date:20170526

Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

2017-05-26 Thread David van der Spoel


On 26/05/17 22:05, Erik Marklund wrote:

“Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which is 
why they are sometimes fewer than the hbonds.


Therefore I would assume they are more instead.


Kind regards,
Erik


On 26 May 2017, at 19:38, Adarsh V. K.  wrote:

Dear all,

The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "

I would like to edit the file before viewing in 'Xmgrace'

I opened the hbnum.xvg using 'gedit'. It shows following details (see below)

Can you please tell me what is there in the third column of the file?

-
# gmx hbond is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@title "Hydrogen Bonds"
@xaxis  label "Time (ps)"
@yaxis  label "Number"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
02   7
   10   2   5
   20   4   3
   30   3   2
   40   3   3
   50   5   1
   60   3   6
   70   3   6
   80   2   3
   90   5   1
  100  3   3
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Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

2017-05-26 Thread Erik Marklund

“Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which is 
why they are sometimes fewer than the hbonds.

Kind regards,
Erik

> On 26 May 2017, at 19:38, Adarsh V. K.  wrote:
> 
> Dear all,
> 
> The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "
> 
> I would like to edit the file before viewing in 'Xmgrace'
> 
> I opened the hbnum.xvg using 'gedit'. It shows following details (see below)
> 
> Can you please tell me what is there in the third column of the file?
> 
> -
> # gmx hbond is part of G R O M A C S:
> #
> # GROtesk MACabre and Sinister
> #
> @title "Hydrogen Bonds"
> @xaxis  label "Time (ps)"
> @yaxis  label "Number"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.35 nm"
> 02   7
>10   2   5
>20   4   3
>30   3   2
>40   3   3
>50   5   1
>60   3   6
>70   3   6
>80   2   3
>90   5   1
>   100  3   3
> -- 
> Gromacs Users mailing list
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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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[gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

2017-05-26 Thread Adarsh V. K.

Dear all,

The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "

I would like to edit the file before viewing in 'Xmgrace'

I opened the hbnum.xvg using 'gedit'. It shows following details (see below)

Can you please tell me what is there in the third column of the file?

-
# gmx hbond is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@title "Hydrogen Bonds"
@xaxis  label "Time (ps)"
@yaxis  label "Number"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
 02   7
10   2   5
20   4   3
30   3   2
40   3   3
50   5   1
60   3   6
70   3   6
80   2   3
90   5   1
   100  3   3
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Re: [gmx-users] RMSF per residue

2017-05-26 Thread Mohsen Ramezanpour

Hi Justin,

Here is what I understand. I would like to know if I understood correctly.

Given a selection, which has all the heavy atoms (5 atoms) in the side
chain of one specific residue (say Lysine), I want to have only "one value"
for the average fluctuation of this selection.
Thus, I will use "-res" option in gmx_rmsf command.

If I understood correctly, the RMSF for each atom in this selection is
calculated first. So, we will have the rmsf(i) values, which i=1 to 5.
Next, a mass-weighted average will be taken over all of these atoms. Thus,
the final value I get as output is the following:

RMSF per selection = (Sum (m(i)*rmsf(i)))/(Sum m(i)) where m(i) is the mass
for atom i.

Is this correct?

If yes, why the RMSF per selection should be a mass-weighted?
In other words, whey the usual average is not used, e.g. (Sum (rmsf(i))/5)
where 5 is the total number of atoms in this selection.

Thanks
Mohsen

On Thu, May 25, 2017 at 12:54 PM, Justin Lemkul  wrote:

>
>
> On 5/24/17 4:12 PM, Mohsen Ramezanpour wrote:
>
>> Dear Gromacs users,
>>
>> I have a question on RMSF calculation:
>>
>> I am not sure how -res works in RMSF and I could not find any useful
>> explanation for it.
>>
>> It will give the average fluctuations per residue, fine. but how exactly?
>>
>> 1) it calculates the RMSF for each atom in that residue first. Then, it
>> averages over all of these atoms and reports it as the average for the
>> residue.
>>
>> 2) it takes the center of mass or specific atom of the residue and
>> calculates the RMSF for that.
>>
>> Or something else?
>>
>>
>> I am interested in the average fluctuation for sidechain of one residue
>> (excluding H atoms from this calculation). I want to have only one value
>> as
>> the average fluctuation for this group.
>>
>> I choose the residue-sidechain-H group (which I made in an index file)
>> when
>> prompted in the following command:
>>
>> gmx rmsf  -f  md.xtc  -fit   -s  md.tpr   -n index.ndx  -o
>>  residues-sidechain-H.xvg  -res
>>
>>
>> an alternative would be to use the following command and make an average
>> over all atoms manually:
>>
>> gmx rmsf  -f  md.xtc  -fit   -s  md.tpr   -n index.ndx  -o
>>  residues-sidechain-H.xvg
>>
>>
>> The results are NOT the same as expected. I think I should use the second
>> command and make the average manually. What do you think?
>>
>>
> The total RMSF of the selection is computed, then a mass-weighted average
> over each of the atoms is computed and that subsequent value assigned for
> output. See the "average_residues" function in
> src/gromacs/gmxana/gmx_rmsf.cpp
>
> -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
>
> ==
> --
> 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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Re: [gmx-users] Perturbation Thermodynamic Integration

2017-05-26 Thread Dan Gil

Hello,

I've run Gromacs following the suggestions, but I still get nonzero
contributions from the mass changing. I will outline in-depth what I did.
Thank you very much for your help!

