Re: [gmx-users] Atom type CB ERROR

[Kashif]

I got parameter file (ligand.par) from swissparam. What should I add from
this file and where? means the topol.top file created during the
simulation, should I use that file to include CB parameter? Please find the
parameter data generated from swiss para and help me what to add regarding
CB atom type.

* 
* Built parameters for ligand.mol2
*by user vzoete Mon May 29 09:38:13 CEST 2017
* 
*
BONDS
HCMM CB381.853 1.0840
HCMM CR342.991 1.0930
HCMM C=O   334.643 1.1010
HCMM C=C   372.066 1.0830
CR   CR306.432 1.5080
CR   NC=O  335.651 1.4360
CR   NC=C  354.218 1.4460
NC=O C=O   419.491 1.3690
CR   CB356.737 1.4860
CB   CB401.068 1.3740
C=O  CB322.985 1.4570
C=O  O=C   931.963 1.2220
NC=C C5B   478.144 1.3510
C=C  NPYL  443.600 1.3680
C=C  CB360.335 1.4490
C=C  C=C   684.039 1.3330
NPYL N5A   396.750 1.3390
NPYL C5A   453.459 1.3640
N5A  C5B   594.297 1.3350
C5B  N5B   320.682 1.3690
CSP  CB391.856 1.4240
CSP  NSP   1193.344 1.1600
C5A  N5B   599.191 1.3130
C5A  N=C   491.098 1.3450
C=O  N=C   725.204 1.2900
C=O  C=C   328.526 1.4680

ANGLES
CB   CB   CB 48.145119.9770
CB   CB   HCMM   40.517120.5710
CB   CB   CR 57.788120.4190
CB   CB   C=O57.429114.4750
NPYL C=C  CB 71.966120.
NPYL C=C  C=C70.239122.3600
CB   C=C  C=C43.035117.5080
C=C  NPYL N5A64.769133.2200
C=C  NPYL C5A61.747130.2750
N5A  NPYL C5A92.404112.0870
NPYL N5A  C5B   125.076101.5500
N5A  C5B  N5B75.924115.3690
N5A  C5B  NC=C   68.943129.1250
N5B  C5B  NC=C   71.966120.
C=C  CB   CB 51.240119.6950
NPYL C5A  N5B72.829110.8650
NPYL C5A  N=C76.859121.7410
N5B  C5A  N=C65.633133.0200
C5B  N5B  C5A86.791103.7790
N=C  C=O  C=C59.803122.2530
N=C  C=O  HCMM   44.835119.4910
C=C  C=O  HCMM   64.841115.3500
C5A  N=C  C=O89.741109.9890
CB   CB   CSP65.201119.6140
C=C  C=C  C=O39.221111.2970
C=C  C=C  HCMM   38.502121.0040
C=O  C=C  HCMM   35.047117.2910
HCMM CR   HCMM   37.134108.8360
HCMM CR   CR 45.770110.5490
HCMM CR   NC=O   53.255107.6460
CR   CR   NC=O   75.564109.9600
HCMM CR   NC=C   51.743109.8700
CR   CR   NC=C   81.321108.6780
CR   NC=O C=O59.084119.6000
CR   NC=O CR 80.386117.9090
CB   CR   HCMM   45.122109.4910
CB   CR   CR 54.406108.6170
CR   CR   CR 61.243109.6080
CB   C=O  NC=O   79.234112.4950
CB   C=O  O=C52.823119.9680
NC=O C=O  O=C65.273127.1520
C5B  NC=C CR 76.571115.4830
CR   NC=C CR 76.571113.7030
CB   CSP  NSP33.968180.

