Re: [gmx-users] Question on energygrps setting

[Justin Lemkul]

On 5/7/20 10:57 AM, Devargya Chakraborty wrote:

I think I couldn't frame the question correctly. Let's say I have a silica
surface and I have water droplet on it and after a proper nvt simulation I
want to calculate the interaction energy of the water droplet with the
surface then how can I use the energy grps option for analysis.


You would specify groups (with an index file or from default groups) e.g.

energygrps = SOL Surface

-Justin


Thanks
Devargya Chakraborty

On Thu 7 May, 2020, 8:23 PM Justin Lemkul,  wrote:



On 5/7/20 10:49 AM, Devargya Chakraborty wrote:

Suppose my system contains an anion a cation and water and I have done an
nvt simulation.after the completion I want to see the energy profile of

the

individual groups like the cation or the anion etc. Can anybody guide me
how to use the energy grps option in analysing that.

You wouldn't. The energygrps setting is specifically for computing
interaction energies between two groups. It cannot be used to give you
the energy of a group.

You could do that by extracting coordinates of interest from the
trajectory with trjconv, making a matching .tpr with convert-tpr, and
then using mdrun -rerun to recompute the energies. While you *can* do
this, note that these values will generally have no physical meaning.

-Justin


Thanks
Devargya Chakraborty

On Thu 7 May, 2020, 5:48 PM Justin Lemkul,  wrote:


On 5/6/20 6:31 PM, Lei Qian wrote:

Dear users,

I know interaction energy calculation is carried out via energygrps

setting

in mdp file.
Because free energy-related settings do not include this energygrps
setting, so I think this energygrps setting may NOT be related to free
energy settings.
Could I ask whether my idea is correct or not?

The two have nothing to do with one another. In general, energygrps
shouldn't be used during an MD simulation anyway, and should be treated
as an analysis method.

-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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==

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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--
==

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] Question on energygrps setting

[Devargya Chakraborty]

I think I couldn't frame the question correctly. Let's say I have a silica
surface and I have water droplet on it and after a proper nvt simulation I
want to calculate the interaction energy of the water droplet with the
surface then how can I use the energy grps option for analysis.

Thanks
Devargya Chakraborty

On Thu 7 May, 2020, 8:23 PM Justin Lemkul,  wrote:

>
>
> On 5/7/20 10:49 AM, Devargya Chakraborty wrote:
> > Suppose my system contains an anion a cation and water and I have done an
> > nvt simulation.after the completion I want to see the energy profile of
> the
> > individual groups like the cation or the anion etc. Can anybody guide me
> > how to use the energy grps option in analysing that.
>
> You wouldn't. The energygrps setting is specifically for computing
> interaction energies between two groups. It cannot be used to give you
> the energy of a group.
>
> You could do that by extracting coordinates of interest from the
> trajectory with trjconv, making a matching .tpr with convert-tpr, and
> then using mdrun -rerun to recompute the energies. While you *can* do
> this, note that these values will generally have no physical meaning.
>
> -Justin
>
> > Thanks
> > Devargya Chakraborty
> >
> > On Thu 7 May, 2020, 5:48 PM Justin Lemkul,  wrote:
> >
> >>
> >> On 5/6/20 6:31 PM, Lei Qian wrote:
> >>> Dear users,
> >>>
> >>> I know interaction energy calculation is carried out via energygrps
> >> setting
> >>> in mdp file.
> >>> Because free energy-related settings do not include this energygrps
> >>> setting, so I think this energygrps setting may NOT be related to free
> >>> energy settings.
> >>> Could I ask whether my idea is correct or not?
> >> The two have nothing to do with one another. In general, energygrps
> >> shouldn't be used during an MD simulation anyway, and should be treated
> >> as an analysis method.
> >>
> >> -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
> >>
> >> jalem...@vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==
> >>
> >> --
> >> 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
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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Re: [gmx-users] Question on energygrps setting

[Justin Lemkul]

On 5/7/20 10:49 AM, Devargya Chakraborty wrote:

Suppose my system contains an anion a cation and water and I have done an
nvt simulation.after the completion I want to see the energy profile of the
individual groups like the cation or the anion etc. Can anybody guide me
how to use the energy grps option in analysing that.


You wouldn't. The energygrps setting is specifically for computing 
interaction energies between two groups. It cannot be used to give you 
the energy of a group.


You could do that by extracting coordinates of interest from the 
trajectory with trjconv, making a matching .tpr with convert-tpr, and 
then using mdrun -rerun to recompute the energies. While you *can* do 
this, note that these values will generally have no physical meaning.


-Justin


Thanks
Devargya Chakraborty

On Thu 7 May, 2020, 5:48 PM Justin Lemkul,  wrote:



On 5/6/20 6:31 PM, Lei Qian wrote:

Dear users,

I know interaction energy calculation is carried out via energygrps

setting

in mdp file.
Because free energy-related settings do not include this energygrps
setting, so I think this energygrps setting may NOT be related to free
energy settings.
Could I ask whether my idea is correct or not?

The two have nothing to do with one another. In general, energygrps
shouldn't be used during an MD simulation anyway, and should be treated
as an analysis method.

-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Gromacs Users mailing list

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posting!

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send a mail to gmx-users-requ...@gromacs.org.



--
==

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Question on energygrps setting

[Devargya Chakraborty]

Suppose my system contains an anion a cation and water and I have done an
nvt simulation.after the completion I want to see the energy profile of the
individual groups like the cation or the anion etc. Can anybody guide me
how to use the energy grps option in analysing that.

Thanks
Devargya Chakraborty

On Thu 7 May, 2020, 5:48 PM Justin Lemkul,  wrote:

>
>
> On 5/6/20 6:31 PM, Lei Qian wrote:
> > Dear users,
> >
> > I know interaction energy calculation is carried out via energygrps
> setting
> > in mdp file.
> > Because free energy-related settings do not include this energygrps
> > setting, so I think this energygrps setting may NOT be related to free
> > energy settings.
> > Could I ask whether my idea is correct or not?
>
> The two have nothing to do with one another. In general, energygrps
> shouldn't be used during an MD simulation anyway, and should be treated
> as an analysis method.
>
> -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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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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Re: [gmx-users] Question on energygrps setting

[Justin Lemkul]

On 5/6/20 6:31 PM, Lei Qian wrote:

Dear users,

I know interaction energy calculation is carried out via energygrps setting
in mdp file.
Because free energy-related settings do not include this energygrps
setting, so I think this energygrps setting may NOT be related to free
energy settings.
Could I ask whether my idea is correct or not?


The two have nothing to do with one another. In general, energygrps 
shouldn't be used during an MD simulation anyway, and should be treated 
as an analysis method.


-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

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Re: [gmx-users] Question about Mean Square Displacement (MSD)

[Kevin Boyd]

Can you send links to the results Gromacs gives you and the results you're
getting, along with the code that you're using to calculate the MSD?

On Sun, Apr 19, 2020 at 2:38 AM Sina Omrani  wrote:

> *Message sent from a system outside of UConn.*
>
>
> Dear Kevin, Thanks for your suggestions but the problem is the difference
> between my answer and GROMACS in calculated MSD. I performed 6 ns
> simulation just for checking my MSD results and I'm not going to calculate
> the diffusion coefficient from it.
>
> On Sun, 19 Apr 2020 at 02:33, Kevin Boyd  wrote:
>
> > What are you trying to calculate MSD for? I doubt that would be
> sufficient
> > sampling to calculate the diffusion coefficient of anything except maybe
> > water. For lipids, you don't start getting accurate readings until you
> > reach a **lag** time of 10 ns, and you need 100s of ns of data to get a
> > good reading even at that lag time. That's with many lipids in a
> bilayer. I
> > don't have experience with calculating diffusion coefficients for
> > proteins, but I'd imagine you need microseconds of sampling, since
> they're
> > much slower tumblers and you usually only have one per simulation box.
> >
> > Your save rate is fine, and could be even more granular.
> >
> > On Sat, Apr 18, 2020 at 12:54 PM Sina Omrani 
> > wrote:
> >
> > > *Message sent from a system outside of UConn.*
> > >
> > >
> > > Thanks, Kevin,
> > > I am looking for the MSD vs lag plot. I use the saved frames that
> > specified
> > > in mdp file. Is that the problem? I saved positions every 10 ps for a
> > 6000
> > > ps simulation. should I lower this or is there another way for using
> more
> > > trajectories?
> > >
> > > On Sun, 19 Apr 2020 at 00:10, Kevin Boyd  wrote:
> > >
> > > > Hi,
> > > >
> > > > Are you talking about the reported diffusion coefficient or the MSD
> vs
> > > lag
> > > > plot? You should be very careful about where you fit. By default,
> > Gromacs
> > > > calculates MSDs at much longer lag times than you typically have good
> > > data
> > > > for. Use the -beginfit and -endfit options to restrict the fit to the
> > lag
> > > > times where the MSD plot is linear.
> > > >
> > > > >I use trjconv command and use the output .gro file
> > > >
> > > > This doesn't make much sense, how many frames are you analyzing?
> > > >
> > > >
> > > > On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth  >
> > > > wrote:
> > > >
> > > > > *Message sent from a system outside of UConn.*
> > > > >
> > > > >
> > > > > Unless you give you give details how you calculate the MSD it will
> > not
> > > be
> > > > > possible to help.
> > > > > Are you using unwrapped co-ordinates in your calculations for MSD?
> > > > >
> > > > > Arun
> > > > >
> > > > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani <
> sinaomran...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > > I am trying to post-processing my results and calculate MSD (mean
> > > > square
> > > > > > displacement) but my answer is different from the MSD value that
> > > > GROMACS
> > > > > > calculated. I use trjconv command and use the output .gro file. I
> > > tried
> > > > > to
> > > > > > understand the GROMACS code but I am not a good programmer. Is
> > there
> > > > any
> > > > > > specific detail except the Einstein relation in the manual?
> > > > > >
> > > > > > sorry if here is not the right place to ask this question.
> > > > > > Best regards.
> > > > > >
> > > > > > Sina Omrani.
> > > > > > --
> > > > > > 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
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> > > > > posting!
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> > or
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> > > > >
> > > > --
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> > >

Re: [gmx-users] Question about Mean Square Displacement (MSD)

[Sina Omrani]

Dear Kevin, Thanks for your suggestions but the problem is the difference
between my answer and GROMACS in calculated MSD. I performed 6 ns
simulation just for checking my MSD results and I'm not going to calculate
the diffusion coefficient from it.

On Sun, 19 Apr 2020 at 02:33, Kevin Boyd  wrote:

> What are you trying to calculate MSD for? I doubt that would be sufficient
> sampling to calculate the diffusion coefficient of anything except maybe
> water. For lipids, you don't start getting accurate readings until you
> reach a **lag** time of 10 ns, and you need 100s of ns of data to get a
> good reading even at that lag time. That's with many lipids in a bilayer. I
> don't have experience with calculating diffusion coefficients for
> proteins, but I'd imagine you need microseconds of sampling, since they're
> much slower tumblers and you usually only have one per simulation box.
>
> Your save rate is fine, and could be even more granular.
>
> On Sat, Apr 18, 2020 at 12:54 PM Sina Omrani 
> wrote:
>
> > *Message sent from a system outside of UConn.*
> >
> >
> > Thanks, Kevin,
> > I am looking for the MSD vs lag plot. I use the saved frames that
> specified
> > in mdp file. Is that the problem? I saved positions every 10 ps for a
> 6000
> > ps simulation. should I lower this or is there another way for using more
> > trajectories?
> >
> > On Sun, 19 Apr 2020 at 00:10, Kevin Boyd  wrote:
> >
> > > Hi,
> > >
> > > Are you talking about the reported diffusion coefficient or the MSD vs
> > lag
> > > plot? You should be very careful about where you fit. By default,
> Gromacs
> > > calculates MSDs at much longer lag times than you typically have good
> > data
> > > for. Use the -beginfit and -endfit options to restrict the fit to the
> lag
> > > times where the MSD plot is linear.
> > >
> > > >I use trjconv command and use the output .gro file
> > >
> > > This doesn't make much sense, how many frames are you analyzing?
> > >
> > >
> > > On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth 
> > > wrote:
> > >
> > > > *Message sent from a system outside of UConn.*
> > > >
> > > >
> > > > Unless you give you give details how you calculate the MSD it will
> not
> > be
> > > > possible to help.
> > > > Are you using unwrapped co-ordinates in your calculations for MSD?
> > > >
> > > > Arun
> > > >
> > > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani 
> > > > wrote:
> > > >
> > > > > Hi,
> > > > > I am trying to post-processing my results and calculate MSD (mean
> > > square
> > > > > displacement) but my answer is different from the MSD value that
> > > GROMACS
> > > > > calculated. I use trjconv command and use the output .gro file. I
> > tried
> > > > to
> > > > > understand the GROMACS code but I am not a good programmer. Is
> there
> > > any
> > > > > specific detail except the Einstein relation in the manual?
> > > > >
> > > > > sorry if here is not the right place to ask this question.
> > > > > Best regards.
> > > > >
> > > > > Sina Omrani.
> > > > > --
> > > > > 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
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> > > > posting!
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> > > >
> > > --
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Re: [gmx-users] Question about Mean Square Displacement (MSD)

[Kevin Boyd]

What are you trying to calculate MSD for? I doubt that would be sufficient
sampling to calculate the diffusion coefficient of anything except maybe
water. For lipids, you don't start getting accurate readings until you
reach a **lag** time of 10 ns, and you need 100s of ns of data to get a
good reading even at that lag time. That's with many lipids in a bilayer. I
don't have experience with calculating diffusion coefficients for
proteins, but I'd imagine you need microseconds of sampling, since they're
much slower tumblers and you usually only have one per simulation box.

Your save rate is fine, and could be even more granular.

