb
> > file, added two different solvents (A, B) and made two different systems
> > say, A-(Diglycine+solvent1), B-(Diglycine+solvent2). I generated the
> > topology file from charmm36 FF by gmx pdb2gmx process for both the
> systems
> > A and B correctly (but in system A there is no [ cmap ] line in topology,
> > but system B has [ cmap ] in topology).. Why is this in one system i am
> > getting but in other i am not..?  Is there any error...or what is it...
> >
> > 2] And  during gmx grompp  -f min.mdp -c mixture.gro -p topol.top -o
> > min.tpr
> >
> > for system A (whr there is no [cmap] in topology), the gmx grompp command
> > works well...
> > But for system B (which has [cmap] in topology), the error comes as:-
> >
> > > ERROR 1 [file topol.top, line 8231]:
> > >  Unknown cmap torsion between atoms 8 10 12 15 18
> >
> > How can i solve this ...??
> >
> > Thank you...
> >
> >
> > On Mon, Aug 21, 2017 at 10:18 PM, Mark Abraham <mark.j.abra...@gmail.com
> >
> > wrote:
> >
> > > Hi,
> > >
> > > On Mon, Aug 21, 2017 at 6:33 PM Dilip H N <cy16f01.di...@nitk.edu.in>
> > > wrote:
> > >
> > > > Hello,
> > > > I have created a peptide from chimera software and got the pdb file,
> > and
> > > i
> > > > have added solvents to it the resultant is mixture.gro, and used gmx
> > > > pdb2gmx to generate the topology using charmm36 FF. I got the
> topology
> > > > correct, but nw if i give the command for energy minimization :-
> > > > gmx grompp -f min.mdp -c mixture.gro -p topol.top -o min.tpr
> > > >
> > > > I am getting error as:-
> > > >
> > > > NOTE 1 [file min.mdp]:
> > > >   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20.
> Note
> > > >   that with the Verlet scheme, nstlist has no effect on the accuracy
> of
> > > >   your simulation.
> > > >
> > > > Setting the LD random seed to -1

Re: [gmx-users] Regarding Unknown cmap torsion between atoms

[Dilip H N]

1] I created Diglycine peptide from chimera software, and got the .pdb
file, added two different solvents (A, B) and made two different systems
say, A-(Diglycine+solvent1), B-(Diglycine+solvent2). I generated the
topology file from charmm36 FF by gmx pdb2gmx process for both the systems
A and B correctly (but in system A there is no [ cmap ] line in topology,
but system B has [ cmap ] in topology).. Why is this in one system i am
getting but in other i am not..?  Is there any error...or what is it...

2] And  during gmx grompp  -f min.mdp -c mixture.gro -p topol.top -o min.tpr

for system A (whr there is no [cmap] in topology), the gmx grompp command
works well...
But for system B (which has [cmap] in topology), the error comes as:-

> ERROR 1 [file topol.top, line 8231]:
>  Unknown cmap torsion between atoms 8 10 12 15 18

How can i solve this ...??

Thank you...


On Mon, Aug 21, 2017 at 10:18 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> On Mon, Aug 21, 2017 at 6:33 PM Dilip H N <cy16f01.di...@nitk.edu.in>
> wrote:
>
> > Hello,
> > I have created a peptide from chimera software and got the pdb file, and
> i
> > have added solvents to it the resultant is mixture.gro, and used gmx
> > pdb2gmx to generate the topology using charmm36 FF. I got the topology
> > correct, but nw if i give the command for energy minimization :-
> > gmx grompp -f min.mdp -c mixture.gro -p topol.top -o min.tpr
> >
> > I am getting error as:-
> >
> > NOTE 1 [file min.mdp]:
> >   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
> >   that with the Verlet scheme, nstlist has no effect on the accuracy of
> >   your simulation.
> >
> > Setting the LD random seed to -1490567170
> > Generated 97877 of the 97903 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 1
> > Generated 64492 of the 97903 1-4 parameter combinations
> >
> > ERROR 1 [file topol.top, line 8231]:
> >   Unknown cmap torsion between atoms 8 10 12 15 18
> >
> > There was 1 note
> > ---
> > Program: gmx grompp, version 2016.3
> > Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1622)
> >
> > Fatal error:
> > There was 1 error in input file(s)
> >
> > 1] What is this cmap all about..??
> >
>
> That's part of how the CHARMM force field works for modelling peptides. You
> should have a basic understanding of that from your background reading that
> led to the choice of this force field.
>
>
> > 2] How do i correct this error..?
> >
>
> Whether you can do so depends whether chimera has generated a structure
> that has a valid CHARMM36 representation, ie there exists a CMAP definition
> for the types of those atoms.
>
> Mark
>
>
> > Any suggestions will be helpful...
> >
> > Thank you...
> >
> >
> >
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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>



-- 
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DILIP.H.N
Ph.D Student
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[gmx-users] Regarding Unknown cmap torsion between atoms

[Dilip H N]

Hello,
I have created a peptide from chimera software and got the pdb file, and i
have added solvents to it the resultant is mixture.gro, and used gmx
pdb2gmx to generate the topology using charmm36 FF. I got the topology
correct, but nw if i give the command for energy minimization :-
gmx grompp -f min.mdp -c mixture.gro -p topol.top -o min.tpr

I am getting error as:-

NOTE 1 [file min.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to -1490567170
Generated 97877 of the 97903 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 64492 of the 97903 1-4 parameter combinations

ERROR 1 [file topol.top, line 8231]:
  Unknown cmap torsion between atoms 8 10 12 15 18

There was 1 note
---
Program: gmx grompp, version 2016.3
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1622)

Fatal error:
There was 1 error in input file(s)

1] What is this cmap all about..??
2] How do i correct this error..?

Any suggestions will be helpful...

Thank you...




-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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Re: [gmx-users] Regarding naming dipeptide in charmm36 Forcefield

[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...


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On Fri, Aug 18, 2017 at 10:32 PM, Justin Lemkul <jalem...@vt.edu> 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
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
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Ph.D Student
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Re: [gmx-users] Regarding naming dipeptide in charmm36 Forcefield

[Dilip H N]

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...
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

Thank you...



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On Thu, Aug 17, 2017 at 5:41 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 8/17/17 12:01 AM, Dilip H N wrote:
>
>> Thank you Justin Sir for replying...
>> Yes, the term "dipeptide" is ambiguous
>> But is there any other smallest  molecule with an amide linkage (two
>> aminoacids linked through peptide bond) or any other small peptide
>> molecule
>> that can be found in CHARMM36 FF..  with the corresponding residue naming
>> in charmm...
>>
>
> As I said, no, there's not.  You have the smallest possible polypeptide,
> two amino acids linked in the normal way.  So that means you have a
> sequence of GLY GLY, and the tool to produce that topology is pdb2gmx.
>
> -Justin
>
> Thank you...
>>
>>
>>
>> <https://mailtrack.io/> Sent with Mailtrack
>> <https://mailtrack.io/install?source=signature=en
>> ral=cy16f01.di...@nitk.edu.in=22>
>>
>>
>> On Wed, Aug 16, 2017 at 9:26 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>> On 8/16/17 11:41 AM, Dilip H N wrote:
>>>
>>> Hello,
>>>> I want to simulate a small dipeptide with mixture of solvents in
>>>> charmm36
>>>> forcefield, (the solvents are already in charmm36 forcefield), but i am
>>>> unable to find any small dipeptide molecule in charmm36 FF, since i have
>>>> solvent molecules in charmm36 FF, but not the dipeptide, which would
>>>> also
>>>> be easy in getting the topology file by gmx pdb2gmx command...
>>>> So can anybody help me how to find the dipeptide molecules (eg.,
>>>> diglycine)
>>>> in charmm36 FF...??
>>>>
>>>> There is no such special residue.  For diglycine, you have two GLY. It's
>>> like any peptide sequence.  The only dipeptide that CHARMM has is alanine
>>> dipeptide, but it's not ALA-ALA, it's ALA capped with acetyl and N-methyl
>>> groups, so there are two peptide bonds, but not two residues (hence why
>>> the
>>> term "dipeptide" is ambiguous).
>>>
>>> -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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>>>
>>>
>>
>>
> --
> ==
>
> 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

[Dilip H N]

Thank you Justin Sir for replying...
Yes, the term "dipeptide" is ambiguous
But is there any other smallest  molecule with an amide linkage (two
aminoacids linked through peptide bond) or any other small peptide molecule
that can be found in CHARMM36 FF..  with the corresponding residue naming
in charmm...

Thank you...



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On Wed, Aug 16, 2017 at 9:26 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 8/16/17 11:41 AM, Dilip H N wrote:
>
>> Hello,
>> I want to simulate a small dipeptide with mixture of solvents in charmm36
>> forcefield, (the solvents are already in charmm36 forcefield), but i am
>> unable to find any small dipeptide molecule in charmm36 FF, since i have
>> solvent molecules in charmm36 FF, but not the dipeptide, which would also
>> be easy in getting the topology file by gmx pdb2gmx command...
>> So can anybody help me how to find the dipeptide molecules (eg.,
>> diglycine)
>> in charmm36 FF...??
>>
>
> There is no such special residue.  For diglycine, you have two GLY. It's
> like any peptide sequence.  The only dipeptide that CHARMM has is alanine
> dipeptide, but it's not ALA-ALA, it's ALA capped with acetyl and N-methyl
> groups, so there are two peptide bonds, but not two residues (hence why the
> term "dipeptide" is ambiguous).
>
> -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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[gmx-users] Regarding naming dipeptide in charmm36 Forcefield

[Dilip H N]

Hello,
I want to simulate a small dipeptide with mixture of solvents in charmm36
forcefield, (the solvents are already in charmm36 forcefield), but i am
unable to find any small dipeptide molecule in charmm36 FF, since i have
solvent molecules in charmm36 FF, but not the dipeptide, which would also
be easy in getting the topology file by gmx pdb2gmx command...
So can anybody help me how to find the dipeptide molecules (eg., diglycine)
in charmm36 FF...??

Any suggestions are highly appreciated

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Regarding indexing to calculate hydrogen bond autocorrelation function

[Dilip H N]

yes thn how can i index the groups (say i want to calculate hbond b/w NH of
glycine and O of water)...
with commands...