DIHEDRALS
CB   CB   CB   CB   3.500  2   180.00
CB   CB   CB   HCMM 3.500  2   180.00
CB   CB   C=O  NC=O 1.250  2   180.00
CB   CB   C=O  O=C  1.250  2   180.00
CB   CB   CSP  NSP  0.000  1 0.00
CB   CB   CR   HCMM-0.210  2   180.00
CB   CB   CR   HCMM 0.196  3 0.00
CB   CB   CR   CR   0.225  2   180.00
CB   CB   CB   C=C  3.500  2   180.00
CB   CR   CR   HCMM 0.195  3 0.00
CB   CR   CR   CR   0.150  3 0.00
CB   CB   CB   CSP  3.500  2   180.00
CB   C=O  NC=O CR   3.000  2   180.00
C=C  NPYL N5A  C5B  0.000  1 0.00
C=C  NPYL C5A  N5B  3.000  2   180.00
C=C  NPYL C5A  N=C  3.000  2   180.00
C=C  CB   CB   HCMM 1.000  2   180.00
C=C  C=C  C=O  N=C  1.250  2   180.00
C=C  C=C  C=O  HCMM 1.250  2   180.00
NPYL C=C  CB   CB   1.000  2   180.00
NPYL C=C  C=C  C=O  0.900  2   180.00
NPYL C=C  C=C  HCMM 0.900  2   180.00
NPYL N5A  C5B  N5B  3.500  2   180.00
NPYL N5A  C5B  NC=C 3.500  2   180.00
NPYL C5A  N5B  C5B  3.500  2   180.00
NPYL C5A  N=C  C=O  0.900  2   180.00
N5A  NPYL C=C  CB   3.000  2   180.00
N5A  NPYL C=C  C=C  3.000  2   180.00
N5A  NPYL C5A  N5B  2.000  2   180.00
N5A  NPYL C5A  N=C  2.000  2   180.00
N5A  C5B  N5B  C5A  3.500  2   180.00
N5A  C5B  NC=C CR   1.800  2   180.00
C5B  N5A  NPYL C5A  2.000  2   180.00
C5B  N5B  C5A  N=C  3.500  2   180.00
C5B  NC=C CR   HCMM 0.125  3 0.00
C5B  NC=C CR   CR   0.125  3 0.00
CB   CB   CB   CR   3.500  2   180.00
CB   CB   C=C  C=C  1.000  2   180.00
CB   C=C  NPYL C5A  3.000  2   180.00
CB   C=C  C=C  C=O  0.900  2   180.00
CB   C=C  C=C  HCMM 0.900  2   180.00
C5A  NPYL C=C  C=C  3.000  2   180.00
C5A  N5B  C5B  NC=C 3.500  2   180.00
C5A  N=C  C=O  C=C  0.900  2   180.00
C5A  N=C  C=O  HCMM 0.900  2   180.00
N5B  C5B  NC=C CR   1.800  2   180.00
N5B  C5A  N=C  C=O  0.900  2   180.00
CB   CB   CB   C=O  3.500  2   180.00
N=C  C=O  C=C  HCMM-0.145  1 0.00
N=C  C=O  C=C  HCMM 0.760  2   180.00
N=C  C=O  C=C  HCMM-0.235  3 0.00
HCMM CB   CB   HCMM 3.500  2   180.00
HCMM CB   CB   

Re: [gmx-users] calculation of energy of individual water molecules in gromacs

[Saumyak Mukherjee]

Thanks Justin for the reply.

Supposing that I have 2300 (average) water molecules in a 1 nm hydration
shell around a protein, I need to calculate the interaction energy of each
and everyone of them in all the time frames, with the rest of the system. I
believe this is not possible using energygrps. Is there any other way?

On 31 May 2017 at 05:39, Justin Lemkul  wrote:

>
>
> On 5/30/17 1:52 AM, Saumyak Mukherjee wrote:
>
>> Dear users,
>>
>> I need to calculate the energy of individual water molecules in a 1 nm
>> shell around protein. That is, there will be n number of energy terms in
>> each time frame if there are n number of water molecules in the said
>> hydration shell at that time step. Is there a way to do it in GROMACS?
>>
>>
> The internal energy of a water molecule?  If you're using standard rigid
> waters, that quantity is by definition zero.  Interaction energy is another
> matter and can be calculated using energygrps.  Whether or not that's
> useful depends on the force field, as I just commented in another thread.
>
> -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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> Gromacs Users mailing list
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>



-- 

*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukher...@gmail.com
smukher...@sscu.iisc.ernet.in

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[gmx-users] EM error

[‪Mohammad Roostaie‬ ‪]

Hi All,
I wanted to run energy minimization process by this command: gmx mdrun -v 
-deffnm em. But, I got this error:
tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted
I do not know what the problem exactly is. Can you please help me?
Thanks,Mohammad

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[gmx-users] please help clarifying units for potential energy and enthalpy from gmx energy

[Christopher Neale]

Dear Users:


I am trying to figure out what “potential energy” and “enthalpy” really mean in 
the output from gmx energy. It took me a while to realize that even when the 
(more hidden than it should be) option -nmol is not used and therefore is set 
to its default value of 1, the .xvg output indicates units of kJ/mol for the 
potential energy, when in that default case it is likely reporting simply kJ, 
or perhaps kJ/unit cell.