On Sat, Apr 18, 2020 at 12:54 PM Sina Omrani  wrote:

> *Message sent from a system outside of UConn.*
>
>
> Thanks, Kevin,
> I am looking for the MSD vs lag plot. I use the saved frames that specified
> in mdp file. Is that the problem? I saved positions every 10 ps for a 6000
> ps simulation. should I lower this or is there another way for using more
> trajectories?
>
> On Sun, 19 Apr 2020 at 00:10, Kevin Boyd  wrote:
>
> > Hi,
> >
> > Are you talking about the reported diffusion coefficient or the MSD vs
> lag
> > plot? You should be very careful about where you fit. By default, Gromacs
> > calculates MSDs at much longer lag times than you typically have good
> data
> > for. Use the -beginfit and -endfit options to restrict the fit to the lag
> > times where the MSD plot is linear.
> >
> > >I use trjconv command and use the output .gro file
> >
> > This doesn't make much sense, how many frames are you analyzing?
> >
> >
> > On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth 
> > wrote:
> >
> > > *Message sent from a system outside of UConn.*
> > >
> > >
> > > Unless you give you give details how you calculate the MSD it will not
> be
> > > possible to help.
> > > Are you using unwrapped co-ordinates in your calculations for MSD?
> > >
> > > Arun
> > >
> > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani 
> > > wrote:
> > >
> > > > Hi,
> > > > I am trying to post-processing my results and calculate MSD (mean
> > square
> > > > displacement) but my answer is different from the MSD value that
> > GROMACS
> > > > calculated. I use trjconv command and use the output .gro file. I
> tried
> > > to
> > > > understand the GROMACS code but I am not a good programmer. Is there
> > any
> > > > specific detail except the Einstein relation in the manual?
> > > >
> > > > sorry if here is not the right place to ask this question.
> > > > Best regards.
> > > >
> > > > Sina Omrani.
> > > > --
> > > > 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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> or
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> > > >
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Re: [gmx-users] Question about Mean Square Displacement (MSD)

[Sina Omrani]

Thanks, Kevin,
I am looking for the MSD vs lag plot. I use the saved frames that specified
in mdp file. Is that the problem? I saved positions every 10 ps for a 6000
ps simulation. should I lower this or is there another way for using more
trajectories?

On Sun, 19 Apr 2020 at 00:10, Kevin Boyd  wrote:

> Hi,
>
> Are you talking about the reported diffusion coefficient or the MSD vs lag
> plot? You should be very careful about where you fit. By default, Gromacs
> calculates MSDs at much longer lag times than you typically have good data
> for. Use the -beginfit and -endfit options to restrict the fit to the lag
> times where the MSD plot is linear.
>
> >I use trjconv command and use the output .gro file
>
> This doesn't make much sense, how many frames are you analyzing?
>
>
> On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth 
> wrote:
>
> > *Message sent from a system outside of UConn.*
> >
> >
> > Unless you give you give details how you calculate the MSD it will not be
> > possible to help.
> > Are you using unwrapped co-ordinates in your calculations for MSD?
> >
> > Arun
> >
> > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani 
> > wrote:
> >
> > > Hi,
> > > I am trying to post-processing my results and calculate MSD (mean
> square
> > > displacement) but my answer is different from the MSD value that
> GROMACS
> > > calculated. I use trjconv command and use the output .gro file. I tried
> > to
> > > understand the GROMACS code but I am not a good programmer. Is there
> any
> > > specific detail except the Einstein relation in the manual?
> > >
> > > sorry if here is not the right place to ask this question.
> > > Best regards.
> > >
> > > Sina Omrani.
> > > --
> > > 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] Question about Mean Square Displacement (MSD)

[Kevin Boyd]

Hi,

Are you talking about the reported diffusion coefficient or the MSD vs lag
plot? You should be very careful about where you fit. By default, Gromacs
calculates MSDs at much longer lag times than you typically have good data
for. Use the -beginfit and -endfit options to restrict the fit to the lag
times where the MSD plot is linear.

>I use trjconv command and use the output .gro file

This doesn't make much sense, how many frames are you analyzing?


On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth  wrote:

> *Message sent from a system outside of UConn.*
>
>
> Unless you give you give details how you calculate the MSD it will not be
> possible to help.
> Are you using unwrapped co-ordinates in your calculations for MSD?
>
> Arun
>
> On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani 
> wrote:
>
> > Hi,
> > I am trying to post-processing my results and calculate MSD (mean square
> > displacement) but my answer is different from the MSD value that GROMACS
> > calculated. I use trjconv command and use the output .gro file. I tried
> to
> > understand the GROMACS code but I am not a good programmer. Is there any
> > specific detail except the Einstein relation in the manual?
> >
> > sorry if here is not the right place to ask this question.
> > Best regards.
> >
> > Sina Omrani.
> > --
> > 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] Question about Mean Square Displacement (MSD)

[Arun Srikanth]

Unless you give you give details how you calculate the MSD it will not be
possible to help.
Are you using unwrapped co-ordinates in your calculations for MSD?

Arun

On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani  wrote:

> Hi,
> I am trying to post-processing my results and calculate MSD (mean square
> displacement) but my answer is different from the MSD value that GROMACS
> calculated. I use trjconv command and use the output .gro file. I tried to
> understand the GROMACS code but I am not a good programmer. Is there any
> specific detail except the Einstein relation in the manual?
>
> sorry if here is not the right place to ask this question.
> Best regards.
>
> Sina Omrani.
> --
> Gromacs Users mailing list
>
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Re: [gmx-users] Question on running gmx trjconv without 2 prompts

[Lei Qian]

Thank you Dr. Lemkul, these two websites are very helpful. Thanks!

On Thu, Apr 16, 2020 at 8:17 PM Justin Lemkul  wrote:

>
>
> On 4/16/20 8:12 PM, Lei Qian wrote:
> > Dear users,
> >
> > Could I ask: how to run gmx trjconv without 2 prompts?
> > I select 'Protein' to center, and 'System' to output.
> >
> > I put indexes of 'Protein' and 'System' into 1 .ndx file, add -n
> > Protein_System.ndx to gmx trjconv command, however, Gromacs cannot do the
> > selection automatically and asked me to choose from 'Protein' or
> 'System'.
>
> http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
>
> -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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] Question on running gmx trjconv without 2 prompts

[Justin Lemkul]

On 4/16/20 8:12 PM, Lei Qian wrote:

Dear users,

Could I ask: how to run gmx trjconv without 2 prompts?
I select 'Protein' to center, and 'System' to output.

I put indexes of 'Protein' and 'System' into 1 .ndx file, add -n
Protein_System.ndx to gmx trjconv command, however, Gromacs cannot do the
selection automatically and asked me to choose from 'Protein' or 'System'.


http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Question about gromacs mailing list

[Alessandra Villa]

Hi,

On Thu, Feb 6, 2020 at 4:02 AM Amit Kumar  wrote:

> Dear gromacs users,
> After subscribing to the gromacs mailing list I am getting only daily
> digest, I am not getting a question-answer thread, so posting my question
> once I cannot reply in the thread.
>
>
You have probably selected "digest mode" when you enrolled in the
mailing-list. You could change this setting by login to the subscription
page.
To do that use the link you find in the welcome email that you got once you
enrolled.
In your case should be something like

https://maillist.sys.kth.se/mailman/options/gromacs.org_gmx-users/ak543714%40gmail.com


Best regards
Alessandra
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Re: [gmx-users] question on dihedrals propers func 3 and impropers func 1

[Alan]

Which version of ACPYPE are you using? Please, get the latest here:
https://github.com/alanwilter/acpype

Check also about option:

-z, --gmx4write RB dihedrals old GMX 4.0

Thanks for using ACPYPE!

Alan

On Sat, 1 Feb 2020 at 18:21, Lei Qian  wrote:

> Dear users,
>
> Could I ask a question on dihedrals func types? Thanks!
>
> I used acpype to convert prmtop file and inpcrd file into gromacs files.
> However, in new generated top file,
> The dihedrals propers func is 3. and The dihedrals impropers func is 1.
>
> These two func types are different from propers func 9 and impropers func
> 4.
> (func type 9 and func type 4 can be found in Gromacs documents).
>
> Could I ask the meaning of func type 3 and func type 1 ?
>
> Thanks!
> Lei
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And many thanks!
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Re: [gmx-users] question regarding gmx helix orientation

[SHAHEE ISLAM]

hello,
by using gmx gangle, i am trying to calculate the angle between protein and
bilayer,
gmx gangle -f *.xtc -s *.tpr -n *.ndx -g1 vector -g2 plane -group1 -group2.
but the error i am getting is
Number of positions in selection 1 in the first group not divisible by 2
my questions are
1. how can i select the index file so that angle will be calculated between
protein and bilayer.
2. should i mention group name in the gmx gangle calculation command.
the total atoms of protein is 283
and for bilayer it is 9360.

thanking you
shahee

On Sat, Dec 14, 2019 at 6:23 AM Justin Lemkul  wrote:

>
>
> On 12/13/19 7:06 AM, SHAHEE ISLAM wrote:
> > Yes ,I am using cg model.
>
> Use gmx gangle.
>
> -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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] Question about the SASA value per residue

[Justin Lemkul]

On 12/27/19 2:36 PM, Pandya, Akash wrote:

Hi all,

I have a quick question about the value obtained for the SASA calculation on a 
per residue basis (-or flag). Is this value the absolute SASA for each residue?


Yes.

-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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Re: [gmx-users] question regarding gmx helix orientation

[Justin Lemkul]

On 12/13/19 7:06 AM, SHAHEE ISLAM wrote:

Yes ,I am using cg model.


Use gmx gangle.

-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] question regarding gmx helix orientation

[SHAHEE ISLAM]

Yes ,I am using cg model.

On Dec 13, 2019 2:37 PM, "Alessandra Villa" <
alessandra.villa.bio...@gmail.com> wrote:

Hi,

On Thu, Dec 12, 2019 at 1:09 PM SHAHEE ISLAM  wrote:

> hi,
> i want to calculate the tilt angle of helix against the bilayer normal.
> First i made a index file which contains the backbone of the residues of
> large helix. I am using this command
> *gmx helixorient -s *.tpr -f *.xtc -n helix.ndx -oaxis -ocenter -orise
> -oradius -otwist -obending -otilt -orot*
> my questions are
>
> 1. Should i mention any other residues in index file so that the angle can
> be calculated along the bilayer normal.
>

As far as I know, four Calpha coordinates are used to define the local
direction of the helix
axis (
http://manual.gromacs.org/current/onlinehelp/gmx-helixorient.html?highlight=
gmx%20helixorient
)
. but I am not sure to what those Calphas correspond since you are using a
CG model.

Best regards
Alessandra

2. by using this command i am able to analyse for 1 us coarse grained
> simulation. But for the next 1 us run i am getting this error
> "too many iterations in routine jacobi"
> can anyone please guide me.
> thanking you
> shahee
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Re: [gmx-users] question regarding gmx helix orientation

[Alessandra Villa]

Hi,

On Thu, Dec 12, 2019 at 1:09 PM SHAHEE ISLAM  wrote:

> hi,
> i want to calculate the tilt angle of helix against the bilayer normal.
> First i made a index file which contains the backbone of the residues of
> large helix. I am using this command
> *gmx helixorient -s *.tpr -f *.xtc -n helix.ndx -oaxis -ocenter -orise
> -oradius -otwist -obending -otilt -orot*
> my questions are
>
> 1. Should i mention any other residues in index file so that the angle can
> be calculated along the bilayer normal.
>

As far as I know, four Calpha coordinates are used to define the local
direction of the helix
axis (
http://manual.gromacs.org/current/onlinehelp/gmx-helixorient.html?highlight=gmx%20helixorient
)
. but I am not sure to what those Calphas correspond since you are using a
CG model.

Best regards
Alessandra

2. by using this command i am able to analyse for 1 us coarse grained
> simulation. But for the next 1 us run i am getting this error
> "too many iterations in routine jacobi"
> can anyone please guide me.
> thanking you
> shahee
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Re: [gmx-users] Question: How to delete water

[Justin Lemkul]

On 12/11/19 5:43 AM, John Whittaker wrote:

To add on to your answer, Justin:

The usage listed in the tutorial instructs you to use the "-nwater" flag
to specify the number of atoms in a water molecule.

The actual script uses "-water" as a flag, without the "n". I noticed this
in a previous version of the script before the usage in the help message
was changed.

Just letting you know that the command on the tutorial page:

(http://www.mdtutorials.com/gmx/membrane_protein/03_solvate.html)

is different than the correct command, but only for that one flag.


Fixed, thank you!

-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Question: How to delete water

[John Whittaker]

To add on to your answer, Justin:

The usage listed in the tutorial instructs you to use the "-nwater" flag
to specify the number of atoms in a water molecule.

The actual script uses "-water" as a flag, without the "n". I noticed this
in a previous version of the script before the usage in the help message
was changed.

Just letting you know that the command on the tutorial page:

(http://www.mdtutorials.com/gmx/membrane_protein/03_solvate.html)

is different than the correct command, but only for that one flag.

- John

>
>
> On 12/10/19 8:24 PM, 변진영 wrote:
>> Dear All,
>> I have gone through the Justin Lemku tutorial for KALP_15 in DPPC. I
>> have reach the last command line in step3 and faced one problem.
>> When I tried  to delete water in my system by running the command line:
>>
>>   Perl water_deletor.pl -in system_solv.gro -out system_solv.fix.gro
>> -ref 033 -middle C50 -nwater 3
>
> Your problem is you are specifying the reference atom as 033
> (zero-three-three) instead of O33 (oh-thre-three, for Oxygen). Hence, no
> reference atoms are found and the bilayer can't be subdivided.
>
> -Justin
>
>> The result message says that
>>
>>   Starting water deletion process…
>>   Option -nwater not set, assuming 3 atoms in the water model.
>>   Defining the middle of the bilayer as z = 3.27570634920635.
>>   ntop = 0
>>   Illegal division by zero at water_deletor.pl line 219.
>>
>> The tutorial said that the -nwater flag defines how many atoms
>> constitute a water molecule and for SPC, there are 3 atoms and so I used
>> the -nwater option in my command line.
>> But the message says “Option -nwater not set, assuming 3 atom in the
>> water model.” How can I set the -nwater option?
>> Any idea on what caused this problem?
>>
>> -Jinyoung
>
> --
> ==
>
> 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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] Question: How to delete water

[Justin Lemkul]

On 12/10/19 8:24 PM, 변진영 wrote:

Dear All,
I have gone through the Justin Lemku tutorial for KALP_15 in DPPC. I have reach 
the last command line in step3 and faced one problem.
When I tried  to delete water in my system by running the command line:
  
  Perl water_deletor.pl -in system_solv.gro -out system_solv.fix.gro -ref 033 -middle C50 -nwater 3


Your problem is you are specifying the reference atom as 033 
(zero-three-three) instead of O33 (oh-thre-three, for Oxygen). Hence, no 
reference atoms are found and the bilayer can't be subdivided.