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On Wed, Jul 26, 2017 at 10:56 PM, Erik Marklund <erik.markl...@kemi.uu.se>
wrote:

>
>
> On 26 Jul 2017, at 19:04, Dilip H N <cy16f01.di...@nitk.edu.in cy16f01.di...@nitk.edu.in>> wrote:
>
> but i dont have any OH or NH groups in glycine,water mixture...
>
> Your water is packed with OH, and glycine has both NH and OH.
>
> Kind regards,
> Erik
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[gmx-users] Regarding indexing to calculate hydrogen bond autocorrelation function

[Dilip H N]

Hello all,
i am trying to make the indexing of groups by gmx make_ndx in order to
calculate hydrogen bond autocorrelation function.
I have glycine and water mixture...in the gmx make_ndx manual it tells tht
OH and NH groups are regarded as donors and  O, N being acceptor...but how
can i make those donors indexes..
but i dont have any OH or NH groups in glycine,water mixture...
how can i resolve this, with set of commands for indexing...

Thank you..



-- 
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DILIP.H.N
Ph.D Student



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[gmx-users] Regarding calculation of coordination number

[Dilip H N]

Hello,
i have calculated the radial distribution function through the commands as:-
gmx rdf -f ab.ttr -s ab.tpr -n ab.ndx -o rdf_ab.xvg -ref x -sel y -cn
cn_ab.xvg

1] my doubt is tht whether -cn option is calculating the co-ordination
number ie., running coordination number [N(r)] or just the coordination
number [CN]..??
Because when i compare the 1st minima of rdf value to the corresponding
coordination number tht i have got by -cn flag is not matching.. i am
getting very less coordination number even with the corresponding
second/third minima value of rdf also..
can anybody help??
2] And if want to calculate coordination number by the formula, how can i
do tht.?? should i manually integrate and calculate the values till 1st
minima or do i need to write a small code for tht.?? how could i solve this
issue..??
-- 
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DILIP.H.N
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[gmx-users] Regarding precision in gromacs

[Dilip H N]

Hello,
i have installed gromacs 2016.2, and in the command line if i type gmx
--version i am getting as:-
GROMACS version:2016.2
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:disabled
SIMD instructions:  AVX2_256
FFT library:fftw-3.3.3-sse2-avx
RDTSCP usage:   enabled
TNG support:enabled
Hwloc support:  disabled
Tracing support:disabled
Built on:   Sun Jul 16 13:28:27 IST 2017
Built by:   root@DILIP [CMAKE]
Build OS/arch:  Linux 3.13.0-24-generic x86_64
Build CPU vendor:   Intel
Build CPU brand:Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz
Build CPU family:   6   Model: 60   Stepping: 3
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf
mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2
sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/gcc GNU 4.8.4
C compiler flags:-march=core-avx2 -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast
C++ compiler:   /usr/bin/c++ GNU 4.8.4
C++ compiler flags:  -march=core-avx2-std=c++0x   -O3 -DNDEBUG
-funroll-all-loops -fexcess-precision=fast

My doubt is tht how does the precision have any effect on the
simulation..?? and how can i convert/make the gromacs version tht i have
installed(2016.2), from single precision to double precision...?? what are
the commands tht i need to give ...??

Thank you...
-- 
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DILIP.H.N
Ph.D Student
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[gmx-users] Regarding creating indexing with atoms having same labelling in different molecules

[Dilip H N]

Hello,
I am having problems during creating the indexes for atoms which have same
atom labelling for the two/three different molecules in the system (say
nitrogen atom that is labelled as N in both the molecules).
 whn i gave the command:-
gmx make_ndx -f md.gro -o a.ndx
i am getting the prompt as :-
Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are: 1Protein residues
There are:10  Other residues
There are:   200  Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...

  0 System   :  750 atoms
  1 Protein:10 atoms
  2 Protein-H: 5 atoms
  3 C-alpha  : 1 atoms
  4 Backbone   : 3 atoms
  5 MainChain  : 3 atoms
  6 MainChain+Cb   : 3 atoms
  7 MainChain+H : 6 atoms
  8 SideChain  : 4 atoms
  9 SideChain-H  : 2 atoms
 10 Prot-Masses :10 atoms
 11 non-Protein   :  890 atoms
 12 Other:   140 atoms
 13 TMAO  :   140 atoms
 14 Water   :   600 atoms
 15 SOL :   600 atoms
 16 non-Water   :   374 atoms

Here i need say the nitrogen present in protein (1 protein: 10 atoms) index
and the nitrogen's present in tmao (13 TMAO: 140 atoms) in the .ndx file.ie.,
i need the nitrogen present in protein and nitrogen's present in tmao in
the index file..
How can i get this..?? wht will be the commands for this... i tried with
various commands but in vain


Thank you...

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding creating topology for molecule

[Dilip H N]

Hello,
1] I want to simulate A and B mixtures...but the problem is tht in both the
say atoms of nitrogen's of both A and B molecules are labelled as N
onlywhich during the indexing for RDF creates problems...

So in the CHARMM FF .rtp file, i changed the nitrogen (of B molecule) N
into N1 and thn saved it, and thn did the changes in atom type from N to N1
in  .pdb/gro file (of B molecule), since now both the nitrogen is labelled
different in B molecule, and hence now the nitrogen's are labelled
differently in A and B molecules.
thn i ran the command as :-
  gmx pdb2gmx -f a.pdb -o a.gro

but still i am getting the error as:-
Atom N1 in residue XXX 2 was not found in rtp entry XXX with x atoms
while sorting atoms.

Why is this error coming inspite of changing the atom type from N to N1
(ie.,redefined the atoms and checked there is no mismatch between them) in
the .rtp file, Or still should i do any changes in any other files..??
 but still i am getting this error... how to solve this error..??

2] In general, if the atoms are labelled in same type/name for different
molecules in the .rtp files/any other files, thn how can i correct it and
get a correct topology file, and get the index's correctly of the atoms
named same in different molecules, without getting overlapped..??


Thank you...

-- 
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DILIP.H.N
Ph.D Student



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[gmx-users] Fwd: Regarding getting the trajectories at certain time intervals

[Dilip H N]

Hello,
I have ran an md simulation  which has 6 frames (3000 / 500 ie.,
nsteps / nstxout, nsteps = 0.001 * 3000 = 3 ps),  and now i need to
get the trajectories, but this will be of very huge data (which gives
trajectories of interval of every 0.5 ps)...So how can i get the
trajectories from intial to final run but with interval of say 1000 ps , i
tried with the following command as :-

gmx trjconv -f md.trr -s md.tpr -o mdtrj.gro -b 0 -e 6

but i am getting trajectories for every 0.5 ps interval, but i need it for
say 1000 ps interval.
How can i do this..??

Thank you...

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding getting the trajectories at certain time intervals

[Dilip H N]

Hello,
I have ran an md simulation  which has 6 frames (3000 / 500 ie.,
nsteps / nstxout, nsteps = 0.001 * 3000 = 3 ps),  and now i need to
get the trajectories, but this will be of very huge data (which gives
trajectories of interval of every 0.5 ps)...So how can i get the
trajectories from intial to final run but with interval of say 1000 ps , i
tried with the following command as :-

gmx trjconv -f md.trr -s md.tpr -o mdtrj.gro -b 0 -e 6

but i am getting trajectories for every 0.5 ps interval, but i need it for
say 1000 ps interval.
How can i do this..??

Thank you...

-- 
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DILIP.H.N
Ph.D Student
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[gmx-users] Regarding change in residue name during conversion from pdb 2 gro file

[Dilip H N]

Hello all,
I have a .pdb file with residue name as DMAM , so while i try to convert
the .pdb file into .gro file by the command :-
gmx editconf -f abc.pdb -o abc.gro
the .gro file is generated but the residue name is being changed to
DMA...which during the simulation mixture setup gives errors as residue not
found it residue topology...
So how do i avoid this residue name getting changed during the conversion
from .pdb file to .gro file...??

Thank you

-- 
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DILIP.H.N
Ph.D Student



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[gmx-users] Regarding conversion of charmm ff to gromacs by cgenff_charmm2gmx.py script

[Dilip H N]

Hello all,
I uploaded a molecule in mol.2 format in cgenff and thn i got the output
file in .str format. and now i am converting the .str which is in charmm
format to gromacs format using the script cgenff_charmm2gmx.py by the
following command as:-

python cgenff_charmm2gmx.py abc abc.str abc.mol2 charmm26-nov2016.ff

but i am getting the following errors..

NOTE1: Code tested with python 2.7.3. Your version:
NOTE2: Please be sure to use the same version of CGenFF in your simulations
that was used during parameter generation:
Traceback (most recent call last):
  File "cgenff_charmm2gmx.py", line 777, in 
check_versions(rtp_name,ffdir + "/forcefield.doc")
  File "cgenff_charmm2gmx.py", line 60, in check_versions
f = open(ffdoc_filename, 'r')
FileNotFoundError: [Errno 2] No such file or directory: 'charmm26
nov2016.ff/forcefield.doc'

How to solve this error..??

Thank you...
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding creating a itp for molecule from CGenFF

[Dilip H N]

Hello all,

I want to simulate methylamine with amino acid misture in CHARMM FF, so i
have created methylamine in mol2 format and created the .itp and .pdb files
from the CGenFF (which creates itp in CHARMM FF for GROMACS). and i have
included it in topology file also as:-  #Include "methylamine.itp", have
solvated the system,
But if i give the command for energy minimization:-
gmx grompp -f em.mdp -c abc.gro -p topol.top -o em.tpr
i am getting the error as

NOTE 1 [file em.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to -1252943664
Generated 85052 of the 85078 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 55198 of the 85078 1-4 parameter combinations

ERROR 1 [file Dimethylamine.itp, line 9]:
  Atomtype 7 not found

How can i solve these error..??
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Regarding the charge of the atom in the .rtp file

[Dilip H N]

No, its not related to parameterization methodology. it is a different
question...

how can i identify the molecule as methylamine (for example) since in the
.rtp the molecule type is written as [MAM1]
[ MAM1 ]
  [ atoms ]
   N1 NG321-0.990  0
   C1 CG3AM2 -0.060  1
  HN1 HGPAM20.390  2
  HN2 HGPAM20.390  3
  HC1 HGAAM20.090  4
  HC2 HGAAM20.090  5
  HC3 HGAAM20.090  6
  [ bonds ]
   N1C1
   N1   HN1
   N1   HN2
   C1   HC1
   C1   HC2
   C1   HC3
Is thr any hint such tht i can identify the molecule type written in .rtp
file.??
Or should i manually find it out..??... but in case of Glycine the molecule
type is [GLY] which is easy to find
How can i solve this issue..??