But then what about the “enthalpy”? It also is given units of kJ/mol in the 
.xvg output from gmx energy, but that numerical output is not affected at all 
by the value of -nmol.


I show some output below to prove scaling of the output “potential energy” but 
no the “enthalpy” with the -nmol option to gmx energy, but that is just to show 
the change with different options to gmx energy on the same .edr file.


Thank you for the help.

Chris.


## without -nmol (default to 1)


# Command line:

#   gmx energy -f FEMSMNM.edr -o a.xvg

# gmx energy is part of G R O M A C S:

#

# GRowing Old MAkes el Chrono Sweat

#

@title "GROMACS Energies"

@xaxis  label "Time (ps)"

@yaxis  label "(kJ/mol)"

@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 "Potential"

@ s1 legend "Enthalpy"

0.00  -555356.062500  -425480.937500

0.20  -530695.812500  -415548.406250

0.40  -528639.75  -410765.75

0.60  -527722.50  -407132.125000

0.80  -526586.687500  -404519.687500

1.00  -526814.125000  -402872.875000

1.20  -525852.625000  -401044.656250

1.40  -525089.25  -399389.187500

1.60  -524979.625000  -398347.593750

1.80  -524312.50  -396957.187500

2.00  -524930.062500  -396691.562500




# Command line:

#   gmx energy -f FEMSMNM.edr -o b.xvg -nmol 100

# gmx energy is part of G R O M A C S:

#

# GROwing Monsters And Cloning Shrimps

#

@title "GROMACS Energies"

@xaxis  label "Time (ps)"

@yaxis  label "(kJ/mol)"

@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 "Potential"

@ s1 legend "Enthalpy"

0.00  -5553.560547  -425480.937500

0.20  -5306.958008  -415548.406250

0.40  -5286.397461  -410765.75

0.60  -5277.225098  -407132.125000

0.80  -5265.866699  -404519.687500

1.00  -5268.141113  -402872.875000

1.20  -5258.526367  -401044.656250

1.40  -5250.892578  -399389.187500

1.60  -5249.796387  -398347.593750

1.80  -5243.125000  -396957.187500

2.00  -5249.300781  -396691.562500
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[gmx-users] How to perform final MD simulation after extending a NPT simulation

[Adarsh V. K.]

Dear all,

*I used following command to extend a NPT simulation*

gmx convert-tpr -s npt.tpr -extend 500 -o tpxout.tpr
gmx mdrun -deffnm tpxout -cpi npt_prev.cpt -v

*Now to do final MD simulation what command I should use?*

gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
md_0_1.tpr
gmx mdrun -deffnm md_0_1 -v

or

gmx grompp -f md.mdp -c npt.gro -t tpxout.cpt -p topol.top -n index.ndx -o
md_0_1.tpr
gmx mdrun -deffnm md_0_1 -v
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Re: [gmx-users] Deuterium Order Parameter Calculations

[Justin Lemkul]

On 5/30/17 7:16 PM, Sanim Rahman wrote:

Hello everyone,

I have a question about calculating Deuterium Order Parameters using
g_order. Is it common to get unrealistic values for Scd if you have not run
the simulation long enough (over 25 ns?)? I ran the calculations after
equilibration on a POPC bilayer just to experiment with the command and I
received "NaN" values for two of my carbons for my calculations on Sn1.



This means something is wrong with your inputs, likely incorrectly specified 
index groups.