(1) Heptane molecule was inserted into a box of size 10x10x10 nm3 with 7833
water molecules using Gromacs insert-molecules. Bad contacts were resolved
using the steep algorithm. The pressure was increased to a 10 bar using the
Berendsen pressure couple until a condensed liquid phase was formed. The
system was equilibrated at standard conditions (1 bar, 300 K) using the
Parinello-Rahman couple and velocity-rescaling thermostat. Step size of 2
femtoseconds with the stochastic integrator was used.
(2) New directories were created with copies of the configuration generated
in step (1). Each directory also contained grompp.mdp which defined the
lambda value (i.e. 1 through 10) for each directory. The configurations
were further equilibrated at this stage for 2 ns. The topology is shown
below. The topology is defined so that "A" is a hydrocarbon and "B" is a
fluorocarbon.
(3) Data collection simulations began after step (2), using grompp,mdp
shown below.
(4) Steps (2) and (3) were repeated for heptane in the gas phase with no
water molecules.
(5) Results: I've ran two alchemical transformation steps. A(aq)->B(aq) and
A(gas)->B(gas). The free energy change difference of the two steps is the
difference in solvation free energy. That is, deltaF(A(aq)->B(aq)) -
deltaF(A(gas)->B(gas)). Mass contribution is large. I will also leave a
matrix of the mean and variance of each contribution at the bottom.

--Topology--

 [ moleculetype ]
HEPT 3

 [ atoms ]
 1   opls_135  1   HEPTCH3  1 -0.180 12.011
 opls_9610.36012.011
 2   opls_136  1   HEPTCH2  2 -0.120 12.011
 opls_9620.24012.011
 3   opls_136  1   HEPTCH2  3 -0.120 12.011
 opls_9620.24012.011
 4   opls_136  1   HEPTCH2  4 -0.120 12.011
 opls_9620.24012.011
 5   opls_136  1   HEPTCH2  5 -0.120 12.011
 opls_9620.24012.011
 6   opls_136  1   HEPTCH2  6 -0.120 12.011
 opls_9620.24012.011
 7   opls_135  1   HEPTCH3  7 -0.180 12.011
 opls_9610.36012.011
 8   opls_140  1   HEPT  H  1  0.060  1.008
 opls_965   -0.12018.998
 9   opls_140  1   HEPT  H  1  0.060  1.008
 opls_965   -0.12018.998
10   opls_140  1   HEPT  H  1  0.060  1.008
 opls_965   -0.12018.998
11   opls_140  1   HEPT  H  2  0.060  1.008
 opls_965   -0.12018.998
12   opls_140  1   HEPT  H  2  0.060  1.008
 opls_965   -0.12018.998
13   opls_140  1   HEPT  H  3  0.060  1.008
 opls_965   -0.12018.998
14   opls_140  1   HEPT  H  3  0.060  1.008
 opls_965   -0.12018.998
15   opls_140  1   HEPT  H  4  0.060  1.008
 opls_965   -0.12018.998
16   opls_140  1   HEPT  H  4  0.060  1.008
 opls_965   -0.12018.998
17   opls_140  1   HEPT  H  5  0.060  1.008
 opls_965   -0.12018.998
18   opls_140  1   HEPT  H  5  0.060  1.008
 opls_965   -0.12018.998
19   opls_140  1   HEPT  H  6  0.060  1.008
 opls_965   -0.12018.998
20   opls_140  1   HEPT  H  6  0.060  1.008
 opls_965   -0.12018.998
21   opls_140  1   HEPT  H  7  0.060  1.008
 opls_965   -0.12018.998
22   opls_140  1   HEPT  H  7  0.060  1.008
 opls_965   -0.12018.998
23   opls_140  1   HEPT  H  7  0.060  1.008
 opls_965   -0.12018.998
 [ bonds ]
 1 2 1
 1 8 1
 1 9 1
 110 1
...

-- MDP Options --

;Integration Method and Parameters
integrator   = sd
nsteps   = 100
dt = 0.002
nstenergy= 1000
nstlog   = 5000

;Output Control
nstxout = 0
nstvout = 0

;Cutoff Schemes
cutoff-scheme= group
rlist= 1.0
vdw-type = cut-off
rvdw = 2.0

;Coulomb interactions
coulombtype  = pme
rcoulomb = 1.0
fourierspacing   = 0.4

;Constraints
constraints  = none

;Temperature coupling
tcoupl   = v-rescale
tc-grps  = system
tau-t= 0.1
ref-t= 300

;Pressure coupling
pcoupl = parrinello-rahman
ref-p = 1.01325
compressibility = 4.5e-5
tau-p = 5

;Free energy calculation
free-energy  = yes
init-lambda-state= 0
delta-lambda = 0
fep-lambdas

Re: [gmx-users] RMSF per residue

2017-05-26 Thread Justin Lemkul




On 5/26/17 2:22 AM, Mohsen Ramezanpour wrote:

Hi Justin,

I have a naive question on tool development for gromacs.