Thank you...





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On Thu, Jun 22, 2017 at 4:38 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> I don't understand what you are asking. How does it relate to
> parameterization methodology?
>
> Mark
>
> On Thu, Jun 22, 2017 at 7:20 AM Dilip H N <cy16f01.di...@nitk.edu.in>
> wrote:
>
> > Thank you for reply..
> >
> > But how can i identify the molecule as methylamine (for example) since in
> > the .rtp the molecule type is written as [MAM1]
> > [ MAM1 ]
> >   [ atoms ]
> >N1 NG321-0.990  0
> >C1 CG3AM2 -0.060  1
> >   HN1 HGPAM20.390  2
> >   HN2 HGPAM20.390  3
> >   HC1 HGAAM20.090  4
> >   HC2 HGAAM20.090  5
> >   HC3 HGAAM20.090  6
> >   [ bonds ]
> >N1C1
> >N1   HN1
> >N1   HN2
> >C1   HC1
> >C1   HC2
> >C1   HC3
> > Is thr any hint such tht i can identify the molecule type written in .rtp
> > file.??
> > Or should i manually find it out..??... but in case of Glycine the
> molecule
> > type is [GLY] which is easy to find
> > How can i solve this issue..??
> >
> > Thank you...
> >
> >
> >
> >   <https://mailtrack.io/> Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature=en;
> referral=cy16f01.di...@nitk.edu.in=22
> > >
> >
> > On Wed, Jun 21, 2017 at 4:23 PM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > On Wed, Jun 21, 2017 at 11:59 AM Dilip H N <cy16f01.di...@nitk.edu.in>
> > > wrote:
> > >
> > > > Hello all.
> > > > 1] I want to knw how the charges are designated/assigned for the each
> > > atoms
> > > > in molecule in the .rtp file.  ie., as example for methylamine in
> > CHARMM
> > > > FF:-
> > > >
> > > > [ MAM1 ]
> > > >   [ atoms ]
> > > >   N1 NG321-0.990  0
> > > >   C1 CG3AM2 -0.060  1
> > > >  HN1 HGPAM20.390  2
> > > >  HN2 HGPAM20.390  3
> > > >  HC1 HGAAM20.090  4
> > > >  HC2 HGAAM20.090  5
> > > >  HC3 HGAAM20.090  6
> > > >   [ bonds ]
> > > >   N1C1
> > > >   N1   HN1
> > > >   N1   HN2
> > > >   C1   HC1
> > > >   C1   HC2
> > > >   C1   HC3
> > > >  ie how are the charges -0.990, -0.060, 0.390 etc., are assigned...
> > > >
> > >
> > > The parameterization methodology is unique to each force field, and
> > perhaps
> > > to each tool that generates compatible topologies. You need to read
> that
> > > documentation and literature to understand how they were derived.
> > >
> > >
> > > > 2] and if i get the topology/itp file from the automated topology
> > builder
> > > > as in SwissParam for CHARMM forcefield, how can i confirm that the
> > > charges
> > > > assigned are exact..??
> > > >
> > >
> > > You can see if they are correct in the sense of being a valid model of
> > > reality by running a simulation and observing whether you can get
> > > reasonable agreement with suitable e.g. experimental data.
> > >
> > > Mark
> > >
> > >
> > > > Any help/suggestion is most welcome.
> > > > Thank you...
> > > > --
> > > > With Best Regards,
> > > >
> > > > DILIP.H.N
> > > > Ph.D Student
> > > >
> > > >
> > > >
> > > >   <https://mailtrack.io/> Sent with Mailtrack
> > > > <
> > > > https://mailtrac

Re: [gmx-users] Regarding the charge of the atom in the .rtp file

[Dilip H N]

Thank you for reply..

But how can i identify the molecule as methylamine (for example) since in
the .rtp the molecule type is written as [MAM1]
[ MAM1 ]
  [ atoms ]
   N1 NG321-0.990  0
   C1 CG3AM2 -0.060  1
  HN1 HGPAM20.390  2
  HN2 HGPAM20.390  3
  HC1 HGAAM20.090  4
  HC2 HGAAM20.090  5
  HC3 HGAAM20.090  6
  [ bonds ]
   N1C1
   N1   HN1
   N1   HN2
   C1   HC1
   C1   HC2
   C1   HC3
Is thr any hint such tht i can identify the molecule type written in .rtp
file.??
Or should i manually find it out..??... but in case of Glycine the molecule
type is [GLY] which is easy to find
How can i solve this issue..??

Thank you...



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On Wed, Jun 21, 2017 at 4:23 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> On Wed, Jun 21, 2017 at 11:59 AM Dilip H N <cy16f01.di...@nitk.edu.in>
> wrote:
>
> > Hello all.
> > 1] I want to knw how the charges are designated/assigned for the each
> atoms
> > in molecule in the .rtp file.  ie., as example for methylamine in CHARMM
> > FF:-
> >
> > [ MAM1 ]
> >   [ atoms ]
> >   N1 NG321-0.990  0
> >   C1 CG3AM2 -0.060  1
> >  HN1 HGPAM20.390  2
> >  HN2 HGPAM20.390  3
> >  HC1 HGAAM20.090  4
> >  HC2 HGAAM20.090  5
> >  HC3 HGAAM20.090  6
> >   [ bonds ]
> >   N1C1
> >   N1   HN1
> >   N1   HN2
> >   C1   HC1
> >   C1   HC2
> >   C1   HC3
> >  ie how are the charges -0.990, -0.060, 0.390 etc., are assigned...
> >
>
> The parameterization methodology is unique to each force field, and perhaps
> to each tool that generates compatible topologies. You need to read that
> documentation and literature to understand how they were derived.
>
>
> > 2] and if i get the topology/itp file from the automated topology builder
> > as in SwissParam for CHARMM forcefield, how can i confirm that the
> charges
> > assigned are exact..??
> >
>
> You can see if they are correct in the sense of being a valid model of
> reality by running a simulation and observing whether you can get
> reasonable agreement with suitable e.g. experimental data.
>
> Mark
>
>
> > Any help/suggestion is most welcome.
> > Thank you...
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> >
> >
> >
> >   <https://mailtrack.io/> Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature=en;
> referral=cy16f01.di...@nitk.edu.in=22
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
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DILIP.H.N
Ph.D Student
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[gmx-users] Regarding the charge of the atom in the .rtp file

[Dilip H N]

Hello all.
1] I want to knw how the charges are designated/assigned for the each atoms
in molecule in the .rtp file.  ie., as example for methylamine in CHARMM
FF:-

[ MAM1 ]
  [ atoms ]
  N1 NG321-0.990  0
  C1 CG3AM2 -0.060  1
 HN1 HGPAM20.390  2
 HN2 HGPAM20.390  3
 HC1 HGAAM20.090  4
 HC2 HGAAM20.090  5
 HC3 HGAAM20.090  6
  [ bonds ]
  N1C1
  N1   HN1
  N1   HN2
  C1   HC1
  C1   HC2
  C1   HC3
 ie how are the charges -0.990, -0.060, 0.390 etc., are assigned...

2] and if i get the topology/itp file from the automated topology builder
as in SwissParam for CHARMM forcefield, how can i confirm that the charges
assigned are exact..??

Any help/suggestion is most welcome.
Thank you...
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding Creating a molecule and fitting it to CHARMM forcefield

[Dilip H N]

Hello all,
I want to create a molecule (methylamine) and want to run  the simulation
in CHARMM forcefield..
1] How can i create the molecule methylamine such tht its residues fit into
CHARMM forcefield..??
2] How do i get its topology/itp for running the simulation..???
3] If the required molecule is not there in the specific force filed (say
CHARMM), than how can i add the desired molecule into the forcefield tht i
needed with all its information (itp,rtp,etc..)..??

Thank you


-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding hydrogen bond dynamics

[Dilip H N]

Hello,
I want to study the hydrogen bond dynamics (continuous and intermittent) of
my system of amino acid with solvent mixture.
I have tried gmx hbond..but i am unable to figure it out
Is there any other means to study the hydrogen bonding of the above
system

Thank you.

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding hydrogen bond dynamics

[Dilip H N]

Hello,
I want to study the hydrogen bond dynamics (continuous and intermittent) of
my system of amino acid with solvent mixture.
I have tried gmx hbond..but i am unable to figure it out
Is there any other means to study the hydrogen bonding of the above
system

Thank you.

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding the forcefield, topology..

[Dilip H N]

Hello,
1] I want to simulate molecules such as Methylamine(CH3NH2),Dimethy
lamine((CH3)2NH), Trimethylamine((CH3)3N), TrimethylamineN-oxide((CH3)3NO-).
Can anybody suggest me the right forcefield in gromacs for these
moleculesin which forcefield is this available along with its residues..
2] Are the forcefields for all these molecules available in the same
forcefield..?
3] and thn i want to simulate an aminoacid with the above molecules...how
can i simulate if the aminoacid and the above said molecules are in
different forcefields..??

Thank you

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding the forcefield, topology..

[Dilip H N]

Hello,
1] I want to simulate molecules such as Methylamine(CH3NH2),
Dimethylamine((CH3)2NH), Trimethylamine((CH3)3N), TrimethylamineN-oxide((CH3
)3NO-).
Can anybody suggest me the right forcefield in gromacs for these
moleculesin which forcefield is this available along with its residues..
2] Are the forcefields for all these molecules available in the same
forcefield..?
3] and thn i want to simulate an aminoacid with the above molecules...how
can i simulate if the aminoacid and the above said molecules are in
different forcefields..??

Thank you

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding the forcefield, topology..

[Dilip H N]

Hello,
1] I want to simulate molecules as Methylamine(CH3NH2),Dimethylamine((CH3)2NH),
Trimethylamine((CH3)3N), TrimethylamineN-oxide((CH3)3NO-).
Can anybody suggest me the right forcefield in gromacs for these
moleculesin which forcefield is this available along with its residues..
2] Are the forcefields for all these molecules available in the same
forcefield..?
3] and thn i want to simulate an aminoacid with the above molecules...how
can i simulate if the aminoacid and the above said molecules are in
different forcefields..??

