Re: [gmx-users] POPC: Fatal error:

[shakira shukoor]

Hi
The error states that the number of POPC molecules in your configuration
file and that mentioned in your topology files are not same. The number
refers to the total number of atoms.

On Wed, Apr 29, 2020 at 6:20 PM Dutta, Kunal  wrote:

> Dear Friends,
> I'm trying to learn Tutorial 2: KALP15 in DPPC
> 
> The FOLLOWING PROBLEM APPEARS:
>
> "
> GROMACS:  gmx grompp, version 2018.1
> Executable:   /usr/bin/gmx
> Data prefix:  /usr
> Working dir:  /home/kunal/Documents/MD_Simulation/B2AR in POPC
> Command line:
> gmx grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o popc.tpr
>
>
> NOTE 1 [file minim.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 -2044757183
> Generated 837 of the 2346 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'POPC'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> ---
> Program: gmx grompp, version 2018.1
> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 619)
>
>
>
> *Fatal error:number of coordinates in coordinate file (popc128a.pdb,
> 14036) does not match topology (topol_popc.top, 17621)*
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> "
>
> Thank you for your kind help.
> Sincerely,
> Kunal
>
> --
> *--Every life is precious*
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Re: [gmx-users] Quick question: is TIP3P water model available in GROMOS54a7 force field?

[shakira shukoor]

Hi
As far as I know tip3p water model is modelled to use in combination with
CHARMM force field. However there is nothing wrong in using TIP3P in
combination with GROMOS force field. And u will have both the bonded and
non bonded parameters of that specific water model in tip3p,itp file
itself. You don't have to get it from the force field. Instead you have to
add this itp file to the defined topology file you are giving.

On Tue, Apr 28, 2020 at 4:29 AM Wei-Tse Hsu  wrote:

> Dear gmx users,
> I prepared a topology using Open Forcefiled for my system. To make GROMACS
> able to recognize the water molecules and the ions to be added, I need to
> include itp files (such as tip3p.itp, spc.itp, ions.itp, etc.) in my
> topology file (.top file). I was planning to use GROMOS54a7 with TIP3P
> water model, so I add the following lines to my topology file:
>
> ; Include water topology
> #include "gromos54a7.ff/tip3p.itp"
>
> In gromos54a7.ff, there is indeed a tip3p.itp file. However, getting the
> error of " Atomtype OWT3 not found", I later found that OWT3 was not
> defined in ffnonbonded.itp. I also tried pdb2gmx command using other system
> and chose gromos54a7 force field, but there is no option for selecting
> TIP3P water model. Therefore, I wonder if TIP3P water model is actually not
> available in GROMOS54a7 force field even if there is a tip3p.itp in
> gromos54a7.ff. I might just use SPC water model instead, but I want to make
> sure that my understanding is correct. Thank you!
>
> Best,
> Wei-Tse
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Re: [gmx-users] (no subject)

[shakira shukoor]

Thanks christian for the detailed description.

On Mon, Feb 17, 2020 at 8:00 PM Christian Blau  wrote:

> Hi Shakkira,
>
>
> The simulation box deformation is described by six parameters that
> describe three basis box vectors with the following
> contraints,
>
>   - the first box vector is aligned along the x-axis, with coordinates
> thus has coordinates (xx,0,0)
>
>   - the second box vector is aligned in the x-y plane with coordinates
> (yx,yy,0)
>
>   - the third box vector is free (zx,zy,zz)
>
>
> The six parameters that you give in .mdp files are in the following order
>
> xx, yy, zz, yx, zx, zy
>
>
> The corrent box is then calculated as
>
> box(t_start)+(t-t_start)*deform
>
>
> For more information have a look at the gromacs manual mdp parameter
> description:
>
> http://manual.gromacs.org/current/user-guide/mdp-options.html
>
> under non-equilibrium MD:
>
> (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
> The velocities of deformation for the box elements: a(x) b(y) c(z)
> b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
> is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
> elements are corrected for periodicity. The coordinates are
> transformed accordingly. Frozen degrees of freedom are (purposely)
> also transformed. The time ts is set to t at the first step and at
> steps at which x and v are written to trajectory to ensure exact
> restarts. Deformation can be used together with semiisotropic or
> anisotropic pressure coupling when the appropriate
> compressibilities are set to zero. The diagonal elements can be
> used to strain a solid. The off-diagonal elements can be used to
> shear a solid or a liquid.
>
>
> Best,
>
> Christian
>
> On 2020-02-16 12:12, shakira shukoor wrote:
> >Hi all
> > Can anyone help me with the DEFORM option in Gromacs to change the box
> > values?
> >
> >
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Department of Chemistry
sdmdlab.xyz
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Re: [gmx-users] DEFORM option in gromacs