If I change part of the code, or if I write a new analysis tool in c++ and
add it to this directory (after compiling with g++), shall I still
recompile the whole Gromacs again?



Yes, because GROMACS functions as a single binary now (gmx).  Compiling a new 
source file will have no effect; you'll need to add the new source file to the 
list of cmake build targets so that it gets compiled and built in.


-Justin


Cheers,
Mohsen

On Thu, May 25, 2017 at 1:43 PM, Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:


Thanks Justin!

On Thu, May 25, 2017 at 12:54 PM, Justin Lemkul  wrote:




On 5/24/17 4:12 PM, Mohsen Ramezanpour wrote:


Dear Gromacs users,

I have a question on RMSF calculation:

I am not sure how -res works in RMSF and I could not find any useful
explanation for it.

It will give the average fluctuations per residue, fine. but how exactly?

1) it calculates the RMSF for each atom in that residue first. Then, it
averages over all of these atoms and reports it as the average for the
residue.

2) it takes the center of mass or specific atom of the residue and
calculates the RMSF for that.

Or something else?


I am interested in the average fluctuation for sidechain of one residue
(excluding H atoms from this calculation). I want to have only one value
as
the average fluctuation for this group.

I choose the residue-sidechain-H group (which I made in an index file)
when
prompted in the following command:

gmx rmsf  -f  md.xtc  -fit   -s  md.tpr   -n index.ndx  -o
 residues-sidechain-H.xvg  -res


an alternative would be to use the following command and make an average
over all atoms manually:

gmx rmsf  -f  md.xtc  -fit   -s  md.tpr   -n index.ndx  -o
 residues-sidechain-H.xvg


The results are NOT the same as expected. I think I should use the second
command and make the average manually. What do you think?



The total RMSF of the selection is computed, then a mass-weighted average
over each of the atoms is computed and that subsequent value assigned for
output. See the "average_residues" function in
src/gromacs/gmxana/gmx_rmsf.cpp

-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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--
*Rewards work better than punishment ...*







--
==

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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Re: [gmx-users] RMSF per residue

2017-05-26 Thread Mohsen Ramezanpour

Hi Justin,

I have a naive question on tool development for gromacs.

If I change part of the code, or if I write a new analysis tool in c++ and
add it to this directory (after compiling with g++), shall I still
recompile the whole Gromacs again?

Cheers,
Mohsen

On Thu, May 25, 2017 at 1:43 PM, Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> Thanks Justin!
>
> On Thu, May 25, 2017 at 12:54 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 5/24/17 4:12 PM, Mohsen Ramezanpour wrote:
>>
>>> Dear Gromacs users,
>>>
>>> I have a question on RMSF calculation:
>>>
>>> I am not sure how -res works in RMSF and I could not find any useful
>>> explanation for it.
>>>
>>> It will give the average fluctuations per residue, fine. but how exactly?
>>>
>>> 1) it calculates the RMSF for each atom in that residue first. Then, it
>>> averages over all of these atoms and reports it as the average for the
>>> residue.
>>>
>>> 2) it takes the center of mass or specific atom of the residue and
>>> calculates the RMSF for that.
>>>
>>> Or something else?
>>>
>>>
>>> I am interested in the average fluctuation for sidechain of one residue
>>> (excluding H atoms from this calculation). I want to have only one value
>>> as
>>> the average fluctuation for this group.
>>>
>>> I choose the residue-sidechain-H group (which I made in an index file)
>>> when
>>> prompted in the following command:
>>>
>>> gmx rmsf  -f  md.xtc  -fit   -s  md.tpr   -n index.ndx  -o
>>>  residues-sidechain-H.xvg  -res
>>>
>>>
>>> an alternative would be to use the following command and make an average
>>> over all atoms manually:
>>>
>>> gmx rmsf  -f  md.xtc  -fit   -s  md.tpr   -n index.ndx  -o
>>>  residues-sidechain-H.xvg
>>>
>>>
>>> The results are NOT the same as expected. I think I should use the second
>>> command and make the average manually. What do you think?
>>>
>>>
>> The total RMSF of the selection is computed, then a mass-weighted average
>> over each of the atoms is computed and that subsequent value assigned for
>> output. See the "average_residues" function in
>> src/gromacs/gmxana/gmx_rmsf.cpp
>>
>> -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
>>
>> ==
>> --
>> 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.
>>
>
>
>
> --
> *Rewards work better than punishment ...*
>



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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

[gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

Re: [gmx-users] RMSF per residue

Re: [gmx-users] Perturbation Thermodynamic Integration

Re: [gmx-users] RMSF per residue

Re: [gmx-users] RMSF per residue

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