Thank you

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Regarding python program/code for Hydrogen bond lifetime

[Dilip H N]

Because in the command gmx h_bond it is not calculating Continuous hydrogen
bond correlation function



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On Tue, May 30, 2017 at 10:58 PM, Dilip H N <cy16f01.di...@nitk.edu.in>
wrote:

> I have ran a simulation and extracted the trajectory for t=0.5 ps each in
> gromacs. The trajectory file is as follows..
>
> Generated by trjconv : Glycine-Ammonia-Water t= 0.500
>  28SOL OW  115   1.586   0.579   1.240
>  28SOLHW1  116   1.520   0.524   1.293
>  28SOLHW2  117   1.645   0.519   1.187
>  29SOL OW  118   0.135   0.791   1.373
>  29SOLHW1  119   0.168   0.716   1.316
>  29SOLHW2  120   0.190   0.873   1.355
>  30SOL OW  121   0.279   0.419   0.486
>  30SOLHW1  122   0.366   0.400   0.440
>  30SOLHW2  123   0.204   0.415   0.41
> .
> .
> .
>
> Generated by trjconv : Glycine-Ammonia-Water t=  1.000
>  28SOL OW  115   1.586   0.579   1.240
>  28SOLHW1  116   1.520   0.524   1.293
>  28SOLHW2  117   1.645   0.519   1.187
>  29SOL OW  118   0.135   0.791   1.373
>  29SOLHW1  119   0.168   0.716   1.316
>  29SOLHW2  120   0.190   0.873   1.355
>  30SOL OW  121   0.279   0.419   0.486
>  30SOLHW1  122   0.366   0.400   0.440
>  30SOLHW2  123   0.204   0.415   0.41
> .
> .
> .
>
> Generated by trjconv : Glycine-Ammonia-Water t=  10.000
>  28SOL OW  115   1.586   0.579   1.240
>  28SOLHW1  116   1.520   0.524   1.293
>  28SOLHW2  117   1.645   0.519   1.187
>  29SOL OW  118   0.135   0.791   1.373
>  29SOLHW1  119   0.168   0.716   1.316
>  29SOLHW2  120   0.190   0.873   1.355
>  30SOL OW  121   0.279   0.419   0.486
>  30SOLHW1  122   0.366   0.400   0.440
>  30SOLHW2  123   0.204   0.415   0.41
> .
>
> Can anybody suggest ideas to write a python program/code to calculate the
> hydrogen bond (continuous/intermittent) time correlations..ie., hydrogen
> bond if it exists between oxygen of one water molecule with hydrogen of
> other water molecule at a distance less than 2.45 angstrom or between
> oxygen of one water molecule with oxygen of other water molecule at a
> distance less than 3.5 angstrom.
>
> Any suggestions regarding this...
>
> Thank you
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>   <https://mailtrack.io/> Sent with Mailtrack
> <https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22>
>



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Ph.D Student
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[gmx-users] Regarding python program/code for Hydrogen bond lifetime

[Dilip H N]

I have ran a simulation and extracted the trajectory for t=0.5 ps each in
gromacs. The trajectory file is as follows..

Generated by trjconv : Glycine-Ammonia-Water t= 0.500
 28SOL OW  115   1.586   0.579   1.240
 28SOLHW1  116   1.520   0.524   1.293
 28SOLHW2  117   1.645   0.519   1.187
 29SOL OW  118   0.135   0.791   1.373
 29SOLHW1  119   0.168   0.716   1.316
 29SOLHW2  120   0.190   0.873   1.355
 30SOL OW  121   0.279   0.419   0.486
 30SOLHW1  122   0.366   0.400   0.440
 30SOLHW2  123   0.204   0.415   0.41
.
.
.

Generated by trjconv : Glycine-Ammonia-Water t=  1.000
 28SOL OW  115   1.586   0.579   1.240
 28SOLHW1  116   1.520   0.524   1.293
 28SOLHW2  117   1.645   0.519   1.187
 29SOL OW  118   0.135   0.791   1.373
 29SOLHW1  119   0.168   0.716   1.316
 29SOLHW2  120   0.190   0.873   1.355
 30SOL OW  121   0.279   0.419   0.486
 30SOLHW1  122   0.366   0.400   0.440
 30SOLHW2  123   0.204   0.415   0.41
.
.
.

Generated by trjconv : Glycine-Ammonia-Water t=  10.000
 28SOL OW  115   1.586   0.579   1.240
 28SOLHW1  116   1.520   0.524   1.293
 28SOLHW2  117   1.645   0.519   1.187
 29SOL OW  118   0.135   0.791   1.373
 29SOLHW1  119   0.168   0.716   1.316
 29SOLHW2  120   0.190   0.873   1.355
 30SOL OW  121   0.279   0.419   0.486
 30SOLHW1  122   0.366   0.400   0.440
 30SOLHW2  123   0.204   0.415   0.41
.

Can anybody suggest ideas to write a python program/code to calculate the
hydrogen bond (continuous/intermittent) time correlations..ie., hydrogen
bond if it exists between oxygen of one water molecule with hydrogen of
other water molecule at a distance less than 2.45 angstrom or between
oxygen of one water molecule with oxygen of other water molecule at a
distance less than 3.5 angstrom.

Any suggestions regarding this...

Thank you


-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding centering the molecule/protein during Simulation

[Dilip H N]

Hello,
I have ran a md simulation of a amino-acid with solvent mixture. Now i view
the trajectory in vmd and see tht the amino-acid moves sometimes toward the
edge of the box,sometimes towards the corners and so on...
 Now how can i centre only the amino-acid to the centre of the box and rest
(ie.,solvent mixture) to move as it is..ie., if i view the trajectory in
vmd i want to fix only the amino-acid to be in centre,whereas the solvent
mixtures to move around during the trajectory...
How can i do this,...??

Thank you...

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding extending simulations with change in .mdp file

[Dilip H N]

Hello,

I have ran a energy minimization, followed by nvt, followed by md run. My
md run mdp (ie., md.mdp) has

dt = 0.002, nsteps = 3000 ; [0.002 * 3000 = 6 ps (60 ns)]
nstxout = 5000 ; save coordinates every 10.0 ps
nstvout = 5000 ; save velocities every 10.0 ps
nstenergy = 5000 ; save energies every 10.0 ps
nstlog= 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps
   ; nstxout-compressed replaces nstxtcout
This simulation i have ran for 60 ns.

Now i need extend the simulation for another 20ns, but with the change in
md.mdp file as:-
dt = 0.001, and nsteps = 2000
nstxout= 1000 ; save coordinates every 1.0 ps
nstvout= 1000 ; save velocities every 1.0 ps
nstenergy = 1000 ; save energies every 1.0 ps
nstlog = 1000 ; update log file every 1.0 ps
nstxout-compressed =1000; save compressed coordinates every 1.0 ps;
   ;nstxout-compressed replaces
nstxtcout
ie., i want the  dt time step of 0.001 and the outputs
(nstxout,nstvout,etc.,) which can save the coordinates for every 1.0ps, for
the 20ns md run.

And then i need to have a  complete run of total 80ns [(60ns of the 1st
mdrun  of dt=0.002*3000) + (20ns of the 2nd mdrun of
dt=0.001*2000)].


How can i do this..??

Thank you.

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Regarding extending simulations

[Dilip H N]

and which are the commands tht i need to give there.. gmx trjconv or gmx
grommp ..??
Can anybody guide me through this kindly..



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On Sun, May 21, 2017 at 4:40 PM, Dilip H N <cy16f01.di...@nitk.edu.in>
wrote:

> Hello,
> I have ran a energy minimization, followed by nvt, followed by md run. My
> md run mdp (ie., md.mdp) has dt = 0.002, nsteps = 3000 ; [0.002 *
> 3000 = 6 ps (60 ns)]
> nstxout = 5000 ; save coordinates every 10.0 ps
> nstvout = 5000 ; save velocities every 10.0 ps
> nstenergy = 5000 ; save energies every 10.0 ps
> nstlog= 5000 ; update log file every 10.0 ps
> nstxout-compressed = 5000  ; save compressed coordinates every 10.0 ps
> ; nstxout-compressed replaces nstxtcout
> This simulation i have ran for 60 ns.
>
> Now i need extend the simulation for another 20ns, but with the change in
> md.mdp file as:-
> dt = 0.001, and nsteps = 
> nstxout= 1000 ; save coordinates every 1.0 ps
> nstvout= 1000 ; save velocities every 1.0 ps
> nstenergy = 1000 ; save energies every 1.0 ps
> nstlog = 1000 ; update log file every 1.0 ps
> nstxout-compressed =1000; save compressed coordinates every 1.0 ps
> ie., i want the  dt time step of 0.001 and the outputs
> (nstxout,nstvout,etc.,) which can save the coordinates for every 1.0ps, for
> the 20ns run.
> I want to run the simulation for extra another 20ns by changing the md.mdp
> for 0.001 dt and saving the coordinates for every 1.0 ps.
> And thn i will have a complete run of total 80ns [(60ns of the 1st mdrun
>  of dt=0.002*3000) + (next 2nd mdrun of dt=0.001*)].
>
> So wht are the changes tht i need to do in the mdp file.. if i change dt
> to 0.001and wht should be the nsteps() value..and changing the output
> steps tht i want to save, such tht i get a run for 20ns , and which will
> give me a total of 80ns..
>
>
> Thank you
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
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> <https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22>
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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[gmx-users] Regarding extending simulations

[Dilip H N]

Hello,
I have ran a energy minimization, followed by nvt, followed by md run. My
md run mdp (ie., md.mdp) has dt = 0.002, nsteps = 3000 ; [0.002 *
3000 = 6 ps (60 ns)]
nstxout = 5000 ; save coordinates every 10.0 ps
nstvout = 5000 ; save velocities every 10.0 ps
nstenergy = 5000 ; save energies every 10.0 ps
nstlog= 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000  ; save compressed coordinates every 10.0 ps
; nstxout-compressed replaces nstxtcout
This simulation i have ran for 60 ns.