-Justin


The result message says that

  Starting water deletion process…
  Option -nwater not set, assuming 3 atoms in the water model.
  Defining the middle of the bilayer as z = 3.27570634920635.
  ntop = 0
  Illegal division by zero at water_deletor.pl line 219.

The tutorial said that the -nwater flag defines how many atoms constitute a 
water molecule and for SPC, there are 3 atoms and so I used the -nwater option 
in my command line.
But the message says “Option -nwater not set, assuming 3 atom in the water 
model.” How can I set the -nwater option?
Any idea on what caused this problem?

-Jinyoung


--
==

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Question about switching off non-bonded interactions between two molecules for MD simulation

[Alessandra Villa]

Hi,

As far as I understood, you have a protein and ligand (not covalently
bonded) and you want to switch off the interaction
between one aminoacid and the ligand.

Concerning approach 1,
If you have a merged topology (only one topology file with one [molecular
type] in your case  protein and ligand -  see pdb2gmx for more info)
[ exclusions] should working.
(see
http://manual.gromacs.org/current/reference-manual/topologies/molecule-definition.html?highlight=exclusion
)

Concerning approach 2,  you need only energygrp-excl  =  A B ( the group A
and B are already defined ) and you do not want to calculate the energy
between 2 groups
 ("energygrps"  group(s) for which to write short-ranged non-bonded
potential energies to the energy file)

Best regards
 Alessandra

On Wed, Nov 13, 2019 at 8:23 PM Soomin Choi  wrote:

> Dear GROMACS users,
>
> I am new to GROMACS software and have a question about switching off
> pair-wise non-bonded interactions between two molecules.
> I have a simulation box composed of a protein with a substrate inside the
> protein catalytic pocket and there are no covalent bonds between protein
> amino acids and a substrate. I would like to run MD simulation of this
> system after switching off non-bonded interactions between one of the amino
> acids and a substrate (leaving all intra non-bonded interactions & inter
> non-bonded interactions between given amino acids and other amino acids). I
> would appreciate it a lot if you could guide me on how to do this. Below
> are approaches I tried but got warning/error messages:
>
> Approach 1) use [exlucsions] in .top file
> If, let's say, atom # 1,2,3 are for the amino acid and atom# 4,5 is for a
> substrate, I added:
> [ exclusions]
> 1  4 5
> 2  4 5
> 3  4 5
> I have successfully obtained .tpr file from grompp but got a fatal error
> after mdrun:
> 'There is no domain decomposition for 448 ranks that is compatible with the
> given box and a minimum cell size of 25.3862 nm. Change the number of ranks
> or mdrun option -rdd or -dds'
>
> Approach 2) use energygrps and energygrp-excl in .mdp file
> If the name in the index for the amino acid and substrate is A and B
> respectively, I added:
> energygrps  = A B
> energygrp-excl  =  A B
> Also, I knew that energygrp-excl does not support Verlet cut-off scheme, I
> used a 'group'. However, I have got an error message when I used grompp:
> 'The sum of the two largest charge group radii (33.381752) is larger than
> rlist (1.20)'
>
> Just to be clear below is a summary of my system:
> - a system composed of one protein and a small substrate
> - the substrate and amino acid that I would like to switch-off are charged
> (+1 and -1, respectively)
> - protein-substrate complex are solvated in TIP3P waters, total # of atoms
> in the system = ~450,000
>
> First of all, I am not sure whether these approaches are correct to
> switch-off non-bonded interactions between two molecules. Second, if so, I
> would like to know how to correct these issues.
>
> Sincerely,
>
> Soomin
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Re: [gmx-users] Question about default auto setting of mdrun -pin

[aeszter]

On Fri, Oct 18, 2019 at 04:54:49PM +0200, Szilárd Páll wrote:
> 
> The source of total number of hardware threads should not be OpenMP but a
> system call or hwloc -- which should (and was IIRC a while ago at least)
> checked agianst the  gmx_omp_nthreads_get() value.

Yes, that's correct. The number of *hw threads* is determined from
hwloc (if it's compiled in), and the number of mdrun threads is from
OpenMP.

However, the default assumption of OpenMP is that you have the whole
node, and mdrun then concludes that pinning is OK.

A.

-- 
Ansgar Esztermann
Sysadmin Dep. Theoretical and Computational Biophysics
http://www.mpibpc.mpg.de/grubmueller/esztermann
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Re: [gmx-users] Question about default auto setting of mdrun -pin

[Szilárd Páll]

On Fri, Oct 18, 2019 at 4:36 PM  wrote:

> On Thu, Oct 17, 2019 at 10:34:39AM +, Kutzner, Carsten wrote:
> >
> > is it intended that the thread-MPI version of mdrun 2018 does pin to its
> core
> > if started with -nt 1 -pin auto?
>

No, I don't think that's intended.


>
> I think I have a (partial) idea about what's happening.
> get_thread_affinity_layout() performs various checks to determin if
> pinning is possible, and for -pin auto, it looks at the number of
> mdrun threads vs hardware threads. However, the number of mdrun
> threads ultimately comes from gmx_omp_nthreads_get().
> Of course, if OMP_NUM_THREADS is unset, OpenMP will default to the
> whole machine, and the above check will always succeed. And sure
> enough, setting OMP_NUM_THREADS to 1 will turn off pinning in our test
> case.
>

The source of total number of hardware threads should not be OpenMP but a
system call or hwloc -- which should (and was IIRC a while ago at least)
checked agianst the  gmx_omp_nthreads_get() value.

If however the behavior you describe is actually reproducible, please do
file a bug report.

--
Szilárd


>
> A.
>
> --
> Ansgar Esztermann
> Sysadmin Dep. Theoretical and Computational Biophysics
> http://www.mpibpc.mpg.de/grubmueller/esztermann
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Re: [gmx-users] Question about gmx_wham

[Alexander Phillips]

Hi John,

I am trying to determine the binding energy of Vitamin E to various lipid
membranes by pulling it vertically out of the membrane and performing
umbrella sampling during this process.

There are three .mdp files I have but most of them use very similar pull
code, I will differentiate them by slashes
pull-rate1 = A / B / C
Where A B C are the three files
The first file is what I used to initially pull the Vitamin E, the second
file is the npt equilibration that Justin used, and the third is the
production run for umbrella sampling (that justin also used).

The pull code is as follows:

; Pull Code
pull = umbrella
pull-geometry = direction-periodic
pull-start = yes
pull-nstxout = 10
pull-nstfout = 10
pull-ngroups = 1
pull-group0 = Lipids
pull-group1 = PULLING_ATOC
pull-vec1 = 0 0 1
pull-rate1 = 0.00025 /  0 / 0
pull-k1 = 10

The only difference is that I disable the pull rate in the last two of the
three.



Also I installed grace and graphed it just fine, thanks!
Thank you for the paper about gmx_wham that will be very helpful moving
forward,

Alex

On Mon, 14 Oct 2019 at 11:27, John Whittaker <
johnwhitt...@zedat.fu-berlin.de> wrote:

> Hi,
>
> > Hello,
> >
> > I am currently running Umbrella Sampling simulations on Vitamin E (in
> > grommacs version 4.6.5). And I followed the tutorial done by Justin A.
> > Lemkul, however I am uncertain of a few things about the gmx_wham command
> > that he instructs us to use.
> >
> > Namely for the two output files, which by default are 'profile.xvg' and
> > 'histo.xvg'.
> > I was wondering for the profile.xvg file what does the X-axis refer to,
> as
> > it says 'z' in the output file however is that in Angstroms, Nanometers,
> > etc.
> > The graph I have goes to a value that doesn't make sense in context of my
> > simulation (goes to a Z of 70 towards the end which is larger than the
> > Z-axis of my simulation  if it was in Angstroms (did it account for
> > periodic boundary conditions?)).
>
> The x-axis of profile.xvg is whatever the reaction coordinate was for your
> umbrella sampling simulations. The reaction coordinate will change
> depending on what system you have and what you're trying to calculate. For
> example, in Justin's tutorial the reaction coordinate is the z-axis and
> what is outputted (in pullx.xvg) is the distance between the protofibril
> and "peptide A" calculated only in the z direction.
>
> You should post the pulling parameters from your .mdp file and describe
> what you're trying to learn about your system by doing umbrella sampling.
> Otherwise, it's hard to help.
>
> > Secondly I was wondering how to graph the histo.xvg file as I was having
> > issues using GNUPLOT, if I shouldn't use GNUPLOT what different graphing
> > program should I use?
>
> histo.xvg has many columns, not just 2 like you have from something like a
> pullx.xvg file. You're probably not plotting all the columns, but I'm not
> sure because you didn't specify what issue you're having.
>
> To get a quick idea of whether or not my histograms are overlapping, I
> normally just use Grace with a command like:
>
> xmgrace -nxy histo.xvg
>
> -nxy tells Grace to assume the data file is in X Y1 Y2 Y3 ... format so it
> plots all your histograms.
>
>
> > If there are pages where this information is readily available, please
> let
> > me know and I will use them, however I could not find them so I would
> like
> > your help.
> >
>
> maybe the gmx wham paper will be useful:
>
> http://cmb.bio.uni-goettingen.de/pub/Hub_JCTC2010.pdf
>
>
> > Thank You,
> > Alex
> > --
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> >
>
> - John
>
>
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Re: [gmx-users] Question about gmx_wham

[John Whittaker]

Hi,

> Hello,
>
> I am currently running Umbrella Sampling simulations on Vitamin E (in
> grommacs version 4.6.5). And I followed the tutorial done by Justin A.
> Lemkul, however I am uncertain of a few things about the gmx_wham command
> that he instructs us to use.
>
> Namely for the two output files, which by default are 'profile.xvg' and
> 'histo.xvg'.
> I was wondering for the profile.xvg file what does the X-axis refer to, as
> it says 'z' in the output file however is that in Angstroms, Nanometers,
> etc.
> The graph I have goes to a value that doesn't make sense in context of my
> simulation (goes to a Z of 70 towards the end which is larger than the
> Z-axis of my simulation  if it was in Angstroms (did it account for
> periodic boundary conditions?)).

The x-axis of profile.xvg is whatever the reaction coordinate was for your
umbrella sampling simulations. The reaction coordinate will change
depending on what system you have and what you're trying to calculate. For
example, in Justin's tutorial the reaction coordinate is the z-axis and
what is outputted (in pullx.xvg) is the distance between the protofibril
and "peptide A" calculated only in the z direction.

You should post the pulling parameters from your .mdp file and describe
what you're trying to learn about your system by doing umbrella sampling.
Otherwise, it's hard to help.

> Secondly I was wondering how to graph the histo.xvg file as I was having
> issues using GNUPLOT, if I shouldn't use GNUPLOT what different graphing
> program should I use?

histo.xvg has many columns, not just 2 like you have from something like a
pullx.xvg file. You're probably not plotting all the columns, but I'm not
sure because you didn't specify what issue you're having.

To get a quick idea of whether or not my histograms are overlapping, I
normally just use Grace with a command like:

xmgrace -nxy histo.xvg

-nxy tells Grace to assume the data file is in X Y1 Y2 Y3 ... format so it
plots all your histograms.


> If there are pages where this information is readily available, please let
> me know and I will use them, however I could not find them so I would like
> your help.
>

maybe the gmx wham paper will be useful:

http://cmb.bio.uni-goettingen.de/pub/Hub_JCTC2010.pdf


> Thank You,
> Alex
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>

- John


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Re: [gmx-users] question on system blow-up

[Lei Qian]

Hi John,

Thank you very much for your reply.

After checking my log file, it seems my Metal ion cannot form a stable
coordination bonds in simulation.
the first 10 missing interactions, except for exclusions:
   LJ-14 atoms 1180 1572   global  1180  1572
The number 1572 is my metal ion. And 1180 is an atom close to it in space.

Because it says "the first 10 missing interactions", but the file only
shows one missing interaction here LJ-14 atoms 1180 1572. It seems strange.
When I checked the trr file, the metal ion position shift away from its
normal position.
I will try to redo mcpb process.


On Fri, Sep 20, 2019 at 6:22 AM John Whittaker <
johnwhitt...@zedat.fu-berlin.de> wrote:

> Hi,
>
> > Dear gmx-users,
> >
> > Could I ask a question on system blow-up? Thanks!
> > I finished em, nvt, and npt. But when I ran production(npt) 10ns, I found
> > system blow up at around 1ns. ("atoms involved moved further apart than
> > the
> > multi-body cut-off distance")
> >
> > When I checked the trajectory files: nvt.trr, npt.trr, I found the
> > distorted water molecules (very very long H-O bond), although protein
> > looks
> > OK in these traj files. I guess perhaps those distorted water molecules
> > are
> > blow-up and they can gradually affect protein?
>
> It doesn't matter which molecule it is; if a molecule is blowing up, it
> will cause the simulation to fail. After visualizing your system, are you
> able to see what causes the elongated H-O bond? Are molecules overlapping?
> Are there other warnings (like LINCS warnings) in your output? You need to
> provide some more information about the system you are simulating or no
> one will really know how to help.
>
> >
> > I tried to change production npt setting to nvt (pcoupl = no), and change
> > integrator md to sd, change tau_t: 2.0 2.0. However, the following error
> > always show up:
> > "1 of the 20067 bonded interactions could not be calculated because some
> > atoms involved moved further apart than the multi-body cut-off distance
> > (1.18213 nm) or the two-body cut-off distance (1.241 nm)"
>
> These settings are likely not the cause of your problem and they probably
> wouldn't change much about the simulation consistently blowing up. When
> you make these changes, are the same molecules distorted?
>
> Best,
>
> John
>
> >
> > Thank you!
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
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> > posting!
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> >
>
>
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Re: [gmx-users] question on system blow-up

[John Whittaker]

Hi,

> Dear gmx-users,
>
> Could I ask a question on system blow-up? Thanks!
> I finished em, nvt, and npt. But when I ran production(npt) 10ns, I found
> system blow up at around 1ns. ("atoms involved moved further apart than
> the
> multi-body cut-off distance")
>
> When I checked the trajectory files: nvt.trr, npt.trr, I found the
> distorted water molecules (very very long H-O bond), although protein
> looks
> OK in these traj files. I guess perhaps those distorted water molecules
> are
> blow-up and they can gradually affect protein?