-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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Re: [gmx-users] Doubt about gmx wham analysis

[Justin Lemkul]

On 5/30/17 6:49 AM, Varvdekar Bhagyesh Rajendra wrote:

Dear all,

I have followed the Umbrella sampling tutorial 
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html)
 on a Protein-ligand system using gromacs 5.1.1 while making some changes in 
md_pull code with pull_coord1_dim = Y Y Y . Now I have to perform WHAM analysis 
using gmx wham. As my system (Protein-ligand system) has the reaction 
coordinate as the center of masses between the protein and ligand I have to 
supply the .pdo file as suggested in gmx wham help menu. I would appreciate if 
anyone could help me to generate these pdo files because I have not encountered 
any option to generate them.



.pdo files were umbrella sampling output files from ancient versions of GROMACS. 
 Support for their interpretation is maintained only for backwards compatibility.


Look through the tutorial again; nowhere does it use .pdo files and yet it still 
calculates a PMF :)


-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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Re: [gmx-users] Write force on a single particle

[Justin Lemkul]

On 5/30/17 5:48 AM, simon.grosse-h...@fau.de wrote:

Dear All,

is it possible to write the forces of only one (type of) particle to the 
trajectory?


I am using GROMACS to simulate the dispersion of a hydrophobic particle in a big 
box of water and am interested in the force acting on the particle. Simply 
writing all the forces to the trajectory (via nstfout) also writes all the 
forces on the water molecules, which is a lot of data that actually I do not 
need. For the compressed trajectory output I can specify the groups to write, 
which would perfectly solve my problem, if the compressed trajectories could 
hold forces. That, however, is not the case (as far as I know; is that 
correct?). So is there any other way to get only the force acting on the one 
particle?




The only solution of which I am aware is to do a short interval of simulation 
writing a full .trr, post-process to save only what you want, then continue with 
another interval, etc.


-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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Re: [gmx-users] Unexpected behavior in the output of gmx insert-molecules using the -ip option.

[Justin Lemkul]

On 5/29/17 11:11 PM, Abhishek Acharya wrote:

Dear GROMACS users,

I want to insert my molecule of interest in a simulation box at specific
positions, specified by a dat file.

Now, when I run insert-molecules, I find that on "certain occasions" (yes,
it doesn't happen always.), the program also inserts the molecule
at the origin [0 0 0]. It seems that it is appending the input coordinates
of my molecule, provided with -ci,
to the final coordinate file, something which should not happen.

Is this behavior known? Of course, it is trivial to remove the extra
coordinates, but it becomes an effort if a large number of systems need to
be
generated.



Sounds buggy, but without an actual command and set of inputs that reliably 
triggers the behavior, it's hard to track down.  If you can provide that, please 
open a Redmine issue.


-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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Re: [gmx-users] destruction of the structure of a molecule in water after energy minimization

[Justin Lemkul]

On 5/30/17 2:27 AM, Saeed Nasiri wrote:

Dear all

I created the topology and itp files for a molecule manually (the
parameters are not exist in the usual force fields) and build a box of a
molecule and 857 water molecules. The structure of the molecule in water
box is OK. Then the energy minimization step was done by the following
files. After the successful termination, the structure of the molecule has
been destroyed and the atoms of the molecule are spread in the box. In the
following the employed files and the structure of the molecule (in gro
format) before and after minimization (without water molecule) are
presented.
  Any help will highly appreciated.



The problem likely lies in the topology of this molecule.  If it falls apart in 
vacuo, that's the issue and you need to revisit your parametrization.


-Justin


### before minimization ###
 1BMCW1   1.222   1.373   1.397
 1BMCW2   1.349   1.331   1.419
 1BMCR3   1.308   1.498   1.557
 1BM   HCW4   1.148   1.339   1.327
 1BM   HCW5   1.408   1.254   1.371
 1BM   HCR6   1.318   1.570   1.636
 1BMNA7   1.196   1.475   1.486
 1BMNA8   1.400   1.408   1.521
 1BMC19   1.540   1.411   1.566
 1BMH1   10   1.571   1.308   1.584
 1BMH1   11   1.541   1.464   1.662
 1BMC2   12   1.631   1.482   1.466
 1BMHC   13   1.588   1.580   1.446
 1BMHC   14   1.630   1.426   1.372
 1BMCS   15   1.774   1.494   1.518
 1BMHC   16   1.814   1.395   1.542
 1BMHC   17   1.774   1.551   1.611
 1BMCT   18   1.867   1.563   1.418
 1BMHC   19   1.831   1.663   1.394
 1BMHC   20   1.969   1.572   1.458
 1BMHC   21   1.873   1.507   1.324
 1BMC1   22   1.082   1.566   1.484
 1BMH1   23   1.032   1.567   1.581
 1BMH1   24   1.011   1.532   1.409
 1BMH1   25   1.121   1.665   1.461
 2Cl  Cl   26   2.283   1.962   0.221