Now i need extend the simulation for another 20ns, but with the change in
md.mdp file as:-
dt = 0.001, and nsteps = 
nstxout= 1000 ; save coordinates every 1.0 ps
nstvout= 1000 ; save velocities every 1.0 ps
nstenergy = 1000 ; save energies every 1.0 ps
nstlog = 1000 ; update log file every 1.0 ps
nstxout-compressed =1000; save compressed coordinates every 1.0 ps
ie., i want the  dt time step of 0.001 and the outputs
(nstxout,nstvout,etc.,) which can save the coordinates for every 1.0ps, for
the 20ns run.
I want to run the simulation for extra another 20ns by changing the md.mdp
for 0.001 dt and saving the coordinates for every 1.0 ps.
And thn i will have a complete run of total 80ns [(60ns of the 1st mdrun
 of dt=0.002*3000) + (next 2nd mdrun of dt=0.001*)].

So wht are the changes tht i need to do in the mdp file.. if i change dt to
0.001and wht should be the nsteps() value..and changing the output
steps tht i want to save, such tht i get a run for 20ns , and which will
give me a total of 80ns..


Thank you
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Regarding reading .gro file in python

[Dilip H N]

>
> 3] Yes,I want create an automatic tool in Python which sets up calculations
> for me  and possibly runs them...
> So that this Python script calls pdb2gmx, editconf, etc..
>
>
In its simplest form, that's just a bunch of system calls within the Python
script.  You can easily do this as a normal shell script without even
having to invoke Python at all.

Can u suggest me how to write it in the shell script..?? without even
having to invoke Python...


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<#>

On Fri, Apr 28, 2017 at 12:01 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 4/27/17 2:29 PM, Dilip H N wrote:
>
>> Thank you Justin Sir..
>>
>>  Yes this is what i wanted..the source code in gromacs..where is the
>> source
>> written..?? whr/in which files will i be able to get it..??
>>
>>
> Start with "get the source code" on gromacs.org and go from there.  There
> are a few developer pages online for various aspects of the source, but
> generally most programs are contained to source files named just like the
> programs; obviously there are also external functions that are shared by
> different programs, but you can easily find those with grep.
>
> -Justin
>
> Thank you
>>
>>
>>
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>> <https://mailtrack.io/install?source=signature=en
>> ral=cy16f01.di...@nitk.edu.in=22>
>> <#>
>>
>> On Thu, Apr 27, 2017 at 11:56 PM, Dilip H N <cy16f01.di...@nitk.edu.in>
>> wrote:
>>
>> and how are the x,y,z coordinates, velocities assigned with the values..??
>>> the logic behind them in gromacs
>>>
>>> Thank you
>>>
>>>
>>>
>>>   <https://mailtrack.io/> Sent with Mailtrack
>>> <https://mailtrack.io/install?source=signature=en
>>> ral=cy16f01.di...@nitk.edu.in=22>
>>>
>>> On Thu, Apr 27, 2017 at 11:52 PM, Dilip H N <cy16f01.di...@nitk.edu.in>
>>> wrote:
>>>
>>> Thank you Oliver Beckstein Sir, Dawid das Sir,
>>>>
>>>> My questions are..
>>>>
>>>> 1] I got the initial configuration of a molecule in .pdb format and thn
>>>> i
>>>> gave the command
>>>> gmx editconf -f .pdb -o box.gro -c -box x y z
>>>> what happens in the background when this command is given..?? (the C++
>>>> program runs in which gromacs is written)
>>>> so what is the logic in tht program..??
>>>> 2] and i have a initial .gro file and thn i want to insert more number
>>>> of
>>>> molecules of tht to a box created i give the command
>>>> gmx insert-molecules -f .box.gro -ci ab.gro -nmol x -o abc.gro
>>>> so in the above command the molecules tht i want to insert gets inserted
>>>> in the empty spaces of the box...How is this defined in the program
>>>> (such
>>>> tht the molecules should be inserted into the empty spaces only)..??
>>>> 3] Yes,I want create an automatic tool in Python which sets up
>>>> calculations
>>>> for me  and possibly runs them...
>>>> So that this Python script calls pdb2gmx, editconf, etc..
>>>>
>>>> Thank you
>>>>
>>>>
>>>>   <https://mailtrack.io/> Sent with Mailtrack
>>>> <https://mailtrack.io/install?source=signature=en
>>>> ral=cy16f01.di...@nitk.edu.in=22>
>>>> <#m_-6789244521733948564_m_6373284441246192622_>
>>>>
>>>>
>>>> On Thu, Apr 27, 2017 at 10:41 PM, Dawid das <add...@googlemail.com>
>>>> wrote:
>>>>
>>>> Hello Dilip,
>>>>>
>>>>>  I don't really get what your problem is. What do you actually want to
>>>>> do?
>>>>> Read-in and parse a *.gro file which
>>>>> is output from MD simulation? Then for instance, your Python script
>>>>> should
>>>>> calculate something from, e.g. distance
>>>>> between centres of masses of residues of interest?
>>>>> Or do you want create an automatic tool in Python which sets up
>>>>> calculations for you and possibly runs them?
>>>>> So that this Python script calls pdb2gmx, editconf, etc.
>>>>>
>>>>> I have written various scripts for parsing output files from Gromacs
>>>>> simulations for my pretty specific purposes.
>>>>>

Re: [gmx-users] Regarding reading .gro file in python

[Dilip H N]

Thank you Justin Sir..

 Yes this is what i wanted..the source code in gromacs..where is the source
written..?? whr/in which files will i be able to get it..??

Thank you



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<#>

On Thu, Apr 27, 2017 at 11:56 PM, Dilip H N <cy16f01.di...@nitk.edu.in>
wrote:

> and how are the x,y,z coordinates, velocities assigned with the values..??
> the logic behind them in gromacs
>
> Thank you
>
>
>
>   <https://mailtrack.io/> Sent with Mailtrack
> <https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22>
>
> On Thu, Apr 27, 2017 at 11:52 PM, Dilip H N <cy16f01.di...@nitk.edu.in>
> wrote:
>
>> Thank you Oliver Beckstein Sir, Dawid das Sir,
>>
>> My questions are..
>>
>> 1] I got the initial configuration of a molecule in .pdb format and thn i
>> gave the command
>> gmx editconf -f .pdb -o box.gro -c -box x y z
>> what happens in the background when this command is given..?? (the C++
>> program runs in which gromacs is written)
>> so what is the logic in tht program..??
>> 2] and i have a initial .gro file and thn i want to insert more number of
>> molecules of tht to a box created i give the command
>> gmx insert-molecules -f .box.gro -ci ab.gro -nmol x -o abc.gro
>> so in the above command the molecules tht i want to insert gets inserted
>> in the empty spaces of the box...How is this defined in the program (such
>> tht the molecules should be inserted into the empty spaces only)..??
>> 3] Yes,I want create an automatic tool in Python which sets up calculations
>> for me  and possibly runs them...
>> So that this Python script calls pdb2gmx, editconf, etc..
>>
>> Thank you
>>
>>
>>   <https://mailtrack.io/> Sent with Mailtrack
>> <https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22>
>> <#m_-6789244521733948564_m_6373284441246192622_>
>>
>> On Thu, Apr 27, 2017 at 10:41 PM, Dawid das <add...@googlemail.com>
>> wrote:
>>
>>> Hello Dilip,
>>>
>>>  I don't really get what your problem is. What do you actually want to
>>> do?
>>> Read-in and parse a *.gro file which
>>> is output from MD simulation? Then for instance, your Python script
>>> should
>>> calculate something from, e.g. distance
>>> between centres of masses of residues of interest?
>>> Or do you want create an automatic tool in Python which sets up
>>> calculations for you and possibly runs them?
>>> So that this Python script calls pdb2gmx, editconf, etc.
>>>
>>> I have written various scripts for parsing output files from Gromacs
>>> simulations for my pretty specific purposes.
>>> Anyway if you may find them useful, I will be happy to share them with
>>> you.
>>>
>>> Best wishes,
>>> Dawid
>>>
>>> 2017-04-27 18:53 GMT+02:00 Oliver Beckstein <obeck...@asu.edu>:
>>>
>>> > Hi Dilip,
>>> >
>>> > I think the next version of Gromacs will have some Python bindings.
>>> >
>>> > Until then you can use MDAnalysis http://mdanalysis.org : It reads GRO
>>> > files (as well as XTC, TRR, and TPR, … and many other formats) and
>>> loads it
>>> > into a numpy array.
>>> >
>>> > (If you have questions regarding MDAnalysis please ask on the
>>> MDAnanlysis
>>> > user mailing http://users.mdanalysis.org list instead of the Gromacs
>>> > list.)
>>> >
>>> > Best wishes,
>>> > Oliver (disclosure: I am one of the core developers of MDAnalysis)
>>> >
>>> > > On 27 Apr, 2017, at 09:46, Dilip H N <cy16f01.di...@nitk.edu.in>
>>> wrote:
>>> > >
>>> > > Hello,
>>> > >
>>> > > I want to write a python program to read a .gro file in gromacs.. How
>>> > can i
>>> > > write the program / code to read the .gro file...
>>> > >
>>> > > I need to write a python programm to read the .gro file and write as
>>> it
>>> > > is.. can anybody help me regarding this...
>>> > >
>>> > > Thank you..
>>> > >
>>> > > --
>>> > > With Best Regards,
>>> > >
>>> > > DILIP.H.N
>>> > > Ph.D Student
>>> > >
>>> >
>>> >

Re: [gmx-users] Regarding reading .gro file in python

[Dilip H N]

and how are the x,y,z coordinates, velocities assigned with the values..??
the logic behind them in gromacs

Thank you



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On Thu, Apr 27, 2017 at 11:52 PM, Dilip H N <cy16f01.di...@nitk.edu.in>
wrote:

> Thank you Oliver Beckstein Sir, Dawid das Sir,
>
> My questions are..
>
> 1] I got the initial configuration of a molecule in .pdb format and thn i
> gave the command
> gmx editconf -f .pdb -o box.gro -c -box x y z
> what happens in the background when this command is given..?? (the C++
> program runs in which gromacs is written)
> so what is the logic in tht program..??
> 2] and i have a initial .gro file and thn i want to insert more number of
> molecules of tht to a box created i give the command
> gmx insert-molecules -f .box.gro -ci ab.gro -nmol x -o abc.gro
> so in the above command the molecules tht i want to insert gets inserted
> in the empty spaces of the box...How is this defined in the program (such
> tht the molecules should be inserted into the empty spaces only)..??
> 3] Yes,I want create an automatic tool in Python which sets up calculations
> for me  and possibly runs them...
> So that this Python script calls pdb2gmx, editconf, etc..
>
> Thank you
>
>
>   <https://mailtrack.io/> Sent with Mailtrack
> <https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22>
> <#m_6373284441246192622_>
>
> On Thu, Apr 27, 2017 at 10:41 PM, Dawid das <add...@googlemail.com> wrote:
>
>> Hello Dilip,
>>
>>  I don't really get what your problem is. What do you actually want to do?
>> Read-in and parse a *.gro file which
>> is output from MD simulation? Then for instance, your Python script should
>> calculate something from, e.g. distance
>> between centres of masses of residues of interest?
>> Or do you want create an automatic tool in Python which sets up
>> calculations for you and possibly runs them?
>> So that this Python script calls pdb2gmx, editconf, etc.
>>
>> I have written various scripts for parsing output files from Gromacs
>> simulations for my pretty specific purposes.
>> Anyway if you may find them useful, I will be happy to share them with
>> you.
>>
>> Best wishes,
>> Dawid
>>
>> 2017-04-27 18:53 GMT+02:00 Oliver Beckstein <obeck...@asu.edu>:
>>
>> > Hi Dilip,
>> >
>> > I think the next version of Gromacs will have some Python bindings.
>> >
>> > Until then you can use MDAnalysis http://mdanalysis.org : It reads GRO
>> > files (as well as XTC, TRR, and TPR, … and many other formats) and
>> loads it
>> > into a numpy array.
>> >
>> > (If you have questions regarding MDAnalysis please ask on the
>> MDAnanlysis
>> > user mailing http://users.mdanalysis.org list instead of the Gromacs
>> > list.)
>> >
>> > Best wishes,
>> > Oliver (disclosure: I am one of the core developers of MDAnalysis)
>> >
>> > > On 27 Apr, 2017, at 09:46, Dilip H N <cy16f01.di...@nitk.edu.in>
>> wrote:
>> > >
>> > > Hello,
>> > >
>> > > I want to write a python program to read a .gro file in gromacs.. How
>> > can i
>> > > write the program / code to read the .gro file...
>> > >
>> > > I need to write a python programm to read the .gro file and write as
>> it
>> > > is.. can anybody help me regarding this...
>> > >
>> > > Thank you..
>> > >
>> > > --
>> > > With Best Regards,
>> > >
>> > > DILIP.H.N
>> > > Ph.D Student
>> > >
>> >
>> > --
>> > Oliver Beckstein, DPhil * oliver.beckst...@asu.edu
>> > http://becksteinlab.physics.asu.edu/
>> >
>> > Assistant Professor of Physics
>> > Arizona State University
>> > Center for Biological Physics and Department of Physics
>> > Tempe, AZ 85287-1504
>> > USA
>> >
>> > Office: PSF 348
>> > Phone: +1 (480) 727-9765
>> > FAX: +1 (480) 965-4669
>> >
>> > Department of Physics: https://physics.asu.edu/content/oliver-beckstein
>> > Center for Biological Physics: https://cbp.asu.edu/content/
>> > oliver-beckstein
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > --
>> > Gromacs Users mailing list
>> >

Re: [gmx-users] Regarding reading .gro file in python

[Dilip H N]

Thank you Oliver Beckstein Sir, Dawid das Sir,

My questions are..

1] I got the initial configuration of a molecule in .pdb format and thn i
gave the command
gmx editconf -f .pdb -o box.gro -c -box x y z
what happens in the background when this command is given..?? (the C++
program runs in which gromacs is written)
so what is the logic in tht program..??
2] and i have a initial .gro file and thn i want to insert more number of
molecules of tht to a box created i give the command
gmx insert-molecules -f .box.gro -ci ab.gro -nmol x -o abc.gro
so in the above command the molecules tht i want to insert gets inserted in
the empty spaces of the box...How is this defined in the program (such tht
the molecules should be inserted into the empty spaces only)..??
3] Yes,I want create an automatic tool in Python which sets up calculations
for me  and possibly runs them...
So that this Python script calls pdb2gmx, editconf, etc..

Thank you


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<#>

On Thu, Apr 27, 2017 at 10:41 PM, Dawid das <add...@googlemail.com> wrote:

> Hello Dilip,
>
>  I don't really get what your problem is. What do you actually want to do?
> Read-in and parse a *.gro file which
> is output from MD simulation? Then for instance, your Python script should
> calculate something from, e.g. distance
> between centres of masses of residues of interest?
> Or do you want create an automatic tool in Python which sets up
> calculations for you and possibly runs them?
> So that this Python script calls pdb2gmx, editconf, etc.
>
> I have written various scripts for parsing output files from Gromacs
> simulations for my pretty specific purposes.
> Anyway if you may find them useful, I will be happy to share them with you.
>
> Best wishes,
> Dawid
>
> 2017-04-27 18:53 GMT+02:00 Oliver Beckstein <obeck...@asu.edu>:
>
> > Hi Dilip,
> >
> > I think the next version of Gromacs will have some Python bindings.
> >
> > Until then you can use MDAnalysis http://mdanalysis.org : It reads GRO
> > files (as well as XTC, TRR, and TPR, … and many other formats) and loads
> it
> > into a numpy array.
> >
> > (If you have questions regarding MDAnalysis please ask on the MDAnanlysis
> > user mailing http://users.mdanalysis.org list instead of the Gromacs
> > list.)
> >
> > Best wishes,
> > Oliver (disclosure: I am one of the core developers of MDAnalysis)
> >
> > > On 27 Apr, 2017, at 09:46, Dilip H N <cy16f01.di...@nitk.edu.in>
> wrote:
> > >
> > > Hello,
> > >
> > > I want to write a python program to read a .gro file in gromacs.. How
> > can i
> > > write the program / code to read the .gro file...
> > >
> > > I need to write a python programm to read the .gro file and write as it
> > > is.. can anybody help me regarding this...
> > >
> > > Thank you..
> > >
> > > --
> > > With Best Regards,
> > >
> > > DILIP.H.N
> > > Ph.D Student
> > >
> >
> > --
> > Oliver Beckstein, DPhil * oliver.beckst...@asu.edu
> > http://becksteinlab.physics.asu.edu/
> >
> > Assistant Professor of Physics
> > Arizona State University
> > Center for Biological Physics and Department of Physics
> > Tempe, AZ 85287-1504
> > USA
> >
> > Office: PSF 348
> > Phone: +1 (480) 727-9765
> > FAX: +1 (480) 965-4669
> >
> > Department of Physics: https://physics.asu.edu/content/oliver-beckstein
> > Center for Biological Physics: https://cbp.asu.edu/content/
> > oliver-beckstein
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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[gmx-users] Regarding reading .gro file in python

[Dilip H N]

Hello,

I want to write a python program to read a .gro file in gromacs.. How can i
write the program / code to read the .gro file...

I need to write a python programm to read the .gro file and write as it
is.. can anybody help me regarding this...

Thank you..

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Regarding finding orientation of angles of solvent with desired atom

[Dilip H N]

Hello,

I have simulated amino acid (eg., glycine) with water solvent mixture in
gromacs..
my question is ..
1] How can i find out the solvent orientation (angle made) ie.,angle made
by water (HOH) with respect to alpha carbon of amino acid (eg.,
glycine)...??
2] I have tried with gmx sorient command ..it gives me five outputs..sori,
snor, sord, scum, scount. With sori (it gives from solvent orientation -
cos theta -1 to 0) and snor (it gives from solvent normal orientation - cos
theta 0 to 1) , but with what respect is it giving i am not able to
understand...
3] I wanted to calculate the angle formed between water (HOH) and alpha
carbon of glycine. but if it consider the .gro file, i can calculate the
angle for only the last frame... but i want to calculate the angle for the
full frame (tpr/trr). How can i do it ...Can anybody kindly help me
regarding this..

Thank you...



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<#>

On Mon, Apr 24, 2017 at 1:22 PM, Dilip H N <cy16f01.di...@nitk.edu.in>
wrote:

> Hello,
>
> I have simulated amino acid (eg., glycine) with water solvent mixture in
> gromacs..
> my question is ..
> 1] How can i find out the solvent orientation (angle made) ie.,angle made
> by water (HOH) with respect to alpha carbon of amino acid (eg.,
> glycine)...??
> 2] I have tried with gmx sorient command ..it gives me five outputs..sori,
> snor, sord, scum, scount. With sori (it gives from solvent orientation -
> cos theta -1 to 0) and snor (it gives from solvent normal orientation - cos
> theta 0 to 1) , but with what respect is it giving i am not able to
> understand...ie theta 1 and theta 2
> 3] I wanted to calculate the angle formed between water (HOH) and alpha
> carbon of glycine. but if it consider the .gro file, i can calculate the
> angle for only the last frame... but i want to calculate the angle for the
> full frame (tpr/trr). How can i do it sir...Can u kindly help me regarding
> this..
> Since i am referring one of ur research paper - [Glycine in aqueous
> solution: solvation shells, interfacial water, and vibrational spectroscopy
> from ab initio molecular dynamics]. and in other paper - [MONTE CARLO
> SIMULATION STUDIES OF THE SOLVATION OF IONS. 2. GLYCINE ZWITTERION] they
> have calculated the cos theta distribution functions...so i wanted to
> calculate ..
>
> Thank you sir...
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
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> <https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22>
> <#m_1046049965356203242_>
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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[gmx-users] Regarding finding orientation of angles of solvent with desired atom

[Dilip H N]

Hello,

I have simulated amino acid (eg., glycine) with water solvent mixture in
gromacs..
my question is ..
1] How can i find out the solvent orientation (angle made) ie.,angle made
by water (HOH) with respect to alpha carbon of amino acid (eg.,
glycine)...??
2] I have tried with gmx sorient command ..it gives me five outputs..sori,
snor, sord, scum, scount. With sori (it gives from solvent orientation -
cos theta -1 to 0) and snor (it gives from solvent normal orientation - cos
theta 0 to 1) , but with what respect is it giving i am not able to
understand...ie theta 1 and theta 2
3] I wanted to calculate the angle formed between water (HOH) and alpha
carbon of glycine. but if it consider the .gro file, i can calculate the
angle for only the last frame... but i want to calculate the angle for the
full frame (tpr/trr). How can i do it sir...Can u kindly help me regarding
this..
Since i am referring one of ur research paper - [Glycine in aqueous
solution: solvation shells, interfacial water, and vibrational spectroscopy
from ab initio molecular dynamics]. and in other paper - [MONTE CARLO
SIMULATION STUDIES OF THE SOLVATION OF IONS. 2. GLYCINE ZWITTERION] they
have calculated the cos theta distribution functions...so i wanted to
calculate ..