It doesn't matter which molecule it is; if a molecule is blowing up, it
will cause the simulation to fail. After visualizing your system, are you
able to see what causes the elongated H-O bond? Are molecules overlapping?
Are there other warnings (like LINCS warnings) in your output? You need to
provide some more information about the system you are simulating or no
one will really know how to help.

>
> I tried to change production npt setting to nvt (pcoupl = no), and change
> integrator md to sd, change tau_t: 2.0 2.0. However, the following error
> always show up:
> "1 of the 20067 bonded interactions could not be calculated because some
> atoms involved moved further apart than the multi-body cut-off distance
> (1.18213 nm) or the two-body cut-off distance (1.241 nm)"

These settings are likely not the cause of your problem and they probably
wouldn't change much about the simulation consistently blowing up. When
you make these changes, are the same molecules distorted?

Best,

John

>
> Thank you!
> --
> Gromacs Users mailing list
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> * Please search the archive at
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Re: [gmx-users] Question about distance restraints

[Justin Lemkul]

On 8/31/19 5:27 PM, Tanos Franca wrote:

    Dear users,

    I´m trying to run a MD simulation using different distance 
restraints for several pairs of atoms (example: 0.1 nm - 0.2 nm; 0.2 
nm - 0.3 nm, ...) but it´s not working. GROMACS is only accepting one 
range of restraint (example: 0.1 nm - 0.2 nm for all pairs) per 
simulation. If I try including different ranges I got fatal error 
mesage. Does someone knows how to run the different range of distances 
in the same MD simulation?




You will need to share all relevant topology snippets, commands, and 
exact error messages.


-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] question on ffG43a1p force field

[Justin Lemkul]

On 8/27/19 11:17 AM, Lei Qian wrote:

Hi Dr. Lemkul,

Thank you for your reply.
I have sent the links to you. Hope they could reach to you.
The links include three log files.
1. WT protein running for 1ns production step.(wall time: 1h40min).
2. WT protein running for 10ns production step (wall time: 6d09h17).
3. Mutant protein running for 1ns production step. (wall time: 17h30min).

 From the log, I can find each of them was run on one node with 24 cores.
It seems the wall times for all these three files do not have linearly
proportional relationship.


Please share the .log files with the list, not just with me.

-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] question on ffG43a1p force field

[Lei Qian]

Hi Dr. Lemkul,

Thank you for your reply.
I have sent the links to you. Hope they could reach to you.
The links include three log files.
1. WT protein running for 1ns production step.(wall time: 1h40min).
2. WT protein running for 10ns production step (wall time: 6d09h17).
3. Mutant protein running for 1ns production step. (wall time: 17h30min).

>From the log, I can find each of them was run on one node with 24 cores.
It seems the wall times for all these three files do not have linearly
proportional relationship.
Thanks for your time and help!
Lei















On Fri, Aug 23, 2019 at 3:42 PM Justin Lemkul  wrote:

>
>
> On 8/23/19 2:27 AM, Lei Qian wrote:
> > Thank you Dr. Lemkul,
> > I continued to use the GROMOS 43a1p for my simulation.
> >
> > I did simulation for 2 proteins separately: one is WT, the other one is
> its
> > one-residue mutant.
> > And I finished em, NVT, NPT and 1 ns Production (4 steps) for both
> proteins.
> >
> > However, I found for each of these 4 above steps, the wall time was a lot
> > more longer for mutant than WT protein.
> > Actually I used the same set of parameters for both proteins: e.g. same
> mdp
> > files for both protein in each step.
> > Both proteins get acceptable results after 100-step NVT, 100-step NPT
> etc.,
> > but the wall-time for mutant was much more longer than WT.
> > Could I ask the reason for this?
> > Sorry for this inconvenience. Thank you for your time and all your help!
>
> There is no way to know what is going on without seeing the .log files
> from the runs and knowing the commands you gave. If you want to share
> files, upload them to a file-sharing server and provide a link. The
> mailing list does not accept attachments.
>
> -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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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Re: [gmx-users] Question about Gromacs

[David van der Spoel]

Den 2019-08-26 kl. 20:53, skrev Najla Hosseini:

Dear David,

Hope you are doing well.
I am Gromacs user and I need to change the partial charge of molecules 
in force field or itp file as a function of distance during the run in 
Gromacs. Is it possible? How I should do that?
Please pose your questions on the mailing list, however this is not 
possible to dynamically.


If not, I should use two itp file with a condition for finishing one 
of them and starting the new tpr file based on another itp file, how I 
should do that?


Thank you so much.
I really appreciate your consideration and time.

Best Regards, Najla

--
/*Kind Regards,
*/
/*Najla *
/



--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se

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Re: [gmx-users] question on ffG43a1p force field

[Justin Lemkul]

On 8/23/19 2:27 AM, Lei Qian wrote:

Thank you Dr. Lemkul,
I continued to use the GROMOS 43a1p for my simulation.

I did simulation for 2 proteins separately: one is WT, the other one is its
one-residue mutant.
And I finished em, NVT, NPT and 1 ns Production (4 steps) for both proteins.

However, I found for each of these 4 above steps, the wall time was a lot
more longer for mutant than WT protein.
Actually I used the same set of parameters for both proteins: e.g. same mdp
files for both protein in each step.
Both proteins get acceptable results after 100-step NVT, 100-step NPT etc.,
but the wall-time for mutant was much more longer than WT.
Could I ask the reason for this?
Sorry for this inconvenience. Thank you for your time and all your help!


There is no way to know what is going on without seeing the .log files 
from the runs and knowing the commands you gave. If you want to share 
files, upload them to a file-sharing server and provide a link. The 
mailing list does not accept attachments.


-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] question on ffG43a1p force field

[Lei Qian]

Thank you Dr. Lemkul,
I continued to use the GROMOS 43a1p for my simulation.

I did simulation for 2 proteins separately: one is WT, the other one is its
one-residue mutant.
And I finished em, NVT, NPT and 1 ns Production (4 steps) for both proteins.

However, I found for each of these 4 above steps, the wall time was a lot
more longer for mutant than WT protein.
Actually I used the same set of parameters for both proteins: e.g. same mdp
files for both protein in each step.
Both proteins get acceptable results after 100-step NVT, 100-step NPT etc.,
but the wall-time for mutant was much more longer than WT.
Could I ask the reason for this?
Sorry for this inconvenience. Thank you for your time and all your help!
Lei








On Tue, Aug 20, 2019 at 8:23 AM Justin Lemkul  wrote:

>
>
> On 8/20/19 2:11 AM, Lei Qian wrote:
> > Thank you Dr. Lemkul,
> > Could I ask one more question? Thank you!
> >
> > When I did the step for adding ions and minimization and equilibration
> > steps, one warning always showed up.
> > So I had to add -maxwarn 2 after the command gmx grompp.
> > This warning is as follows:
> >
> > WARNING 1 [file topol.top, line 48]:
> >The GROMOS force fields have been parametrized with a physically
> >incorrect multiple-time-stepping scheme for a twin-range cut-off. When
> >used with a single-range cut-off (or a correct Trotter
> >multiple-time-stepping scheme), physical properties, such as the
> density,
> >might differ from the intended values. Check if molecules in your
> system
> >are affected by such issues before proceeding. Further information
> may be
> >available at https://redmine.gromacs.org/issues/2884.
> >
> > It seems this warning is related to the GROMOS force field (for
> > phosphorylation) you sent to me last week.
> > Could I disregard this warning?
>
> There are significant concerns about the reproducibility of GROMOS force
> fields. The authors of a recent study (
> https://pubs.acs.org/doi/10.1021/acs.jctc.8b00425) allege that GROMACS
> has bugs that affect results, but the GROMACS developers maintain that
> the GROMOS force fields were developed with incorrect algorithms in the
> GROMOS software (hence the warning, and see the related Redmine issue
> linked in the message).
>
> The issue is not specifically related to 43a1p (which is anyway an
> extremely old force field), but all of the GROMOS parameter sets.
>
> Proceed with caution. There are other force field options available that
> have been confirmed to work as expected across different software.
>
> -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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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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Re: [gmx-users] question on ffG43a1p force field

[Justin Lemkul]

On 8/20/19 2:11 AM, Lei Qian wrote:

Thank you Dr. Lemkul,
Could I ask one more question? Thank you!

When I did the step for adding ions and minimization and equilibration
steps, one warning always showed up.
So I had to add -maxwarn 2 after the command gmx grompp.
This warning is as follows:

WARNING 1 [file topol.top, line 48]:
   The GROMOS force fields have been parametrized with a physically
   incorrect multiple-time-stepping scheme for a twin-range cut-off. When
   used with a single-range cut-off (or a correct Trotter
   multiple-time-stepping scheme), physical properties, such as the density,
   might differ from the intended values. Check if molecules in your system
   are affected by such issues before proceeding. Further information may be
   available at https://redmine.gromacs.org/issues/2884.

It seems this warning is related to the GROMOS force field (for
phosphorylation) you sent to me last week.
Could I disregard this warning?


There are significant concerns about the reproducibility of GROMOS force 
fields. The authors of a recent study (
https://pubs.acs.org/doi/10.1021/acs.jctc.8b00425) allege that GROMACS 
has bugs that affect results, but the GROMACS developers maintain that 
the GROMOS force fields were developed with incorrect algorithms in the 
GROMOS software (hence the warning, and see the related Redmine issue 
linked in the message).


The issue is not specifically related to 43a1p (which is anyway an 
extremely old force field), but all of the GROMOS parameter sets.


Proceed with caution. There are other force field options available that 
have been confirmed to work as expected across different software.


-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] question on ffG43a1p force field

[Lei Qian]

Thank you Dr. Lemkul,
Could I ask one more question? Thank you!

When I did the step for adding ions and minimization and equilibration
steps, one warning always showed up.
So I had to add -maxwarn 2 after the command gmx grompp.
This warning is as follows:

WARNING 1 [file topol.top, line 48]:
  The GROMOS force fields have been parametrized with a physically
  incorrect multiple-time-stepping scheme for a twin-range cut-off. When
  used with a single-range cut-off (or a correct Trotter
  multiple-time-stepping scheme), physical properties, such as the density,
  might differ from the intended values. Check if molecules in your system
  are affected by such issues before proceeding. Further information may be
  available at https://redmine.gromacs.org/issues/2884.

It seems this warning is related to the GROMOS force field (for
phosphorylation) you sent to me last week.
Could I disregard this warning?
Thanks!

Lei









On Sun, Aug 18, 2019 at 10:54 AM Justin Lemkul  wrote:

>
>
> On 8/18/19 3:24 AM, Lei Qian wrote:
> > Could I ask one more question about your *gromos43a1p.ff* force filed ?
> > Thanks!
> > I ran $ gmx pdb2gmx -f myfile.pdb -o sort_processed.gro -water spce
> >
> > It shows a fatal error:
> > "Fatal error:
> > The residues in the chain xxx--xxx do not have a consistent type. The
> first
> > residue has type 'Protein', while residue *SEP is of type 'Other'*.
> > Either there is a mistake in your chain, or it includes nonstandard
> residue
> > names that have not yet been added to the *residuetypes.dat file* in the
> > GROMACS library directory."
> >
> > Then I found the *residuetypes.dat *in gromacs-2019.2/share/top, and add
> > "SEP   protein" to the list.
> > However, the fatal error still shows up after this change.
> > Could I ask how to solve this problem?
>
> You need to change the installed residuetypes.dat file, not the one in
> the source.
>
> -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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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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Re: [gmx-users] question on ffG43a1p force field

[Justin Lemkul]

On 8/18/19 3:24 AM, Lei Qian wrote:

Could I ask one more question about your *gromos43a1p.ff* force filed ?
Thanks!
I ran $ gmx pdb2gmx -f myfile.pdb -o sort_processed.gro -water spce

It shows a fatal error:
"Fatal error:
The residues in the chain xxx--xxx do not have a consistent type. The first
residue has type 'Protein', while residue *SEP is of type 'Other'*.
Either there is a mistake in your chain, or it includes nonstandard residue
names that have not yet been added to the *residuetypes.dat file* in the
GROMACS library directory."

Then I found the *residuetypes.dat *in gromacs-2019.2/share/top, and add
"SEP   protein" to the list.
However, the fatal error still shows up after this change.
Could I ask how to solve this problem?


You need to change the installed residuetypes.dat file, not the one in 
the source.


-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] question on ffG43a1p force field

[Lei Qian]

Could I ask one more question about your *gromos43a1p.ff* force filed ?
Thanks!
I ran $ gmx pdb2gmx -f myfile.pdb -o sort_processed.gro -water spce

It shows a fatal error:
"Fatal error:
The residues in the chain xxx--xxx do not have a consistent type. The first
residue has type 'Protein', while residue *SEP is of type 'Other'*.
Either there is a mistake in your chain, or it includes nonstandard residue
names that have not yet been added to the *residuetypes.dat file* in the
GROMACS library directory."

Then I found the *residuetypes.dat *in gromacs-2019.2/share/top, and add
"SEP   protein" to the list.
However, the fatal error still shows up after this change.
Could I ask how to solve this problem?
Thanks!





On Fri, Aug 16, 2019 at 6:22 AM Justin Lemkul  wrote:

>
>
> On 8/16/19 2:15 AM, Lei Qian wrote:
> > Sorry for this basic question.
> > I read previous emails and tried to make pdb2gmx find ffG43a1p.ff.
> > I added #include "ffG43a1p.itp" in FF.dat in ffG43a1p.ff folder. Also
> tried
> > to create a file called forcefield.doc and wrote "ffG43a1p" into it.
> > I put these files in working directory
> > and /usr/local/gromacs/share/gromacs/top/ directory. However, neither of
> > them worked.
> > Could I ask how to solve this problem?
>
> It sounds like you are trying to modify a very old and outdated version
> of the files (potentially with an outdated version of GROMACS - FF.dat
> is no longer used). The files you want for any post-4.0 version of
> GROMACS are in:
>
> http://www.gromacs.org/@api/deki/files/235/=gromos43a1p-4.5.1.tgz
>
> -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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
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Re: [gmx-users] question on ffG43a1p force field

[Lei Qian]

Thank you very much Dr. Lemkul,

I downloaded your file and it works!
Actually I downloaded the previous file from Gromacs web:
http://www.gromacs.org/Downloads/User_contributions/Force_fields
Thanks again for your help!