 after minimization ###
 1BMCW1   1.030   1.807   0.330
 1BMCW2   1.253   0.613   1.483
 1BMCR3   0.962   1.561   1.355
 1BM   HCW4   0.754   0.906   0.667
 1BM   HCW5   1.875   0.398   0.729
 1BM   HCR6   0.982   2.417   2.358
 1BMNA7   0.291   0.861   1.603
 1BMNA8   0.845   0.979   2.444
 1BMC19   1.834   0.830   2.413
 1BMH1   10   1.844   0.003   1.938
 1BMH1   11   1.443   1.743   2.290
 1BMC2   12   1.917   1.355   1.566
 1BMHC   13   1.404   2.327   1.676
 1BMHC   14   1.558   1.096   0.699
 1BMCS   15   2.661   1.364   2.237
 1BMHC   16   2.317   0.518   1.479
 1BMHC   17   2.099   2.175   2.002
 1BMCT   18   2.036   1.892   0.626
 1BMHC   19   2.109   2.565   1.277
 1BMHC   20   2.648   1.892   1.400
 1BMHC   21   2.494   1.027   0.829
 1BMC1   22   0.417   2.454   1.333
 1BMH1   23   0.484   1.849   2.126
 1BMH1   24   0.182   1.535   0.847
 1BMH1   25   1.280   2.539   0.925
 2Cl  Cl   26   2.580   2.241   2.823

# minimum.mdp 
; minim.mdp - used as input into grompp to generate em.tpr

integrator= steep; Algorithm (steep = steepest descent
minimization)
emtol= 10.0  ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps= 50  ; Maximum number of (minimization) steps to
perform
define = -DFLEXIBLE

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist   = 1; Frequency to update the neighbor
list and long range forces
cutoff-scheme   = Verlet
ns_type= grid; Method to determine neighbor list
(simple, grid)
coulombtype= PME; Treatment of long range electrostatic
interactions
rcoulomb= 1.0; Short-range electrostatic cut-off
rvdw= 1.0; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

## topol.top


#include "oplsaa.ff/forcefield.itp"


#include "ff_BM.itp"
#include "BM.itp"
#include "Cl.itp"

; Include water topology
#include "oplsaa.ff/tip3p.itp"

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

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
11   1000   1000   1000
#endif

[system]
BM Cl

[molecules]
BM1
Cl  1
SOL   857



--
==

Justin A. Lemkul, Ph.D.

Re: [gmx-users] calculation of energy of individual water molecules in gromacs

[Justin Lemkul]

On 5/30/17 1:52 AM, Saumyak Mukherjee wrote:

Dear users,

I need to calculate the energy of individual water molecules in a 1 nm
shell around protein. That is, there will be n number of energy terms in
each time frame if there are n number of water molecules in the said
hydration shell at that time step. Is there a way to do it in GROMACS?



The internal energy of a water molecule?  If you're using standard rigid waters, 
that quantity is by definition zero.  Interaction energy is another matter and 
can be calculated using energygrps.  Whether or not that's useful depends on the 
force field, as I just commented in another thread.


-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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Re: [gmx-users] Non-bonded interaction energy

[Justin Lemkul]

On 5/29/17 11:03 PM, Мижээ Батсайхан wrote:

Dear gmx users,

I would like to calculate non-bonded interaction energy between two groups.
I performed mdrun -rerun for the groups. How reliable is sum of LJ and
Coulombic energies? Please, is there any suggestion and discussion?



If the force field was parametrized such that it is based on some real quantity 
(e.g. how CHARMM considers individual water interactions specifically based on 
QM so a molecule's interaction energy with water should be a real 
representation), it can be useful.  If the force field did not do this, then I 
don't see any physical meaning in the interaction energy.