[shakira shukoor]

I want to gradually decrease the box along xy direction in my simulation. I
m confused what does this six values in the deform options mean?

On Sun, Feb 16, 2020 at 6:41 PM Justin Lemkul  wrote:

>
>
> On 2/16/20 1:44 AM, shakira shukoor wrote:
> > Hi all
> > Can anyone help me with the DEFORM option in Gromacs to change the box
> > values?
>
> What are you trying to do and what problem are you encountering?
>
> Please don't repeatedly post the same question. It often takes time for
> people to see posts and have time to reply, especially on weekends.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
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> ==
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Department of Chemistry
sdmdlab.xyz
IIT Patna
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[gmx-users] (no subject)

[shakira shukoor]

  Hi all
Can anyone help me with the DEFORM option in Gromacs to change the box
values?


-- 
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Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
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[gmx-users] DEFORM option in gromacs

[shakira shukoor]

Hi all
Can anyone help me with the DEFORM option in Gromacs to change the box
values?

-- 
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Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106
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Re: [gmx-users] problem while calculating order parameter

[shakira shukoor]

I guess you have not made your index file correctly. It should contain only
the group for which you will calculate the order parameter.

On Sat, Feb 15, 2020 at 3:21 PM Devargya Chakraborty <
devargyachakraborty@gmail.com> wrote:

> i want to calculate the order prameter between two carbon atom namrd C01
> and C03 in my topology file but while calculating, i am getting the
> following error.
>
>  Taking z axis as normal to the membrane
> Reading file nvt.tpr, VERSION 2019.1 (single precision)
> Using following groups:
> Groupname: System First atomname: C01 First atomnr 0
> Groupname: Other First atomname: C01 First atomnr 0
> Groupname: EMI First atomname: C01 First atomnr 0
> Groupname: NSC First atomname: NBT First atomnr 760
> Groupname: Water First atomname: OW First atomnr 1360
> Groupname: SOL First atomname: OW First atomnr 1360
> Groupname: non-Water First atomname: C01 First atomnr 0
> Groupname: C01 First atomname: C01 First atomnr 0
> Groupname: C04 First atomname: C04 First atomnr 1
> Groupname: C03 First atomname: C03 First atomnr 2
> Groupname: H07 First atomname: H07 First atomnr 3
> Groupname: H09 First atomname: H09 First atomnr 4
> Groupname: H08 First atomname: H08 First atomnr 5
> Groupname: C05 First atomname: C05 First atomnr 6
> Groupname: H0B First atomname: H0B First atomnr 7
> Groupname: H0C First atomname: H0C First atomnr 8
> Groupname: H0D First atomname: H0D First atomnr 9
> Groupname: N00 First atomname: N00 First atomnr 10
> Groupname: C06 First atomname: C06 First atomnr 11
> Groupname: H0F First atomname: H0F First atomnr 12
> Groupname: C0N First atomname: C0N First atomnr 13
> Groupname: H0O First atomname: H0O First atomnr 14
> Groupname: H0P First atomname: H0P First atomnr 15
> Groupname: H0Q First atomname: H0Q First atomnr 16
> Groupname: N02 First atomname: N02 First atomnr 17
> Groupname: H0E First atomname: H0E First atomnr 18
> Groupname: NBT First atomname: NBT First atomnr 760
> Groupname: SBT First atomname: SBT First atomnr 761
> Groupname: OBT First atomname: OBT First atomnr 763
> Groupname: CBT First atomname: CBT First atomnr 764
> Groupname: F1 First atomname: F1 First atomnr 768
>
> Reading frame   0 time0.000   Number of elements in first group:
> 10360
>
> ---
> Program: gmx order, version 2019.1
> Source file: src/gromacs/gmxana/gmx_order.cpp (line 546)
>
> Fatal error:
> grp 1 does not have same number of elements as grp 1
>
> can anybody help.
>
> Thanks
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sdmdlab.xyz
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[gmx-users] Electron density profile calculation