Thank you sir...

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding running coordination number

[Dilip H N]

Hello,
can anybody help me How can i relate the RDF with running coordination
number..??
How can i study both the RDF and unning coordination number, what is the
relation between these two..??


-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding calculation of running coordination number

[Dilip H N]

Hello,
How can i calculate the running coordination number in gromacs..??

I have tried with the gmx rdf command ...ie.,
gmx rdf -f md.trr -s md.tpr -n abc.ndx -o rdf.xvg -cn rdfcn.xvg

and in the gmx rdf description it states that :- Option -cn produces the
cumulative number RDF, i.e. the average number of particles within a
distance r.

Is this the same -cn command that calculates the running coordination
number ..?? or not..??
Thank you

With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding Cos theta functions calculations in gromacs...

[Dilip H N]

Hello,

how do i calculate the cos theta distribution for water belonging to CH2
region of glycine??

1] how to use the gmx sorient command.??, since it will be calculating two
angles between the vector from one or more reference positions of first
atom to each molecule...
why is it calculating two angles
θ_1: the angle with the vector from the first atom of the solvent molecule
to the midpoint between atoms 2 and 3.
θ_2: the angle with the normal of the solvent plane, defined by the same
three atoms, or, when the option -v23 is set, the angle with the vector
between atoms 2 and 3.
2] how to make the indexes for it..??

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Regarding analysing cos theta distribution functions

[Dilip H N]

Thank you,

for calculating the angle distribution, I gave the following command (for
glycine-water mixture molecule) as

gmx mk_angndx -s md.tpr -n angle.ndx

and i got the following indec file as..

[ UB_th=109.5_368.192f ]
 2 1 3 2 1 4 3 1 4
[ UB_th=109.5_251.042f ]
 2 1 5 3 1 5 4 1 5
[ UB_th=107.5_430.952f ]
 1 5 6 1 5 7
[ UB_th=110.0_365.682f ]
 1 5 8
[ UB_th=115.0_301.252f ]
 6 5 7
[ UB_th=109.5_418.402f ]
 6 5 8 7 5 8
[ UB_th=118.0_334.722f ]
 5 8 9 5 810
[ UB_th=124.0_836.802f ]
 9 810

What does the UB_th mean here..??


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On Wed, Apr 12, 2017 at 1:58 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> There's lots of options... see
> http://manual.gromacs.org/documentation/2016.3/user-
> guide/cmdline.html#commands-by-topic
> for
> starters.
>
> Mark
>
> On Wed, Apr 12, 2017 at 10:06 AM Dilip H N <cy16f01.di...@nitk.edu.in>
> wrote:
>
> > Thank you Mark, João Henriques.
> > I have ran a Md simulation of amino acid in water solvent mixture.
> > In gromacs what are all the analysis i can do with my system (amino
> > acid-water solvent mixture)..??
> > For eg., I have just calculated RDF (to knw how atoms are distributed
> > radially around each other),
> > apart from this what are the analysis part tht i can do with gromacs..??
> >
> >
> >
> >   <https://mailtrack.io/> Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature=en;
> referral=cy16f01.di...@nitk.edu.in=22
> > >
> >
> > On Wed, Apr 12, 2017 at 1:23 PM, João Henriques <
> > joao.m.a.henriq...@gmail.com> wrote:
> >
> > > He wants to compute the angular distribution functions, ADFs
> (water-water
> > > O-H vector), of the first hydration layer. I have posted a similar
> > question
> > > (twice, under different formulations) some time ago and got no help.
> I'd
> > > suggest experimenting with MDAnalysis (python module), because default
> > > gromacs tools are unlikely to do the job without some creative
> > > hacking/quick-and-dirty scripting.
> > >
> > > Re-ordering the water molecules by proximity to the protein surface
> (per
> > > snapshot) is easy (use gmx trjorder) and establishing the hydration
> layer
> > > cutoff is also relatively simple (use gmx rdf). Getting the ADFs in the
> > > proper way is not easy/practical. At least I didn't find it easy at all
> > > (and I'm not alone in this). MDAnalysis makes things easy and
> > customizable,
> > > but it can be rather slow.
> > >
> > > See the link below for some examples. I ended up using bits and pieces
> of
> > > the class MDAnalysis.analysis.waterdynamics.AngularDistribution until
> I
> > > got
> > > the desired result.
> > >
> > > https://pythonhosted.org/MDAnalysis/documentation_
> > > pages/analysis/waterdynamics.html
> > >
> > > Good luck!
> > >
> > > /J
> > >
> > >
> > > On Wed, Apr 12, 2017 at 8:19 AM, Mark Abraham <
> mark.j.abra...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > I have no idea what a cos theta distribution is, nor the objective of
> > > your
> > > > study, so it's hard to help. But gmx mk_angndx is intended to help
> with
> > > > such cases.
> > > >
> > > > Mark
> > > >
> > > > On Wed, Apr 12, 2017 at 8:17 AM Dilip H N <cy16f01.di...@nitk.edu.in
> >
> > > > wrote:
> > > >
> > > > > Hello Jonathan,
> > > > >
> > > > > Suppose i want to calculate the cos theta distribution of
> hydrogen's
> > of
> > > > > water  in 1st hydration shell of amino acid (glycine)
> > > > > ie., orientation of  alpha carbon of glycine with oxygen of water
> > > > > molecules... how can i calculate it..??
> > > > >
> > > > > And in  what groups/atoms should i make the indexes..?? (like it
> says
> > > the
> > > > > index file must contain atom triplets for angles)...
> > > > > How to make the atom triplets.. which atom the cos theta is to be
> > found
> > > > out
> > > > > sho

Re: [gmx-users] Regarding analysing cos theta distribution functions

[Dilip H N]

Thank you Mark, João Henriques.
I have ran a Md simulation of amino acid in water solvent mixture.
In gromacs what are all the analysis i can do with my system (amino
acid-water solvent mixture)..??
For eg., I have just calculated RDF (to knw how atoms are distributed
radially around each other),
apart from this what are the analysis part tht i can do with gromacs..??



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On Wed, Apr 12, 2017 at 1:23 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> He wants to compute the angular distribution functions, ADFs (water-water
> O-H vector), of the first hydration layer. I have posted a similar question
> (twice, under different formulations) some time ago and got no help. I'd
> suggest experimenting with MDAnalysis (python module), because default
> gromacs tools are unlikely to do the job without some creative
> hacking/quick-and-dirty scripting.
>
> Re-ordering the water molecules by proximity to the protein surface (per
> snapshot) is easy (use gmx trjorder) and establishing the hydration layer
> cutoff is also relatively simple (use gmx rdf). Getting the ADFs in the
> proper way is not easy/practical. At least I didn't find it easy at all
> (and I'm not alone in this). MDAnalysis makes things easy and customizable,
> but it can be rather slow.
>
> See the link below for some examples. I ended up using bits and pieces of
> the class MDAnalysis.analysis.waterdynamics.AngularDistribution until I
> got
> the desired result.
>
> https://pythonhosted.org/MDAnalysis/documentation_
> pages/analysis/waterdynamics.html
>
> Good luck!
>
> /J
>
>
> On Wed, Apr 12, 2017 at 8:19 AM, Mark Abraham <mark.j.abra...@gmail.com>
> wrote:
>
> > Hi,
> >
> > I have no idea what a cos theta distribution is, nor the objective of
> your
> > study, so it's hard to help. But gmx mk_angndx is intended to help with
> > such cases.
> >
> > Mark
> >
> > On Wed, Apr 12, 2017 at 8:17 AM Dilip H N <cy16f01.di...@nitk.edu.in>
> > wrote:
> >
> > > Hello Jonathan,
> > >
> > > Suppose i want to calculate the cos theta distribution of hydrogen's of
> > > water  in 1st hydration shell of amino acid (glycine)
> > > ie., orientation of  alpha carbon of glycine with oxygen of water
> > > molecules... how can i calculate it..??
> > >
> > > And in  what groups/atoms should i make the indexes..?? (like it says
> the
> > > index file must contain atom triplets for angles)...
> > > How to make the atom triplets.. which atom the cos theta is to be found
> > out
> > > should be placed in the indexing order.. so to find the
> > > angle between alpha carbon of glycine with oxygen of water
> molecules
> > >
> > >
> > >
> > >   <https://mailtrack.io/> Sent with Mailtrack
> > > <
> > > https://mailtrack.io/install?source=signature=en;
> > referral=cy16f01.di...@nitk.edu.in=22
> > > >
> > >
> > > On Wed, Apr 12, 2017 at 11:12 AM, Jonathan Saboury <jsab...@gmail.com>
> > > wrote:
> > >
> > > > For making .ndx files look at the following:
> > > > http://manual.gromacs.org/programs/gmx-make_ndx.html
> > > >
> > > > Best of luck,
> > > > Jonathan
> > > >
> > > > On Tue, Apr 11, 2017 at 10:26 PM, Dilip H N <
> cy16f01.di...@nitk.edu.in
> > >
> > > > wrote:
> > > >
> > > > > gmx sorient -f .xtc/trr -s .tpr -n .ndx...
> > > > >
> > > > > How to make these indexes for this case..?? what are the
> atoms/groups
> > > > > that i need to consider for
> > > > >
> > > > > indexing in this case..
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >   <https://mailtrack.io/> Sent with Mailtrack
> > > > > <https://mailtrack.io/install?source=signature=en;
> > > > > referral=cy16f01.di...@nitk.edu.in=22>
> > > > >
> > > > > On Wed, Apr 12, 2017 at 9:57 AM, Dilip H N <
> > cy16f01.di...@nitk.edu.in>
> > > > > wrote:
> > > > >
> > > > > > Hello,
> > > > > > 1] I want to calculate  cos theta distributions (eg.,cos theta
> > > > > > distributions of hydrogen's of water in first hydration shell
> layer
> > > of
> > > > > > amino acid)..??
>

Re: [gmx-users] Regarding analysing cos theta distribution functions

[Dilip H N]

Hello Jonathan,

Suppose i want to calculate the cos theta distribution of hydrogen's of
water  in 1st hydration shell of amino acid (glycine)
ie., orientation of  alpha carbon of glycine with oxygen of water
molecules... how can i calculate it..??