On Fri, Aug 16, 2019 at 6:22 AM Justin Lemkul  wrote:

>
>
> On 8/16/19 2:15 AM, Lei Qian wrote:
> > Sorry for this basic question.
> > I read previous emails and tried to make pdb2gmx find ffG43a1p.ff.
> > I added #include "ffG43a1p.itp" in FF.dat in ffG43a1p.ff folder. Also
> tried
> > to create a file called forcefield.doc and wrote "ffG43a1p" into it.
> > I put these files in working directory
> > and /usr/local/gromacs/share/gromacs/top/ directory. However, neither of
> > them worked.
> > Could I ask how to solve this problem?
>
> It sounds like you are trying to modify a very old and outdated version
> of the files (potentially with an outdated version of GROMACS - FF.dat
> is no longer used). The files you want for any post-4.0 version of
> GROMACS are in:
>
> http://www.gromacs.org/@api/deki/files/235/=gromos43a1p-4.5.1.tgz
>
> -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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] question on ffG43a1p force field

[Justin Lemkul]

On 8/16/19 2:15 AM, Lei Qian wrote:

Sorry for this basic question.
I read previous emails and tried to make pdb2gmx find ffG43a1p.ff.
I added #include "ffG43a1p.itp" in FF.dat in ffG43a1p.ff folder. Also tried
to create a file called forcefield.doc and wrote "ffG43a1p" into it.
I put these files in working directory
and /usr/local/gromacs/share/gromacs/top/ directory. However, neither of
them worked.
Could I ask how to solve this problem?


It sounds like you are trying to modify a very old and outdated version 
of the files (potentially with an outdated version of GROMACS - FF.dat 
is no longer used). The files you want for any post-4.0 version of 
GROMACS are in:


http://www.gromacs.org/@api/deki/files/235/=gromos43a1p-4.5.1.tgz

-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Question from new gromacs user

[Justin Lemkul]

On 5/27/19 5:22 PM, Nabil Abid wrote:

Dear
i need to get some help concerning gromacs utilities and mainly how to get the 
full structure of protein (all system) from a generated extreme.pdb file (only 
c-alpha). thanks


GROMACS has no ability to rebuild an entire structure. pdb2gmx can build 
missing H atoms but nothing else.


-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Question on generating hydrogens

[Justin Lemkul]

On 4/22/19 5:39 PM, tca1 wrote:

Hi all,

Is it possible to use pdb2gmx to generate hydrogens for a 
configuration file without also creating a topology file? Based on the 
documentation, it seems I can only rename this file, not prevent its 
creation.


Ideally, I'd like to prevent this, because I have many 
identically-structured polymer molecules and building the topology for 
the whole system takes a very long time, but I can use a template 
topology file which includes a single-chain itp file and then just 
tells the code how many chains are present (analogously to how 
solvents are handled). However, my initial input file doesn't have the 
hydrogens included, so I've been forced to use pdb2gmx to handle this 
part. I'd love to be able to decouple the steps, though.




The principal function of pdb2gmx is to produce a topology. Production 
of a force field-compatible structure is actually somewhat of a side 
effect. The only way to prevent the production of a topology is to 
explicitly disable these functions in the code and recompile.


-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] question

[Bratin Kumar Das]

Hi
You need to create the restrain file of co-factor and ligand
separately. Next you have to include the restrain file in the topolog file.
Check the gromacs manual

On Mon 8 Apr, 2019, 5:22 PM m mar  *hello*
>
> *How can I position restraint cofactor and ligand **together?*
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Re: [gmx-users] question about make_ndx

[Ullmann, Thomas]

Hi,

Under Unix/Linux you can use

gmx make_ndx -f struc.gro -o test.ndx << _EOR_
r 1
q
_EOR_

Best,
Thomas.

--
R. Thomas Ullmann, PhD
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Göttingen, Germany
thomas.ullm...@mpibpc.mpg.de
www.bisb.uni-bayreuth.de/People/ullmannt
--


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Carlos Navarro 

Sent: Thursday, April 4, 2019 5:55:26 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] question about make_ndx

Dear gmx users,
I’m trying to feed make_ndx though echo, but I’m having some issues.
When I use echo  "r 1"  | gmx make_ndx -f struc.gro -o test.ndx I got the
following error message:

Fatal error:
Error reading user input

So apparently I have to include also the q argument to close properly
make_ndx, but I don’t know how to do this.
I have tried with echo  "r 1 q"  | gmx make_ndx, echo  "r 1” “q"  | gmx
make_ndx, and other combinations, but non of them worked.
Any ideas?
Best regards,
Carlos

——
Carlos Navarro Retamal
Bioinformatic Engineering. PhD.
Postdoctoral Researcher in Center of Bioinformatics and Molecular
Simulations
Universidad de Talca
Av. Lircay S/N, Talca, Chile
E: carlos.navarr...@gmail.com or cnava...@utalca.cl
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Re: [gmx-users] Question about gmx order ...

[Dallas Warren]

First guess would be the atom at which the property is being calculated
i.e. radial line from the COM through the atom.

On Sat, 23 Mar. 2019, 6:43 am Sergio Garay,  wrote:

> Hi all
>
> I have a micelle trajectory formed by 30 molecules, and I would like to
> obtain the order parameters of each acyl chain moieties. I've tried using
> the option -radial, but I'm not sure about the result. What will be the
> director that it will be used in the calculation? It will be a vector from
> the center of mass to.what? the tool is not asking for any terminal
> atom to calculate the end of the director. Probably I'm wrong, but I'm not
> sure how to continue.
> Any help will be very appreciated!
>
> Sergio
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Re: [gmx-users] Question on gmx editconf, pbc and NPT

[Dallas Warren]

Pressure coupling is explained here ->
http://manual.gromacs.org/documentation/current/reference-manual/algorithms/molecular-dynamics.html#pressure-coupling

There is no pressure applied to the face of a simulation box, as the face
of the simulation box itself is an arbitrary construct done to allow us to
visualise the system.  The particle coordinates and box vectors are what is
adjusted to maintain the pressure.

Sounds more like you want to use this
http://manual.gromacs.org/documentation/current/reference-manual/special/pulling.html#the-pull-code

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Thu, 27 Dec 2018 at 22:14, Sebastian Muraru <
sebastian.mur...@grabtop.upb.ro> wrote:

> Hi there! Please help me figure something out.
>
> I have a setup made out of two molecules and I would like to investigate
> when happens when they meet (graphene + biomolecule). One of them is fixed
> by position restraints, one of them is mobile. When running a simulation
> under NPT conditions I assumed pressure is applied so that everything is
> 'slightly guided' towards the center of the simulation box (given a high
> enough pressure value). Would that assumption be correct? Or is pressure
> presumably applied on the faces of the simulation box?
>
> Thus, I figured, since I want to check what happens when the molecules
> meet, I want molecule_1 to be in the center of the simulation box and have
> molecule_2 slightly guided towards it. However, given that the distance
> between the molecules is known and fixed, placing the box so that
> molecule_1 is at the center leaves a part of molecule_2 out of the box
> through the top face.
>
> I assumed this would not be a problem during a simulation due to pbc being
> on, thus allowing the part of molecule_2 that's out of the box to reenter
> through the bottom layer. However, I also need to go through a solvation
> step and that I think this complicates things because a part of molecule_2
> will not be in solvent. Would you know a workaround for this issue? I try
> to avoid making the box taller / bigger.
>
> Thanks and a Happy Upcoming New Year to the Gromacs Community!
> --
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Re: [gmx-users] Question on gmx editconf, pbc and NPT (Sebastian Muraru)

[Sebastian Muraru]

I think I found a workaround my own problem: 
I initially placed everything in a box that includes all present molecules 
within its borders and solvated it. Then I redefined the box and ran an energy 
minimisation step.
The em.gro file looks as if everything is solvated fine inside the new box 
which has molecule_1 at its center.


- Original Message -
From: "gromacs org gmx-users-request" 

To: "gromacs org gmx-users" 
Sent: Thursday, December 27, 2018 1:32:20 PM GMT +02:00 Athens, Beirut, 
Bucharest, Istanbul
Subject: gromacs.org_gmx-users Digest, Vol 176, Issue 69

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Today's Topics:

   1. Re: how to restart a job in grmacs (sp...@iacs.res.in)
   2. Re: how to restart a job in grmacs (SHAHEE ISLAM)
   3. Question on gmx editconf, pbc and NPT (Sebastian Muraru)
   4. Re: how to restart a job in grmacs (sp...@iacs.res.in)
   5. Re: how to restart a job in grmacs (SHAHEE ISLAM)
   6. electrostatic and LJ energy (Dr Tushar Ranjan Moharana)


--

Message: 1
Date: Thu, 27 Dec 2018 16:28:53 +0530
From: sp...@iacs.res.in
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] how to restart a job in grmacs
Message-ID:
<20181227162853.horde.xoxxxhf68ivvyq27yoz5...@mailweb.iacs.res.in>
Content-Type: text/plain; charset=UTF-8; format=flowed; DelSp=Yes

  - Message from SHAHEE ISLAM  -
? ? Date: Thu, 27 Dec 2018 16:16:18 +0530
? ? From: SHAHEE ISLAM 
Reply-To: gmx-us...@gromacs.org
Subject: [gmx-users] how to restart a job in grmacs
? ? ? To: gmx-us...@gromacs.org

> hi,
> i have run a simulation for 10 ns but after 4 ns due to power off the
> job stopped.Then using this gmx mdrun -s md_0_10ns.tpr -cpi
> md_0_10ns.cpt,continue the left simulation.Now after normal
> termination of 10 ns how i wll do the next 5 ns simulation after this
> 10 ns.
> thanking you
> shahee
> --
> Gromacs Users mailing list
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> * Please search the archive at
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> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or send a mail to gmx-users-requ...@gromacs.org.

Hi
You can extend the job by generating a new tpr file?
gmx convert-tpr -s old.tpr -extend 5000 -o new.tpr?
then restart the job?
gmx mdrun -s new.tpr -cpi state.cpt
?This will continue the run from 10 ns.
Sunipa
- End message from SHAHEE ISLAM  -


--

Message: 2
Date: Thu, 27 Dec 2018 16:41:21 +0530
From: SHAHEE ISLAM 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] how to restart a job in grmacs
Message-ID:

Content-Type: text/plain; charset="UTF-8"

thank you so much for your reply.
-extend 5000 what does it signify.if the time step is 2 fs then by
simply multiplying these two it will give 10 ns.
thanking you

On 12/27/18, sp...@iacs.res.in  wrote:
>   - Message from SHAHEE ISLAM  -
> ? ? Date: Thu, 27 Dec 2018 16:16:18 +0530
> ? ? From: SHAHEE ISLAM 
> Reply-To: gmx-us...@gromacs.org
> Subject: [gmx-users] how to restart a job in grmacs
> ? ? ? To: gmx-us...@gromacs.org
>
>> hi,
>> i have run a simulation for 10 ns but after 4 ns due to power off the
>> job stopped.Then using this gmx mdrun -s md_0_10ns.tpr -cpi
>> md_0_10ns.cpt,continue the left simulation.Now after normal
>> termination of 10 ns how i wll do the next 5 ns simulation after this
>> 10 ns.
>> thanking you
>> shahee
>> --
>> 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
>> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or send a mail to gmx-users-requ...@gromacs.org.
>
> Hi
> You can extend the job by generating a new tpr file
> gmx convert-tpr -s old.tpr -extend 5000 -o new.tpr
> then restart the job
> gmx mdrun -s new.tpr -cpi state.cpt
> ?This will continue the run from 10 ns.
> Sunipa
> - End message from SHAHEE ISLAM  -
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Re: [gmx-users] Question about nsttcouple

[Mark Abraham]

Hi,

Sorry, it looks like the documentation is wrong in that case. Developers
are fond of doing fancy things and not remembering all the things that
depend on it. I imagine that nsttcouple gets 10 chosen, and only later is
nstlist changed. The interpretation and behaviour of nstlist have
unfortunately changed over many years...

Mark

On Thu, Nov 8, 2018 at 12:38 AM minky son  wrote:

> Thank you for reply
>
> [ Input values in mdp file ]
> nstlist = 10
> nsttcouple = -1
>
> After gmx mdrun, ‘nstlist’ is automatically changed from 10 to 50.
>
> I expected that both ‘nstlist’ and ‘nsttcouple’ would be changed to 50,
> because ‘nsttcouple=-1’ means ‘nsttcouple=nstlist’.
> But, nstlist =50 and nsttcouple= 10 were written in log file.
> Which value was used for nsttcouple? 10 or 50?
>
> I’m not sure, because .log file shows input mdp parameter values, not
> automatically changed values (GROMACS 2018).
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Re: [gmx-users] Question about nsttcouple

[Justin Lemkul]

On 11/7/18 9:43 AM, minky son wrote:

Dear gmx users,


In gromacs manual,

“nsttcouple: The default value of -1 sets nsttcouple equal to nstlist,
unless nstlist <=0, then a value of 10 is used.”



When I did grompp with the following mdp options,

nstlist = 20

tcoupl = berendsen

nsttcouple = -1

tau-t = 0.1



I got a warning message.

WARNING 1 [file pr_nvt.mdp]:

   "For proper integration of the Berendsen thermostat, tau-t (0.1) should
be at least 5 times larger than nsttcouple*dt (0.04)"



I think this means that nsttcouple is applied to 20, not 10. This doesn't
match with the one mentioned in the manual. why?


It does match the manual, it's just grammatically complicated. A value 
of 10 is used for nstlist if *both* nsttcouple = -1 and nstlist <= 0. 
You have nstlist = 20, so the presence of nsttcouple = -1 means it is 
set to 20, not 10.