[shakira shukoor]

Hi all
Is anyone familiar with Gromacs analysis of MARTINI modeled lipid bilayer
systems.
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Department of Chemistry
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[gmx-users] MARTINI forcefield

[shakira shukoor]

Hi all
Is anyone familiar about electron density profiles using gmx density for
lipid bilayer modeled with MARTINI forcefield in gromacs. I am confused
with the electrons.dat file to be provided with the calculations. What
should be the number of electrons to be provided in the calculations for
the MARTINI beads.
 Can anyone help me with the calculations?

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Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
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Re: [gmx-users] Error bar for umbrella sampling?

[shakira shukoor]

Error bar will be directly given from gmx wham by bootstrap method.

On Tue, Jan 14, 2020 at 8:13 AM Qing Lv  wrote:

> Thank you Alexander and Quyen. I will try these tools.
>
>
> Qing
>
>
>
>
>
> At 2020-01-14 01:01:31, "Александр Лашков"  wrote:
> >In pymbar package error estimate directly. Example usage this package for
> >umbrella sampling can be  found on github page for this package
> >Alexander
> >
> >пн, 13 янв. 2020 г., 17:35 Qing Lv :
> >
> >> Dear All,
> >>
> >>
> >> I wonder if the error bars are necessary for umbrella sampling in PMF
> >> calculation? If yes, how should the error bars be calculated? Need I do
> 2~3
> >> repeats (with different random initial velocites assigned)?
> >>
> >>
> >> Thanks,
> >> Qing
> >> --
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sdmdlab.xyz
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Re: [gmx-users] Which content is in gmx wham -hist output file?

[shakira shukoor]

That depends on your sampled positions which you will give as pull.xvg
files. And also there is -bins flag option in gmx wham where you can
mention the number of bins if you want to sample more.

On Fri, Jan 10, 2020 at 2:13 PM 변진영  wrote:

> Each column has 0.1nm binning distance or the other distance length??
>
>
> > 2020. 1. 10. 오후 5:28, shakira shukoor  작성:
> >
> > The different columns indicates the counts or probability of different
> > binning distances or the windows you have considered in the simulation.
> >
> > On Fri, Jan 10, 2020 at 1:55 PM 변진영  wrote:
> >
> >> Dear All,
> >> I have tried to run umbrella sampling with GROMACS.
> >> When I tried to analyze the umbrella sampling MD simulation result,  I
> >> used the module, gmx wham so that I got the result file named
> ‘histo.xvg’ .
> >> What I wonder is what does columns mean except the 1st. column(I know
> the
> >> 1st. column is reaction coordinate.)
> >> I think that roughly the other columns except the 1st. Columns mean the
> >> counts or probability for each reaction coordinate, but I don’t know
> what
> >> the columns suggested in detail.
> >>
> >> Do you know what they are
> >>
> >> Thank you
> >> --
> >> 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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> >> send a mail to gmx-users-requ...@gromacs.org.
> >
> >
> >
> > --
> > *Best Regards*
> >
> > Shakkira E
> > PhD student INSPIRE Scholar
> > Department of Chemistry
> > sdmdlab.xyz
> > IIT Patna
> > Bihta
> > Patna 801106
> > --
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PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
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Patna 801106
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Re: [gmx-users] Which content is in gmx wham -hist output file?

[shakira shukoor]

The different columns indicates the counts or probability of different
binning distances or the windows you have considered in the simulation.