-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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[gmx-users] Deuterium Order Parameter Calculations

[Sanim Rahman]

Hello everyone,

I have a question about calculating Deuterium Order Parameters using
g_order. Is it common to get unrealistic values for Scd if you have not run
the simulation long enough (over 25 ns?)? I ran the calculations after
equilibration on a POPC bilayer just to experiment with the command and I
received "NaN" values for two of my carbons for my calculations on Sn1.

I will truly appreciate your response and assistance.

Regards,

Sanim Rahman

*Sanim Rahman*
B.S. Chemical Engineering, 2019
Resident Assistant, Castor Hall Engineering Living Learning Community
2016-2017
Co-Founder and Co-President of the Undergraduate Research Society
Research Assistant, Bhethanabotla-Frisina Neural Plasmonics Stimulation
Group

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[gmx-users] Deuterium Order Parameter Analysis

[Sanim Rahman]

Hello everyone,

I have a question about calculating Deuterium Order Parameters using
g_order. Is it common to get unrealistic values for Scd if you have not run
the simulation long enough (over 25 ns?)? I ran the calculations after
equilibration just to experiment with the command and I received "NaN"
values for two of my carbons for my calculations on Sn1.

I will truly appreciate your response and assistance.

Regards,

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

[Nikhil Maroli]

Hi,
I suggest you use MDAnalysis package, in which built in Python code is
available.

-- 
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Nikhil Maroli
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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



   Sent with Mailtrack


On Tue, May 30, 2017 at 10:58 PM, Dilip H N 
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
>
>
>
>    Sent with Mailtrack
> 
>



-- 
With Best Regards,

DILIP.H.N
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



   Sent with Mailtrack

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Re: [gmx-users] Genion error

[‪Mohammad Roostaie‬ ‪]

Thank you very much Justin. It is good now.
Best,Mohammad

  From: Justin Lemkul 
 To: gmx-us...@gromacs.org 
 Sent: Monday, 29 May 2017, 23:40:06
 Subject: Re: [gmx-users] Genion error
   


On 5/29/17 4:35 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Thank you Justin. Here is the link to access the topology 
> file:https://www.dropbox.com/sh/x58tzpmg0vzkbtg/AADH_efF_s8jKx4OaHN8a7IPa?dl=0
> 
> By the way, I do not know about your advice. Can you please give me the link?

It's somewhere in the archive.  Run the topology through dos2unix and always 
make sure to use a plain text editor.  See if that works.

-Justin

> Kind regards,Mohammad
> 
>        From: Justin Lemkul 
>  To: gmx-us...@gromacs.org
>  Sent: Monday, 29 May 2017, 0:21:10
>  Subject: Re: [gmx-users] Genion error
>    
> 
> 
> On 5/28/17 3:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:
>> Hi All, when I wanted to add ions to the system, I got this error:
>> Fatal error:No line with moleculetype 'SOL' found the [ molecules ] section 
>> of file 'gr.top'For more information and tips for troubleshooting, please 
>> check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
>> However, there is 'SOL' molecule type in the [ molecules ] section of the 
>> topology file. Can you please help me to solve this problem?
> 
> Upload your topology to a file-sharing service and provide the URL to access 
> it.
>    There's no way to know what's going on (and I recall giving some previous
> advice about line endings - have you checked this?)
> 
> -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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Re: [gmx-users] Calculation of nematic order parameter using gromacs

[Antonio Baptista]

Hi Nidhi,

If I remember correctly (and your use of "p2" suggests so), that should be 
the ensemble average of the 2nd-order Legendre polynomial of the angle 
between the molecular axis and the membrane normal, right?


Although the order parameter computed by "gmx order" uses that same 
definition, it takes each C-H bond of the aliphatic lipid tail, not the 
overall molecular axis. So, "gmx order" is not what you want.


You can in principle compute what you need in two steps: (1) use "gmx 
gangle" to compute the angle of interest for all molecules and all 
snapshots (you will have to defined the vector of interest, say as the one 
connecting the tail to the head); (2) do a small script to compute the 
average from those data.


Best,
Antonio


On Tue, 30 May 2017, nidhi sorout wrote:


Dear All,
I want to calculate the nematic order parameter (p2) at each time step.
Is it possible to do this with "gmx order"?
If not than  please suggest the right way.