When I also tried nstlist=10, grompp didn’t show any warning.


Because now nsttcouple*dt is 0.02 (assuming dt = 0.002), and your tau-t 
is, in fact, 5 times larger.



But the value of nstlist was automatically changed to 40 in mdrun.


mdrun always tunes this with the Verlet algorithm.


Is nsttcouple applied to 10 in this case?


Check your .log file.

-Justin

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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Re: [gmx-users] Question about nsttcouple

[Quyen Vu Van]

nsttcouple=10 means that nsstcouple*dt(2fs, I guess)=0.02 and your
tau-t=0.1 (5 fold)
when nsttcouple=20, nsstcouple*dt=0.04 so your tau-t is only 2.5 fold. I
think so

On Wed, Nov 7, 2018 at 3:43 PM minky son  wrote:

> Dear gmx users,
>
>
> In gromacs manual,
>
> “nsttcouple: The default value of -1 sets nsttcouple equal to nstlist,
> unless nstlist <=0, then a value of 10 is used.”
>
>
>
> When I did grompp with the following mdp options,
>
> nstlist = 20
>
> tcoupl = berendsen
>
> nsttcouple = -1
>
> tau-t = 0.1
>
>
>
> I got a warning message.
>
> WARNING 1 [file pr_nvt.mdp]:
>
>   "For proper integration of the Berendsen thermostat, tau-t (0.1) should
> be at least 5 times larger than nsttcouple*dt (0.04)"
>
>
>
> I think this means that nsttcouple is applied to 20, not 10. This doesn't
> match with the one mentioned in the manual. why?
>
>
>
>
>
> When I also tried nstlist=10, grompp didn’t show any warning.
>
> But the value of nstlist was automatically changed to 40 in mdrun.
>
> Is nsttcouple applied to 10 in this case?
>
>
>
> Please give me an advice.
>
> Thank you.
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Re: [gmx-users] Question about Entropy Calculation

[David van der Spoel]

Den 2018-10-11 kl. 09:02, skrev kai.ex...@alumni.uni-ulm.de:

Dear Colleagues,

I would like to calculate the entropy contribution using "gmx anaeig". 
In the explanation of the command, it is written that with -entropy the 
entropy estimate will be computed based on quasi harmonic approach or 
Schlitter's formula. However, I didn't find any option, where to specify 
whether to use the quasi harmonic approximation or Schlitter's formula 
for the entropy calculation.


It will be reinstated in a new verison. For now you can use an older 
version.


My second question is, whether it is possible to tell the program to 
write down the corresponding entropy contributions of translation, 
rotation and vibration separately (as far as I understand, one receives 
an output for the entropy approximation, which constitutes the sum of 
all three terms).
This has been implemented for normal mode analysis but not for the quasi 
harmonic one.


I would be thankful for any help!

With my best regards,
Kai




--
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Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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Re: [gmx-users] Question regarding dihedral angle parameters

[Upendra N]

Dear Justin
Thank you very much.

Yours sincerely
Upendra N



On Thu, Aug 16, 2018 at 8:59 PM, Justin Lemkul  wrote:

>
>
> On 8/16/18 10:52 AM, Upendra N wrote:
>
>> Dear Justin
>> Thank you very much. I also would like to understand why the nature of the
>> potential energy is complex and its origin.
>> Kindly suggest me some reference that contains many examples (i.e
>> different
>> combination of atom types and associated torsional profiles)
>>
>
> Have a look at any primary reference for a paper that derives force field
> parameters; you'll find ample examples.
>
> Also remember that a dihedral potential is not a real physical force. It's
> a band-aid for inaccuracies in nonbonded interactions (primarily 1-4
> interactions). As you rotate about a bond, you're computing the potential
> energy of the molecule, hence asymmetry of the profile in many cases.
> Dihedral terms are added into the potential energy equation to get the
> correct profile (or as close to it as possible).
>
>
> -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.thelemkullab.com
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Re: [gmx-users] Question regarding dihedral angle parameters

[Justin Lemkul]

On 8/16/18 10:52 AM, Upendra N wrote:

Dear Justin
Thank you very much. I also would like to understand why the nature of the
potential energy is complex and its origin.
Kindly suggest me some reference that contains many examples (i.e different
combination of atom types and associated torsional profiles)


Have a look at any primary reference for a paper that derives force 
field parameters; you'll find ample examples.


Also remember that a dihedral potential is not a real physical force. 
It's a band-aid for inaccuracies in nonbonded interactions (primarily 
1-4 interactions). As you rotate about a bond, you're computing the 
potential energy of the molecule, hence asymmetry of the profile in many 
cases. Dihedral terms are added into the potential energy equation to 
get the correct profile (or as close to it as possible).


-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.thelemkullab.com

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Re: [gmx-users] Question regarding dihedral angle parameters

[Upendra N]

Dear Justin
Thank you very much. I also would like to understand why the nature of the
potential energy is complex and its origin.
Kindly suggest me some reference that contains many examples (i.e different
combination of atom types and associated torsional profiles)
Thank you in advance

Yours sincerely
Upendra N



On Thu, Aug 16, 2018 at 5:04 PM, Justin Lemkul  wrote:

>
>
> On 8/16/18 4:16 AM, Upendra N wrote:
>
>> Dear Gromacs users,
>>
>> I am a beginner in gromacs. I was trying to understand how dihedral terms
>> are used and I noticed that for Amber99 ff the ffbonded.itp files have
>> mutliple dihedral parameters for the same dihedral type, each with
>> different force constant, multiplicity and phase angle
>>
>> For instance,
>>
>>   CT  OS  CT  OS9   0.0  0.41840 3  ; Junmei et al, 1999
>>   CT  OS  CT  OS9 180.0  3.55640 2  ; Junmei et al, 1999
>>   CT  OS  CT  OS9 180.0  5.64840 1  ; Junmei et al, 1999
>>
>> I am wondering what determines which of this is assigned to a given
>> dihedral.
>>
>> Also, why is the phase shift different as I understand that phase shift
>> determines where is the minima of the energy in the energy vs torsion
>> plot.
>>
>> I have tried looking for the reason but somehow have not found a
>> satisfactory answer. I would really appreciate if someone can clarify this
>> to me.
>>
>
> 1-D potential energy surfaces are often complex, with multiple local
> minima. The dihedral energy function is such that one can sum up terms with
> different phases and multiplicities to recover the target energy surface
> (QM).
>
> -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.thelemkullab.com
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Re: [gmx-users] Question regarding dihedral angle parameters

[Justin Lemkul]

On 8/16/18 4:16 AM, Upendra N wrote:

Dear Gromacs users,

I am a beginner in gromacs. I was trying to understand how dihedral terms
are used and I noticed that for Amber99 ff the ffbonded.itp files have
mutliple dihedral parameters for the same dihedral type, each with
different force constant, multiplicity and phase angle

For instance,

  CT  OS  CT  OS9   0.0  0.41840 3  ; Junmei et al, 1999
  CT  OS  CT  OS9 180.0  3.55640 2  ; Junmei et al, 1999
  CT  OS  CT  OS9 180.0  5.64840 1  ; Junmei et al, 1999

I am wondering what determines which of this is assigned to a given
dihedral.

Also, why is the phase shift different as I understand that phase shift
determines where is the minima of the energy in the energy vs torsion plot.

I have tried looking for the reason but somehow have not found a
satisfactory answer. I would really appreciate if someone can clarify this
to me.


1-D potential energy surfaces are often complex, with multiple local 
minima. The dihedral energy function is such that one can sum up terms 
with different phases and multiplicities to recover the target energy 
surface (QM).


-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.thelemkullab.com

==

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Re: [gmx-users] Question about water insertion

[Kevin Boyd]

Hi,

You can play around with the -radius and -scale parameters if you're
getting clashes you don't like.

However, it seems like you really should be using gmx solvate. You could
accomplish your goal with

"gmx solvate -cs tip4p.gro -box 10.1103 10.34753 3.958  -maxsol 13853"

Kevin

On Fri, Aug 3, 2018 at 7:27 AM, G R  wrote:

> I have one water molecule in my gro file as below:
> TIP4P
> 4
> 1SOL OW1   0.054   0.005   0.022
> 1SOLHW12   0.009   0.072   0.073
> 1SOLHW23   0.142   0.041   0.008
> 1SOL MW4   0.060   0.018   0.026
>0.00   0.000   0.000
> Then use the command bellow to generate 13853 water molecules in the
> box.
> "insert-molecules -ci water.gro  -box 10.1103 10.34753 3.958 -nmol
> 13853 -o insert.gro"
> But, the water did not settle during energy minimization. When I
> reduced the
> numebr of water to 5000, it works, but it does not have the correct
> density. I need 13853 number of molecules. It seems that gmx insert
> generates water without considering the correct distance between them.
> Do you have any idea to solve this problem?
>
> Thank you in advance!
> Golnaz
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Re: [gmx-users] question about the center of mass motion removal

[Justin Lemkul]

On 8/1/18 10:06 PM, madis...@zju.edu.cn wrote:

Hello GROMACS users,



I have a quick question about comm-grps. I want to study the protein dynamics 
in water with no consideration of diffusion.

The manual suggests me to use groups in removing the center of mass motion by 
saying that it makes sense to use the same groups for temperature coupling and 
center of mass motion removal. But some people suggest using the whole


Where does it say that?


system for center of mass motion removal, such as 
https://www.mail-archive.com/gmx-users@gromacs.org/msg30001.html.


I stand by what I said there. For a protein in water, use "comm-grps = 
System" (which is the default behavior).


-Justin


My t-couple and COM motion removal settings are as follows.

; Temperature coupling is on
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= Protein Non-Protein; two coupling groups - more accurate
tau_t= 0.1  0.1   ; time constant, in ps
ref_t= 310   310   ; reference temperature, one for each group, in K

; COM motion removal
; These options remove motion and rotation of the protein relative to the 
solvent/ions
nstcomm= 100
comm-mode= linear



How to set up the grouping properly for my case?







Best,

Wukai


--
==

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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.thelemkullab.com

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Re: [gmx-users] question

[Alex]

Andrew, you do realize that defects in CNTs make them toxic to living 
organisms, right?


That aside, the presence of water inside CNTs depends on their diameter 
and chirality, so it's kind of hard to tell. But if your setup is 
reasonable and you see water getting inside CNTs, that's your answer: 
water will reside inside CNTs. :)


Alex


On 7/24/2018 4:51 AM, Andrew Bostick wrote:

Dear Mark and Alex,

I want to use CNTs as drug carrier. I think I should consider water
molecules inside the CNT. Do I think right?

Best,
AB


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Re: [gmx-users] question

[Mark Abraham]

Hi,

What physical reality are you trying to model? Will it have water molecules
inside the CNT?

Mark

On Mon, Jul 23, 2018, 16:19 Andrew Bostick 
wrote:

> Hi,
>
> I want to do md simulation of adsorbsion on small molecule on cnt and
> encapsulation small molecule into cnt. Should I remove water molecules
> inside of cnt?
>
> Do these molecules interfere with the interaction between cnt and small
> molecule?
>
> Thanks
> AB
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Re: [gmx-users] question

[Alex]

In reality, assuming your system is possible in reality, is there a 
magical being removing molecules to avoid "interference"?


Alex


On 7/23/2018 8:18 AM, Andrew Bostick wrote:

Hi,

I want to do md simulation of adsorbsion on small molecule on cnt and
encapsulation small molecule into cnt. Should I remove water molecules
inside of cnt?

Do these molecules interfere with the interaction between cnt and small
molecule?

Thanks
AB


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Re: [gmx-users] question regarding high temperature simulation in Gromacs

[Mark Abraham]

Hi,

I don't know, sorry. This is a critical part of your study design, and I
can't do it for you. Look in the literature of its use for any at high
temperature that was actually validated. Or see if e.g. the density and
diffusion rate of your solvent is represented accurately.

Mark

On Fri, Jul 6, 2018 at 1:35 PM Dr. Puspita Halder 
wrote:

> Hi Mark,
>
> I am using OPLS-AA force field for simulating my protein at high
> temperature under nvt condition. Does this work good for high temperature
> system under nvt? Can you suggest which force field I should use then?
>
> Thanks
>
> Puspita
>
> - Original Message -
> From: "Mark Abraham" 
> To: "gmx-users" 
> Cc: "gromacs org gmx-users" 
> Sent: Friday, July 6, 2018 1:40:10 PM
> Subject: Re: [gmx-users] question regarding high temperature simulation
> in  Gromacs
>
> Hi,
>
> You should expect that when you heat something up under constant volume
> that its pressure increases. Average velocity has gone up, so the momentum
> transferred in collisions is also up.
>
> The more important question is what evidence you have that this force field
> provides a useful simulation at this point of V,T?
>
> Mark
>
> On Fri, Jul 6, 2018 at 9:43 AM Dr. Puspita Halder <
> pusp...@cse.iitkgp.ac.in>
> wrote:
>
> > Hi All,
> >
> > Thanks for your helpful suggestions. I'd like to share the method that I
> > am following now for simulating my protein at high temperature. First, I
> > carried out energy minimization run for my protein system using steepest
> > decent method. Then I performed nvt equilibration run for 100-200 ps at
> > 300K followed by npt equilibration at the same temperature and at 1atm
> > pressure for 1-2 ns with protein position restrain. Then I used simulated
> > annealing protocol (without position restrain and under nvt condition)
> for
> > reaching the temperature of the system to 500K starting from the
> structure
> > of 300 K npt simulation with 50K temperature increment each time followed
> > by 2-4 ns of equilibration run at respective temperature. Finally I did
> the
> > production run at 500 K for 30-40 ns under nvt condition. Do you think
> that
> > the protocol I am using is ok ? The problem is I am getting high value of
> > pressure average (~3000-4000) for the simulated annealing run. Please
> share
> > your comments or suggestion
> >  regarding this.
> >
> > Thanks for your help.
> >
> > Puspita Halder
> >
> > - Original Message -
> > From: "Dr. Puspita Halder" 
> > To: "gromacs org gmx-users" 
> > Sent: Wednesday, July 4, 2018 12:41:56 PM
> > Subject: question regarding high temperature simulation in Gromacs
> >
> > Hi All,
> >
> > I have been recently using Gromacs 5.1.4 version for simulating my
> protein
> > systems (mainly prion protein and some of its mutants). I'd like to
> perform
> > high temperature (400K or 500K) simulations with those. Now my question
> is
> > what should be the values of the simulation parameters e.g.,
> > compressibility, tau_p or tau_t at 400K or 500K? I used compressibility =
> > 4.5e-5 and tau_p = 2.0 and tau_t = 0.1 for pressure and temperature
> > coupling for simulations at 300K. What other parameters should I change
> for
> > high temperature simulations? Should I always use simulated annealing
> > protocol for simulations at higher temperature or I can directly heat the
> > system to such higher temperatures? Any comments or suggestions in this
> > regard will be highly appreciated.
> >
> > Thanks for your help in advance.
> >
> > Regards
> > Puspita Halder
> > --
> > 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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Re: [gmx-users] question regarding high temperature simulation in Gromacs

[Dr. Puspita Halder]

Hi Mark,

I am using OPLS-AA force field for simulating my protein at high temperature 
under nvt condition. Does this work good for high temperature system under nvt? 
Can you suggest which force field I should use then?