On Fri, Jan 10, 2020 at 1:55 PM 변진영  wrote:

> Dear All,
> I have tried to run umbrella sampling with GROMACS.
> When I tried to analyze the umbrella sampling MD simulation result,  I
> used the module, gmx wham so that I got the result file named ‘histo.xvg’ .
> What I wonder is what does columns mean except the 1st. column(I know the
> 1st. column is reaction coordinate.)
> I think that roughly the other columns except the 1st. Columns mean the
> counts or probability for each reaction coordinate, but I don’t know what
> the columns suggested in detail.
>
> Do you know what they are
>
> Thank you
> --
> Gromacs Users mailing list
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> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106
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Re: [gmx-users] GROMOS forcefields

[shakira shukoor]

Thank you for such a detailed response. The explanation was very helpful.

On Sat, Jan 4, 2020 at 10:00 PM Kenny Goossens 
wrote:

> Hi Shakkira,
>
> In each of the consecutice iterations of the GROMOS force field, a
> reparameterization of the constants was performed in order to reproduce
> experimental data for various molecules (in the case of the GROMOS suite,
> parameterization is mainly fitted to free enthalpy of solvation). For
> GROMOS54a7, the focus was on improving behaviour of amino acids. Older
> iterations of the force field have less parameters, and are in general less
> accurate. This depends on the system you are working with, however. The
> first number (43,56,...) stands for the number of atom types in the force
> field, the last number stands for the iteration of the force field. Also
> not that A and B versions are designed for different types of applications.
>
> I would advise you to look into the literature on the parameterization of
> the force fields to get an idea of the improvements/changes in every
> iteration of the force field. Furthermore, beware as the GROMOS force field
> does not always show the intended behavior in newer versions of Gromacs,
> and extra caution has to be taken in deciding on the simulation conditions.
> The issues are illustrated i.e. in Reißer 2017m JCTC
> (10.1021/acs.jctc.7b00178) And Silva et al 2018 JCTC
> (10.1021/acs.jctc.8b00758). As far as I'm aware, the Gromacs team has
> decided to discontinue support for GROMOS in the future for this reason.
>
> With kind regards,
> __
> Kenneth Goossens, PhD student
> Laboratory of Medicinal Chemistry (Building A - Room 2.13)
> University of Antwerp - Campus Drie Eiken
> Universiteitsplein 1
> B-2610 Wilrijk
> Belgium
>
>
> 
> Van: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> namens shakira shukoor
> 
> Verzonden: zaterdag 4 januari 2020 16:23
> Aan: gromacs.org_gmx-users@maillist.sys.kth.se <
> gromacs.org_gmx-users@maillist.sys.kth.se>
> Onderwerp: [gmx-users] GROMOS forcefields
>
> Hi all
> Can anyone explain the different code seen in forcefields of GROMOS like
> 53A6, 54A7, 43a1,. what does these numbers mean?
>
> --
> *Best Regards*
>
> Shakkira E
> PhD student INSPIRE Scholar
> Department of Chemistry
> sdmdlab.xyz
> IIT Patna
> Bihta
> Patna 801106
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> Gromacs Users mailing list
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> * Please search the archive at
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> posting!
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-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106
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[gmx-users] GROMOS forcefields

[shakira shukoor]

Hi all
Can anyone explain the different code seen in forcefields of GROMOS like
53A6, 54A7, 43a1,. what does these numbers mean?

-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106
-- 
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[gmx-users] (no subject)

[shakira shukoor]

Dear all
I encountered with following error when running the umbrella sampling
simulation of a protein. What modification should I make in the pull code
to get rid of the error.

ERROR 1 [file npt_umbrella.mdp]:
  When the maximum distance from a pull group reference atom to other atoms
  in the group is larger than 0.5 times half the box size a centrally
  placed atom should be chosen as pbcatom. Pull group 1 is larger than that
  and does not have a specific atom selected as reference atom.

Pull group  natoms  pbc atom  distance at start  reference at t=0
   1   226   113
   2   226   339   1.396 nm  1.396 nm
Estimate for the relative computational load of the PME mesh part: 0.14
This run will generate roughly 13 Mb of data

Thanks in advance

-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106
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Gromacs Users mailing list

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[gmx-users] SIMtoEXP spftware

[shakira shukoor]

Hi
Can anyone guide me on genertaing sim extended file in gromcas to be used
in SIMtoEXP software.

-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106
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