Thank you,
Nidhi
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[gmx-users] Calculation of nematic order parameter using gromacs

[nidhi sorout]

Dear All,
 I want to calculate the nematic order parameter (p2) at each time step.
Is it possible to do this with "gmx order"?
If not than  please suggest the right way.

Thank you,
Nidhi
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[gmx-users] Call for testing: trajectory analysis framework in Python

[Максим Кольцов]

Hi all,

This project was presented at the last Gromacs Workshop in Germany. We
would like to collect some feedback on usability, features and on
whether it is needed at all before going on with the development.

Shortly: we provide Python wrappers for gromacs Trajectory Analysis
framework as described in the docs. Project is currently hosted on
GitHub: https://github.com/PNPI/gromacs-pyapi
There is a Readme file that should be enough for getting stared. If
not, we are open for questions and clarifications.

This API is intended for fast prototyping and writing one-time
throw-away script to test you ideas on trajectory files.

Looking forward to feedback and bug reports!
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[gmx-users] Mail list

[shivani gupta]

My email id is shivanigupta.gup...@gmail.com
Sent from my iPhone
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[gmx-users] Positive potential energy

[Emran Heshmati]

 Hi allI run two simulations on a 16 aa peptide under the same conditions 
(forcefield, simulation duration, ...) except the solvent in one of the 
simulations was TFE instead of water. The potential energy in the TFE 
containing system was positive (about 14 Kj/mol), while in water containing 
system was negative (about -7 Kj/mol). Is it normal? or some kind of error 
has occurred?  Best Regards
Emran Heshmati Ph. D.Biophysicist,Computational  Bio-Chemist
P Save a tree... please don't print this e-mail unless you really need to
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[gmx-users] Doubt about gmx wham analysis

[Varvdekar Bhagyesh Rajendra]

Dear all,

I have followed the Umbrella sampling tutorial 
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html)
 on a Protein-ligand system using gromacs 5.1.1 while making some changes in 
md_pull code with pull_coord1_dim = Y Y Y . Now I have to perform WHAM analysis 
using gmx wham. As my system (Protein-ligand system) has the reaction 
coordinate as the center of masses between the protein and ligand I have to 
supply the .pdo file as suggested in gmx wham help menu. I would appreciate if 
anyone could help me to generate these pdo files because I have not encountered 
any option to generate them.

Thanking in anticipation,
Bhagyesh 
IIIT Hyderabad, India
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[gmx-users] Write force on a single particle

[simon . grosse-holz]

Dear All,

is it possible to write the forces of only one (type of) particle to the 
trajectory?


I am using GROMACS to simulate the dispersion of a hydrophobic particle 
in a big box of water and am interested in the force acting on the 
particle. Simply writing all the forces to the trajectory (via nstfout) 
also writes all the forces on the water molecules, which is a lot of 
data that actually I do not need. For the compressed trajectory output I 
can specify the groups to write, which would perfectly solve my problem, 
if the compressed trajectories could hold forces. That, however, is not 
the case (as far as I know; is that correct?). So is there any other way 
to get only the force acting on the one particle?


Thanks,
Simon
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Re: [gmx-users] Invalid directive impropers

[Saeed Nasiri]

I find the right format for the improper dihedrals.

thanks
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Re: [gmx-users] Unexpected behavior in the output of gmx insert-molecules using the -ip option.

[Abhishek Acharya]

>
>
> Dear GROMACS users,
>
> I want to insert my molecule of interest in a simulation box at specific
> positions, specified by a dat file.
>
> Now, when I run insert-molecules, I find that on "certain occasions" (yes,
> it doesn't happen always.), the program also inserts the molecule
> at the origin [0 0 0]. It seems that it is appending the input coordinates
> of my molecule, provided with -ci,
> to the final coordinate file, something which should not happen.
>
> Is this behavior known? Of course, it is trivial to remove the extra
> coordinates, but it becomes an effort if a large number of systems need to
> be
> generated.
>
> Thank you.
>
> Regards,
> Abhishek Acharya
> Research Associate,
> Department of Molecular Nutrition
> CSIR-Central Food Technological Research Institute,
> Mysuru-570020
>
>
>
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[gmx-users] destruction of the structure of a molecule in water after energy minimization

[Saeed Nasiri]

Dear all

I created the topology and itp files for a molecule manually (the
parameters are not exist in the usual force fields) and build a box of a
molecule and 857 water molecules. The structure of the molecule in water
box is OK. Then the energy minimization step was done by the following
files. After the successful termination, the structure of the molecule has
been destroyed and the atoms of the molecule are spread in the box. In the
following the employed files and the structure of the molecule (in gro
format) before and after minimization (without water molecule) are
presented.
 Any help will highly appreciated.