And in  what groups/atoms should i make the indexes..?? (like it says the
index file must contain atom triplets for angles)...
How to make the atom triplets.. which atom the cos theta is to be found out
should be placed in the indexing order.. so to find the
angle between alpha carbon of glycine with oxygen of water molecules



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On Wed, Apr 12, 2017 at 11:12 AM, Jonathan Saboury <jsab...@gmail.com>
wrote:

> For making .ndx files look at the following:
> http://manual.gromacs.org/programs/gmx-make_ndx.html
>
> Best of luck,
> Jonathan
>
> On Tue, Apr 11, 2017 at 10:26 PM, Dilip H N <cy16f01.di...@nitk.edu.in>
> wrote:
>
> > gmx sorient -f .xtc/trr -s .tpr -n .ndx...
> >
> > How to make these indexes for this case..?? what are the atoms/groups
> > that i need to consider for
> >
> > indexing in this case..
> >
> >
> >
> >
> >   <https://mailtrack.io/> Sent with Mailtrack
> > <https://mailtrack.io/install?source=signature=en;
> > referral=cy16f01.di...@nitk.edu.in=22>
> >
> > On Wed, Apr 12, 2017 at 9:57 AM, Dilip H N <cy16f01.di...@nitk.edu.in>
> > wrote:
> >
> > > Hello,
> > > 1] I want to calculate  cos theta distributions (eg.,cos theta
> > > distributions of hydrogen's of water in first hydration shell layer of
> > > amino acid)..??
> > > 2] and how can i analyze the graph ..??
> > > --
> > > With Best Regards,
> > >
> > > DILIP.H.N
> > > Ph.D Student
> > >
> > >
> > >
> > >   <https://mailtrack.io/> Sent with Mailtrack
> > > <https://mailtrack.io/install?source=signature=en;
> > referral=cy16f01.di...@nitk.edu.in=22>
> > >
> >
> >
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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>
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> Support/Mailing_Lists/GMX-Users_List before posting!
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>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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Re: [gmx-users] Regarding analysing cos theta distribution functions

[Dilip H N]

gmx sorient -f .xtc/trr -s .tpr -n .ndx...

How to make these indexes for this case..?? what are the atoms/groups
that i need to consider for

indexing in this case..




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On Wed, Apr 12, 2017 at 9:57 AM, Dilip H N <cy16f01.di...@nitk.edu.in>
wrote:

> Hello,
> 1] I want to calculate  cos theta distributions (eg.,cos theta
> distributions of hydrogen's of water in first hydration shell layer of
> amino acid)..??
> 2] and how can i analyze the graph ..??
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>   <https://mailtrack.io/> Sent with Mailtrack
> <https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22>
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student
-- 
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[gmx-users] Regarding analysing cos theta distribution functions

[Dilip H N]

Hello,
1] I want to calculate  cos theta distributions (eg.,cos theta
distributions of hydrogen's of water in first hydration shell layer of
amino acid)..??
2] and how can i analyze the graph ..??
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Regarding calculation of angles

[Dilip H N]

Suppose for eg., in glycine how can i calculate the angle between nitrogen
and hydrogen attached to it, angle between C alpha and H alpha etc.,



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On Sun, Apr 9, 2017 at 9:49 PM, Dilip H N <cy16f01.di...@nitk.edu.in> wrote:

> Hello,
> I have ran a amino acid simulation, and i want to calculate the angle
> between the atoms in amino acid molecule. how can i calculate it..??
>
> gmx angle [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-od [<.xvg>]]..
>
> 1] here what index does it refer to .?? is it similar to the the RDF
> indexing ..??
>
> 2] how can i make these indexes...??
>
> Thank you
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>   <https://mailtrack.io/> Sent with Mailtrack
> <https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22>
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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[gmx-users] Regarding calculation of angles

[Dilip H N]

Hello,
I have ran a amino acid simulation, and i want to calculate the angle
between the atoms in amino acid molecule. how can i calculate it..??

gmx angle [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-od [<.xvg>]]..

1] here what index does it refer to .?? is it similar to the the RDF
indexing ..??

2] how can i make these indexes...??

Thank you
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding gmx sorient

[Dilip H N]

Hello,
I have done md simulation of amino acid in solvent mixture, How can i
calculate the gmx sorient..??
I am not able to understand anything in the link
http://manual.gromacs.org/programs/gmx-sorient.html

Is it like for calculating the RDF,(in which we have to first index the
files and thn in gmx rdf  command give -ref and -sel  in end) ..??

How can i calculate it.. what are the steps i need to follow in brief .. is
there anything tht i need to index, etc..,,??

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Regarding restricting to centre of box, cos theta functions

[Dilip H N]

Thank you Justin..

For my query on cos theta distribution functions..
How can i calculate cos theta distributions (eg.,cos theta distributions of
hydrogen's of water in first hydration shell layer of amino acid)..??
Is there any command that i need to give like as in rdf  commands
(indexing,etc.,)  ..??



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On Fri, Apr 7, 2017 at 12:32 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 4/6/17 2:58 PM, Dilip H N wrote:
>
>> Hello,
>> I have ran a md simulation of amino acid with solvent molecules with it.
>> During simulation run, the molecules (amino acid, solvent molecules) move
>> around the box, but i don't want the amino acid to move around during the
>> simulation, want to fix it to centre of box..
>> 1] How can i restrict/fix/keep  only the amino acid molecule in/to the
>> centre of the box during simulation ..? Is it possible..
>>
>>
> It's not necessary.  A simulation with periodic boundary conditions is
> infinite and therefore there is no center.  If it's inconvenient to
> visualize, that has no bearing on the physics.  Don't try to perturb the
> system with biasing potentials; just re-center with trjconv when the
> simulation is done.
>
> 2] How can i calculate the cos theta function in gromacs..??
>>
>>
> Put down GROMACS and pick up a high school trigonometry book.  GROMACS
> isn't a calculator :)
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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DILIP.H.N
Ph.D Student
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[gmx-users] Regarding restricting to centre of box, cos theta functions

[Dilip H N]

Hello,
I have ran a md simulation of amino acid with solvent molecules with it.
During simulation run, the molecules (amino acid, solvent molecules) move
around the box, but i don't want the amino acid to move around during the
simulation, want to fix it to centre of box..
1] How can i restrict/fix/keep  only the amino acid molecule in/to the
centre of the box during simulation ..? Is it possible..

2] How can i calculate the cos theta function in gromacs..??
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Regarding viewing Trajectories

[Dilip H N]

Thamk you ,
But in my RDF i have got a peaks(solvation shells) with Carbon of amino
acid with ammonia in ammonia-water mixture, so i need to analyse why that
peak has been formed, which can be viewed by visualizing the trajectories
 in vmd.
So i need to see that at what time frame/step has the bond
formed/particular molecule is closer to the preferred atom, since with this
i can give justification to my results...
So how can i view those molecules that have been more closer/bond formation
with specific molecule has occurred...since viewing the whole trajectory
time frame (i have 6002 frames) is time consuming...
I wrote in Graphical representation > selected atoms > all within 5 of
protein and i am viewing it for every time frame...



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On Wed, Apr 5, 2017 at 12:07 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> A peak in a distance distribution function by definition is contributed to
> by lots of molecules around that distance from lots of different central
> points. There's no single frame for each point.
>
> If you look at a normal histogram, and see a peak, asking "which single
> data point made this" is not meaningful, because multiple data points have
> normally contributed.
>
> Mark
>
> On Wed, Apr 5, 2017 at 6:40 AM Dilip H N <cy16f01.di...@nitk.edu.in>
> wrote:
>
> > Hello.,
> > In RDF of amino acid with ammonia and water mixture, i have got a 1st
> peak,
> > 2nd peak (solvation shell), and i need to view this in the vmd by making
> > use of the trajectories (trr/xtc files), so while viewing the
> trajectories
> >
> > 1] how can i view that exact trajectory at which i have got the
> particular
> > peak in RDF (since that would mean either H-bond formation/probability of
> > tht molecule close to that)
> > because viewing each frame to find it would take literally lot of time,
> ...
> >
> > Thank you.
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> >
> >
> >
> >   <https://mailtrack.io/> Sent with Mailtrack
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> > https://mailtrack.io/install?source=signature=en;
> referral=cy16f01.di...@nitk.edu.in=22
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DILIP.H.N
Ph.D Student
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[gmx-users] Regarding viewing Trajectories

[Dilip H N]

Hello.,
In RDF of amino acid with ammonia and water mixture, i have got a 1st peak,
2nd peak (solvation shell), and i need to view this in the vmd by making
use of the trajectories (trr/xtc files), so while viewing the trajectories

1] how can i view that exact trajectory at which i have got the particular
peak in RDF (since that would mean either H-bond formation/probability of
tht molecule close to that)
because viewing each frame to find it would take literally lot of time, ...

Thank you.

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding getting trajectories in gromacs..

[Dilip H N]

Hello,
I have ran a md simulation for
nsteps = 500 ; 2 * 500 = 1 ps (10 ns)
dt = 0.002 ; 1e+07 fs
nstxout= 5000 ; save coordinates every 20.0 ps
nstvout= 5000 ; save velocities every 20.0 ps
nstenergy= 5000 ; save energies every 20.0 ps
nstlog= 5000 ; update log file every 20.0 ps
nstxout-compressed  = 5000  ; save compressed coordinates every 20.0 ps

ie., for 10 ns.. and when i view the trr file in vmd , the bonds are
stretched/compressed.. so i tried with the command
gmx trjconv -f md.trr/xtc -s md.tpr -pbc mol -o md-mol.xtc
this above command is for the whole 0 - 10 ns trajectory i got and all the
bonds are intact now..
My question is that if i want to get the trajectories for 0-2ns,
2-4ns,4-6ns,6-8ns, 8-10ns, ie for every 2ns ..how to get it..??
gmx trjconv -f md.trr -s md.tpr -o  new.gro -b 0 -e 200
with this command i got the gro file... but how to view the trajectory of
this file...

1] What are the commands that i need to give to view individual
trajectories of 2 ns intervals
2] and how to view those obtained trajectories of 2ns in vmd without
getting bonds stretched/elongated..

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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