Thanks

Puspita

- Original Message -
From: "Mark Abraham" 
To: "gmx-users" 
Cc: "gromacs org gmx-users" 
Sent: Friday, July 6, 2018 1:40:10 PM
Subject: Re: [gmx-users] question regarding high temperature simulation in  
Gromacs

Hi,

You should expect that when you heat something up under constant volume
that its pressure increases. Average velocity has gone up, so the momentum
transferred in collisions is also up.

The more important question is what evidence you have that this force field
provides a useful simulation at this point of V,T?

Mark

On Fri, Jul 6, 2018 at 9:43 AM Dr. Puspita Halder 
wrote:

> Hi All,
>
> Thanks for your helpful suggestions. I'd like to share the method that I
> am following now for simulating my protein at high temperature. First, I
> carried out energy minimization run for my protein system using steepest
> decent method. Then I performed nvt equilibration run for 100-200 ps at
> 300K followed by npt equilibration at the same temperature and at 1atm
> pressure for 1-2 ns with protein position restrain. Then I used simulated
> annealing protocol (without position restrain and under nvt condition) for
> reaching the temperature of the system to 500K starting from the structure
> of 300 K npt simulation with 50K temperature increment each time followed
> by 2-4 ns of equilibration run at respective temperature. Finally I did the
> production run at 500 K for 30-40 ns under nvt condition. Do you think that
> the protocol I am using is ok ? The problem is I am getting high value of
> pressure average (~3000-4000) for the simulated annealing run. Please share
> your comments or suggestion
>  regarding this.
>
> Thanks for your help.
>
> Puspita Halder
>
> - Original Message -
> From: "Dr. Puspita Halder" 
> To: "gromacs org gmx-users" 
> Sent: Wednesday, July 4, 2018 12:41:56 PM
> Subject: question regarding high temperature simulation in Gromacs
>
> Hi All,
>
> I have been recently using Gromacs 5.1.4 version for simulating my protein
> systems (mainly prion protein and some of its mutants). I'd like to perform
> high temperature (400K or 500K) simulations with those. Now my question is
> what should be the values of the simulation parameters e.g.,
> compressibility, tau_p or tau_t at 400K or 500K? I used compressibility =
> 4.5e-5 and tau_p = 2.0 and tau_t = 0.1 for pressure and temperature
> coupling for simulations at 300K. What other parameters should I change for
> high temperature simulations? Should I always use simulated annealing
> protocol for simulations at higher temperature or I can directly heat the
> system to such higher temperatures? Any comments or suggestions in this
> regard will be highly appreciated.
>
> Thanks for your help in advance.
>
> Regards
> Puspita Halder
> --
> 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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Re: [gmx-users] question regarding high temperature simulation in Gromacs

[Mark Abraham]

Hi,

You should expect that when you heat something up under constant volume
that its pressure increases. Average velocity has gone up, so the momentum
transferred in collisions is also up.

The more important question is what evidence you have that this force field
provides a useful simulation at this point of V,T?

Mark

On Fri, Jul 6, 2018 at 9:43 AM Dr. Puspita Halder 
wrote:

> Hi All,
>
> Thanks for your helpful suggestions. I'd like to share the method that I
> am following now for simulating my protein at high temperature. First, I
> carried out energy minimization run for my protein system using steepest
> decent method. Then I performed nvt equilibration run for 100-200 ps at
> 300K followed by npt equilibration at the same temperature and at 1atm
> pressure for 1-2 ns with protein position restrain. Then I used simulated
> annealing protocol (without position restrain and under nvt condition) for
> reaching the temperature of the system to 500K starting from the structure
> of 300 K npt simulation with 50K temperature increment each time followed
> by 2-4 ns of equilibration run at respective temperature. Finally I did the
> production run at 500 K for 30-40 ns under nvt condition. Do you think that
> the protocol I am using is ok ? The problem is I am getting high value of
> pressure average (~3000-4000) for the simulated annealing run. Please share
> your comments or suggestion
>  regarding this.
>
> Thanks for your help.
>
> Puspita Halder
>
> - Original Message -
> From: "Dr. Puspita Halder" 
> To: "gromacs org gmx-users" 
> Sent: Wednesday, July 4, 2018 12:41:56 PM
> Subject: question regarding high temperature simulation in Gromacs
>
> Hi All,
>
> I have been recently using Gromacs 5.1.4 version for simulating my protein
> systems (mainly prion protein and some of its mutants). I'd like to perform
> high temperature (400K or 500K) simulations with those. Now my question is
> what should be the values of the simulation parameters e.g.,
> compressibility, tau_p or tau_t at 400K or 500K? I used compressibility =
> 4.5e-5 and tau_p = 2.0 and tau_t = 0.1 for pressure and temperature
> coupling for simulations at 300K. What other parameters should I change for
> high temperature simulations? Should I always use simulated annealing
> protocol for simulations at higher temperature or I can directly heat the
> system to such higher temperatures? Any comments or suggestions in this
> regard will be highly appreciated.
>
> Thanks for your help in advance.
>
> Regards
> Puspita Halder
> --
> 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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Re: [gmx-users] question regarding high temperature simulation in Gromacs

[Dr. Puspita Halder]

Hi All,

Thanks for your helpful suggestions. I'd like to share the method that I am 
following now for simulating my protein at high temperature. First, I carried 
out energy minimization run for my protein system using steepest decent method. 
Then I performed nvt equilibration run for 100-200 ps at 300K followed by npt 
equilibration at the same temperature and at 1atm pressure for 1-2 ns with 
protein position restrain. Then I used simulated annealing protocol (without 
position restrain and under nvt condition) for reaching the temperature of the 
system to 500K starting from the structure of 300 K npt simulation with 50K 
temperature increment each time followed by 2-4 ns of equilibration run at 
respective temperature. Finally I did the production run at 500 K for 30-40 ns 
under nvt condition. Do you think that the protocol I am using is ok ? The 
problem is I am getting high value of pressure average (~3000-4000) for the 
simulated annealing run. Please share your comments or suggestion 
 regarding this.

Thanks for your help.

Puspita Halder

- Original Message -
From: "Dr. Puspita Halder" 
To: "gromacs org gmx-users" 
Sent: Wednesday, July 4, 2018 12:41:56 PM
Subject: question regarding high temperature simulation in Gromacs

Hi All,

I have been recently using Gromacs 5.1.4 version for simulating my protein 
systems (mainly prion protein and some of its mutants). I'd like to perform 
high temperature (400K or 500K) simulations with those. Now my question is what 
should be the values of the simulation parameters e.g., compressibility, tau_p 
or tau_t at 400K or 500K? I used compressibility = 4.5e-5 and tau_p = 2.0 and 
tau_t = 0.1 for pressure and temperature coupling for simulations at 300K. What 
other parameters should I change for high temperature simulations? Should I 
always use simulated annealing protocol for simulations at higher temperature 
or I can directly heat the system to such higher temperatures? Any comments or 
suggestions in this regard will be highly appreciated.

Thanks for your help in advance.

Regards
Puspita Halder
-- 
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Re: [gmx-users] question regarding high temperature simulation in Gromacs

[Justin Lemkul]

On 7/4/18 4:08 PM, Quyen V. Vu wrote:

Dear Prof. David,
Could you kindly describe in more detail for give me references which
problems will happen?


What happens when you boil water? It turns to steam and its volume 
expands rapidly. That behavior is not very stable for most barostats. 
Beyond that, force field parameters are usually only validated at 
ambient temperature and there is no guarantee that their properties will 
be valid at extreme temperatures. Using NVT (e.g. constant density) 
circumvents these problems to some extent.


-Justin


On Wed, Jul 4, 2018, 15:13 David van der Spoel  wrote:


Den 2018-07-04 kl. 09:11, skrev Dr. Puspita Halder:

Hi All,

I have been recently using Gromacs 5.1.4 version for simulating my

protein systems (mainly prion protein and some of its mutants). I'd like to
perform high temperature (400K or 500K) simulations with those. Now my
question is what should be the values of the simulation parameters e.g.,
compressibility, tau_p or tau_t at 400K or 500K? I used compressibility =
4.5e-5 and tau_p = 2.0 and tau_t = 0.1 for pressure and temperature
coupling for simulations at 300K. What other parameters should I change for
high temperature simulations? Should I always use simulated annealing
protocol for simulations at higher temperature or I can directly heat the
system to such higher temperatures? Any comments or suggestions in this
regard will be highly appreciated.

Thanks for your help in advance.

Regards
Puspita Halder


Simulating above the boiling temperature of water may be problematic
with pressure coupling. Better turn it off.

--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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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.thelemkullab.com

==

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Re: [gmx-users] question regarding high temperature simulation in Gromacs

[Quyen V. Vu]

Dear Prof. David,
Could you kindly describe in more detail for give me references which
problems will happen?

On Wed, Jul 4, 2018, 15:13 David van der Spoel  wrote:

> Den 2018-07-04 kl. 09:11, skrev Dr. Puspita Halder:
> > Hi All,
> >
> > I have been recently using Gromacs 5.1.4 version for simulating my
> protein systems (mainly prion protein and some of its mutants). I'd like to
> perform high temperature (400K or 500K) simulations with those. Now my
> question is what should be the values of the simulation parameters e.g.,
> compressibility, tau_p or tau_t at 400K or 500K? I used compressibility =
> 4.5e-5 and tau_p = 2.0 and tau_t = 0.1 for pressure and temperature
> coupling for simulations at 300K. What other parameters should I change for
> high temperature simulations? Should I always use simulated annealing
> protocol for simulations at higher temperature or I can directly heat the
> system to such higher temperatures? Any comments or suggestions in this
> regard will be highly appreciated.
> >
> > Thanks for your help in advance.
> >
> > Regards
> > Puspita Halder
> >
> Simulating above the boiling temperature of water may be problematic
> with pressure coupling. Better turn it off.
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
> 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] question regarding high temperature simulation in Gromacs

[Dr. Puspita Halder]

Hi,

Thanks for your reply. I'd try to run my high temperature simulations with 
pressure coupling off as per your suggestion. 
I was wondering about the simulation parameters (as mentioned in the early 
post) that I need to change for running high 
temperature simulations and should I use simulated annealing protocol for all 
such simulations? 

Thanks
Puspita Halder



- Original Message -
From: "David van der Spoel" 
To: "gmx-users" 
Sent: Wednesday, July 4, 2018 1:43:22 PM
Subject: Re: [gmx-users] question regarding high temperature simulation in 
Gromacs

Den 2018-07-04 kl. 09:11, skrev Dr. Puspita Halder:
> Hi All,
> 
> I have been recently using Gromacs 5.1.4 version for simulating my protein 
> systems (mainly prion protein and some of its mutants). I'd like to perform 
> high temperature (400K or 500K) simulations with those. Now my question is 
> what should be the values of the simulation parameters e.g., compressibility, 
> tau_p or tau_t at 400K or 500K? I used compressibility = 4.5e-5 and tau_p = 
> 2.0 and tau_t = 0.1 for pressure and temperature coupling for simulations at 
> 300K. What other parameters should I change for high temperature simulations? 
> Should I always use simulated annealing protocol for simulations at higher 
> temperature or I can directly heat the system to such higher temperatures? 
> Any comments or suggestions in this regard will be highly appreciated.
> 
> Thanks for your help in advance.
> 
> Regards
> Puspita Halder
> 
Simulating above the boiling temperature of water may be problematic 
with pressure coupling. Better turn it off.

-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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Re: [gmx-users] question regarding high temperature simulation in Gromacs

[David van der Spoel]

Den 2018-07-04 kl. 09:11, skrev Dr. Puspita Halder:

Hi All,

I have been recently using Gromacs 5.1.4 version for simulating my protein 
systems (mainly prion protein and some of its mutants). I'd like to perform 
high temperature (400K or 500K) simulations with those. Now my question is what 
should be the values of the simulation parameters e.g., compressibility, tau_p 
or tau_t at 400K or 500K? I used compressibility = 4.5e-5 and tau_p = 2.0 and 
tau_t = 0.1 for pressure and temperature coupling for simulations at 300K. What 
other parameters should I change for high temperature simulations? Should I 
always use simulated annealing protocol for simulations at higher temperature 
or I can directly heat the system to such higher temperatures? Any comments or 
suggestions in this regard will be highly appreciated.

Thanks for your help in advance.

Regards
Puspita Halder

Simulating above the boiling temperature of water may be problematic 
with pressure coupling. Better turn it off.


--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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Re: [gmx-users] Question regarding running Gromacs new graphics card on Centos

[Mark Abraham]

Hi,

On Wed, Jun 20, 2018 at 4:07 AM Tony Myung Keun Cho 
wrote:

> Hi everyone,
> I have been using Gromacs 2016.3 with GPU-acceleration with CUDA on Centos
> 7 for a year.
> I am a beginner as a programmer.
>
> I was using Nvidia GTX1050, but now I replaced it with Nvidia GTX1070Ti.
> For sole purpose of running Gromacs with FFTW and CUDA, will it cause a
> calculation error if I just purge previous CUDA and nvidia software, update
> them, and recompile Gromacs?
>

No need to remove anything, just install the new CUDA version side by side,
making sure that the driver installation comes from the more recent CUDA.
Then configure, compile and install GROMACS again. You

Will it be better to just format and reinstall the OS?
>

That's absolutely not required.