### before minimization ###
1BMCW1   1.222   1.373   1.397
1BMCW2   1.349   1.331   1.419
1BMCR3   1.308   1.498   1.557
1BM   HCW4   1.148   1.339   1.327
1BM   HCW5   1.408   1.254   1.371
1BM   HCR6   1.318   1.570   1.636
1BMNA7   1.196   1.475   1.486
1BMNA8   1.400   1.408   1.521
1BMC19   1.540   1.411   1.566
1BMH1   10   1.571   1.308   1.584
1BMH1   11   1.541   1.464   1.662
1BMC2   12   1.631   1.482   1.466
1BMHC   13   1.588   1.580   1.446
1BMHC   14   1.630   1.426   1.372
1BMCS   15   1.774   1.494   1.518
1BMHC   16   1.814   1.395   1.542
1BMHC   17   1.774   1.551   1.611
1BMCT   18   1.867   1.563   1.418
1BMHC   19   1.831   1.663   1.394
1BMHC   20   1.969   1.572   1.458
1BMHC   21   1.873   1.507   1.324
1BMC1   22   1.082   1.566   1.484
1BMH1   23   1.032   1.567   1.581
1BMH1   24   1.011   1.532   1.409
1BMH1   25   1.121   1.665   1.461
2Cl  Cl   26   2.283   1.962   0.221

 after minimization ###
1BMCW1   1.030   1.807   0.330
1BMCW2   1.253   0.613   1.483
1BMCR3   0.962   1.561   1.355
1BM   HCW4   0.754   0.906   0.667
1BM   HCW5   1.875   0.398   0.729
1BM   HCR6   0.982   2.417   2.358
1BMNA7   0.291   0.861   1.603
1BMNA8   0.845   0.979   2.444
1BMC19   1.834   0.830   2.413
1BMH1   10   1.844   0.003   1.938
1BMH1   11   1.443   1.743   2.290
1BMC2   12   1.917   1.355   1.566
1BMHC   13   1.404   2.327   1.676
1BMHC   14   1.558   1.096   0.699
1BMCS   15   2.661   1.364   2.237
1BMHC   16   2.317   0.518   1.479
1BMHC   17   2.099   2.175   2.002
1BMCT   18   2.036   1.892   0.626
1BMHC   19   2.109   2.565   1.277
1BMHC   20   2.648   1.892   1.400
1BMHC   21   2.494   1.027   0.829
1BMC1   22   0.417   2.454   1.333
1BMH1   23   0.484   1.849   2.126
1BMH1   24   0.182   1.535   0.847
1BMH1   25   1.280   2.539   0.925
2Cl  Cl   26   2.580   2.241   2.823

# minimum.mdp 
; minim.mdp - used as input into grompp to generate em.tpr

integrator= steep; Algorithm (steep = steepest descent
minimization)
emtol= 10.0  ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps= 50  ; Maximum number of (minimization) steps to
perform
define = -DFLEXIBLE

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist   = 1; Frequency to update the neighbor
list and long range forces
cutoff-scheme   = Verlet
ns_type= grid; Method to determine neighbor list
(simple, grid)
coulombtype= PME; Treatment of long range electrostatic
interactions
rcoulomb= 1.0; Short-range electrostatic cut-off
rvdw= 1.0; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

## topol.top


#include "oplsaa.ff/forcefield.itp"


#include "ff_BM.itp"
#include "BM.itp"
#include "Cl.itp"

; Include water topology
#include "oplsaa.ff/tip3p.itp"

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

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

[system]
BM Cl

[molecules]
BM1
Cl  1
SOL   857
-- 
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