Mark


> Thank you very much for reading and your help in advance!
>
> Best regards,
> Tony
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Re: [gmx-users] question

[Dallas Warren]

Pressure can fluctuate a huge amount, hundreds of bar, and since you
are looking for an average of "1" it is unlikely to get that close to
the value.  As long as the pressure has stabilised around reference
pressure, and not continuing to increase/decrease, then it has
essentially reached equilibrium.

For example, which shows the pressure fluctuation for a with 300k
atoms: https://twitter.com/dr_dbw/status/968625462959210496  If have
more atoms, then the fluctuations will be less, less atoms then it
will be larger.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 15 March 2018 at 08:11, s.ghasemlou  wrote:
> Hi all
>
> I performed a 100 ps run for npt step but the average pressure hadn't
> got the desired value. I continued the NPT for more 50 ps but the
> average pressure got higher.is it right to extend an equilibration run?
> or we can only extend md runs?
>
> thanks
> --
> 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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Re: [gmx-users] Question about gmx bar

[Justin Lemkul]

On 2/27/18 6:31 PM, Thanh Le wrote:

Hi Justin,
I assume, in order to get Coulomb energy for the first 10 stages, I should 
change coul-lambdas stages to the same row as bonded-lambdas (0.0 0.01 0.025 
0.05 0.075 0.1 0.2 0.35 0.5 0.75 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.0 1.0 1.0 1.0 
1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0).
Is there another way to do it? Is there a paper I can read to get more details 
about the subject?


No, but there's a tutorial:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html

And other material on, e.g. alchemistry.org.

-Justin


Thanks,
Thanh Le



On 2/27/18 4:13 PM, Thanh Le wrote:

Hi everyone,
I just finished running 2 sets of simulations (ligand in water and RNA+ligand 
in water) for my system to learn about its binding energy. Using the parameter 
for BAR method, I ran 20 simulations for ligand in water and 30 simulations for 
RNA+ligand in water with different lambda stages. What is interesting/confusing 
to me is the 0 energy from stages 0-10. Based on what I have been reading and 
the set up of my prod.mdp, these stages should give Coulomb Energy. If you can 
tell me why or how to fix it, I would greatly appreciate your help.

You've defined only a bonded transformation in those stages:

bonded-lambdas   = 0.0 0.01 0.025 0.05 0.075 0.1 0.2 0.35 0.5 0.75 1.0 
1.00 1.0 1.00 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 
1.0
coul-lambdas = 0.0 0.00 0.000 0.00 0.000 0.0 0.0 0.00 0.0 0.00 0.0 
0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 
1.0
vdw-lambdas  = 0.0 0.00 0.000 0.00 0.000 0.0 0.0 0.00 0.0 0.00 0.0 
0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 
1.0

Your electrostatic terms remain in state A (lambda = 0) and there is no 
difference in bonded energies, so the first windows are essentially doing 
nothing.

-Justin


--
==

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

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

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

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Re: [gmx-users] Question about gmx bar

[Justin Lemkul]

On 2/27/18 4:13 PM, Thanh Le wrote:

Hi everyone,
I just finished running 2 sets of simulations (ligand in water and RNA+ligand 
in water) for my system to learn about its binding energy. Using the parameter 
for BAR method, I ran 20 simulations for ligand in water and 30 simulations for 
RNA+ligand in water with different lambda stages. What is interesting/confusing 
to me is the 0 energy from stages 0-10. Based on what I have been reading and 
the set up of my prod.mdp, these stages should give Coulomb Energy. If you can 
tell me why or how to fix it, I would greatly appreciate your help.


You've defined only a bonded transformation in those stages:

bonded-lambdas   = 0.0 0.01 0.025 0.05 0.075 0.1 0.2 0.35 0.5 0.75 1.0 
1.00 1.0 1.00 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 
1.0
coul-lambdas = 0.0 0.00 0.000 0.00 0.000 0.0 0.0 0.00 0.0 0.00 0.0 
0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 
1.0
vdw-lambdas  = 0.0 0.00 0.000 0.00 0.000 0.0 0.0 0.00 0.0 0.00 0.0 
0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 
1.0

Your electrostatic terms remain in state A (lambda = 0) and there is no 
difference in bonded energies, so the first windows are essentially doing 
nothing.

-Justin




point  0 -  1,   DG  0.00 +/-  0.00
point  1 -  2,   DG  0.00 +/-  0.00
point  2 -  3,   DG  0.00 +/-  0.00
point  3 -  4,   DG  0.00 +/-  0.00
point  4 -  5,   DG  0.00 +/-  0.00
point  5 -  6,   DG  0.00 +/-  0.00
point  6 -  7,   DG  0.00 +/-  0.00
point  7 -  8,   DG  0.00 +/-  0.00
point  8 -  9,   DG  0.00 +/-  0.00
point  9 - 10,   DG  0.00 +/-  0.00
point 10 - 11,   DG 1198.03 +/- 11.41
point 11 - 12,   DG 711.32 +/-  1.58
point 12 - 13,   DG 258.19 +/-  3.80
point 13 - 14,   DG -116.21 +/-  3.81
point 14 - 15,   DG 24.24 +/-  0.17
point 15 - 16,   DG 25.40 +/-  0.18
point 16 - 17,   DG 51.57 +/-  0.42
point 17 - 18,   DG 51.20 +/-  0.57
point 18 - 19,   DG 48.42 +/-  0.97
point 19 - 20,   DG 46.55 +/-  0.56
point 20 - 21,   DG 44.53 +/-  0.23
point 21 - 22,   DG 20.56 +/-  0.12
point 22 - 23,   DG 18.23 +/-  0.11
point 23 - 24,   DG 13.64 +/-  0.16
point 24 - 25,   DG -3.58 +/-  0.84
point 25 - 26,   DG -44.60 +/-  0.29
point 26 - 27,   DG -33.45 +/-  0.07
point 27 - 28,   DG -15.22 +/-  0.02
point 28 - 29,   DG  0.81 +/-  0.12

total  0 - 29,   DG 2299.63 +/-  5.17

Here is the prod.mdp for complex:

;
; Production simulation
;

;
; RUN CONTROL
;
integrator   = sd; stochastic leap-frog integrator
nsteps   = 5000; 2 * 500,000 fs = 1000 ps = 1 ns
dt   = 0.002 ; 2 fs
comm-mode= Linear; remove center of mass translation
nstcomm  = 100   ; frequency for center of mass motion removal

;
; OUTPUT CONTROL
;
nstxout= 0  ; don't save coordinates to .trr
nstvout= 0  ; don't save velocities to .trr
nstfout= 0  ; don't save forces to .trr
nstxout-compressed = 1000   ; xtc compressed trajectory output every 
1000 steps (2 ps)
compressed-x-precision = 1000   ; precision with which to write to the 
compressed trajectory file
nstlog = 1000   ; update log file every 2 ps
nstenergy  = 1000   ; save energies every 2 ps
nstcalcenergy  = 100; calculate energies every 100 steps

;
; BONDS
;
constraint_algorithm   = lincs  ; holonomic constraints
constraints= all-bonds  ; hydrogens only are constrained
lincs_iter = 1  ; accuracy of LINCS (1 is default)
lincs_order= 4  ; also related to accuracy (4 is default)
lincs-warnangle= 30 ; maximum angle that a bond can rotate 
before LINCS will complain (30 is default)
continuation   = yes; formerly known as 'unconstrained-start' - 
useful for exact continuations and reruns

;
; NEIGHBOR SEARCHING
;
cutoff-scheme   = Verlet
ns-type = grid   ; search neighboring grid cells
nstlist = 10 ; 20 fs (default is 10)
rlist   = 1.0; short-range neighborlist cutoff (in nm)
pbc = xyz; 3D PBC

;

Re: [gmx-users] question

[Mark Abraham]

On Sun, Dec 31, 2017, 06:14 RAHUL SURESH  wrote:

> On Sat, 30 Dec 2017 at 9:47 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 12/30/17 1:39 AM, s.ghasemlou wrote:
> > > Hello every one,
> > >
> > > After using the command "g_grompp -f em.mdp -c totalbox1.gro -p
> > > topol.top -o ions.tpr" I get the error:
> > >
> > > ERROR 1 [file topol.top, line 863]:
> > >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.(my box vectors are 31.16343- 31.16343- 31.16343)
> >
> > Check to be sure; it seems impossible to me that conventional cutoffs
> > could trigger such an error with such a large box. Make sure that you're
> > not thinking in A and trying to use nm (GROMACS convention).
> >
> > > I have tried different rlist, r columb and rvdw values. I have also
> > > changed the box vector several times, but I still get the same error. I
> > > don't know how to change them to fix the error.
> > >
> > > There is also the below warning:
> > >
> > > Warning: atom name 1 in topol.top and totalbox1.gro does not match (H55
> > > - OW)
> > > Warning: atom name 2 in topol.top and totalbox1.gro does not match (C2
> -
> > > HW1)
> > > Warning: atom name 3 in topol.top and totalbox1.gro does not match (H53
> > > - HW2)
> > > Warning: atom name 4 in topol.top and totalbox1.gro does not match (H54
> > > - OW)
> > > Warning: atom name 5 in topol.top and totalbox1.gro does not match (C1
> -
> > > HW1)
> > > Warning: atom name 6 in topol.top and totalbox1.gro does not match (H51
> > > - HW2)
> > > Warning: atom name 7 in topol.top and totalbox1.gro does not match (H52
> > > - OW)
> > > Warning: atom name 8 in topol.top and totalbox1.gro does not match (C50
> > > - HW1)
> > > Warning: atom name 9 in topol.top and totalbox1.gro does not match
> (H109
> > > - HW2)
> > > Warning: atom name 10 in topol.top and totalbox1.gro does not match
> > > (H110 - OW)
> > > Warning: atom name 11 in topol.top and totalbox1.gro does not match
> (O43
> > > - HW1)
> > > Warning: atom name 12 in topol.top and totalbox1.gro does not match
> (C42
> > > - HW2)
> > > Warning: atom name 13 in topol.top and totalbox1.gro does not match
> (C44
> > > - OW)
> > > Warning: atom name 14 in topol.top and totalbox1.gro does not match
> (C40
> > > - HW1)
> > > Warning: atom name 15 in topol.top and totalbox1.gro does not match
> (C41
> > > - HW2)
> > > Warning: atom name 16 in topol.top and totalbox1.gro does not match
> > > (H100 - OW)
> > > Warning: atom name 17 in topol.top and totalbox1.gro does not match
> (C46
> > > - HW1)
> > > Warning: atom name 18 in topol.top and totalbox1.gro does not match
> > > (H102 - HW2)
> > > Warning: atom name 19 in topol.top and totalbox1.gro does not match
> (C45
> > > - OW)
> > > Warning: atom name 20 in topol.top and totalbox1.gro does not match
> > > (H101 - HW1)
> >
> > Your topology is out of order with respect to the coordinates. The order
> > of the [molecules] section in your .top must be identical to the order
> > of the appearance of coordinates. This is not the case in your system,
> > so you need to correct it. Do not use -maxwarn under any circumstances;
>
>
> Dear Justin
>
> 1. For The above mentioned error is it advisable to manually edit the gro
> file or top file?
>

Once you've decided what you want to simulate, all the input files must be
consistent with that. Change any that aren't.

2. What will the situation to use the flag “-maxwarn” ?
>

If you understand what is causing the situation and why it is not a
problem. That does not apply in your case.

Mark


> > you will get a physically invalid system.
> >
> > -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.
> >
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> 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.o

Re: [gmx-users] question

[RAHUL SURESH]

On Sat, 30 Dec 2017 at 9:47 PM, Justin Lemkul  wrote:

>
>
> On 12/30/17 1:39 AM, s.ghasemlou wrote:
> > Hello every one,
> >
> > After using the command "g_grompp -f em.mdp -c totalbox1.gro -p
> > topol.top -o ions.tpr" I get the error:
> >
> > ERROR 1 [file topol.top, line 863]:
> >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.(my box vectors are 31.16343- 31.16343- 31.16343)
>
> Check to be sure; it seems impossible to me that conventional cutoffs
> could trigger such an error with such a large box. Make sure that you're
> not thinking in A and trying to use nm (GROMACS convention).
>
> > I have tried different rlist, r columb and rvdw values. I have also
> > changed the box vector several times, but I still get the same error. I
> > don't know how to change them to fix the error.
> >
> > There is also the below warning:
> >
> > Warning: atom name 1 in topol.top and totalbox1.gro does not match (H55
> > - OW)
> > Warning: atom name 2 in topol.top and totalbox1.gro does not match (C2 -
> > HW1)
> > Warning: atom name 3 in topol.top and totalbox1.gro does not match (H53
> > - HW2)
> > Warning: atom name 4 in topol.top and totalbox1.gro does not match (H54
> > - OW)
> > Warning: atom name 5 in topol.top and totalbox1.gro does not match (C1 -
> > HW1)
> > Warning: atom name 6 in topol.top and totalbox1.gro does not match (H51
> > - HW2)
> > Warning: atom name 7 in topol.top and totalbox1.gro does not match (H52
> > - OW)
> > Warning: atom name 8 in topol.top and totalbox1.gro does not match (C50
> > - HW1)
> > Warning: atom name 9 in topol.top and totalbox1.gro does not match (H109
> > - HW2)
> > Warning: atom name 10 in topol.top and totalbox1.gro does not match
> > (H110 - OW)
> > Warning: atom name 11 in topol.top and totalbox1.gro does not match (O43
> > - HW1)
> > Warning: atom name 12 in topol.top and totalbox1.gro does not match (C42
> > - HW2)
> > Warning: atom name 13 in topol.top and totalbox1.gro does not match (C44
> > - OW)
> > Warning: atom name 14 in topol.top and totalbox1.gro does not match (C40
> > - HW1)
> > Warning: atom name 15 in topol.top and totalbox1.gro does not match (C41
> > - HW2)
> > Warning: atom name 16 in topol.top and totalbox1.gro does not match
> > (H100 - OW)
> > Warning: atom name 17 in topol.top and totalbox1.gro does not match (C46
> > - HW1)
> > Warning: atom name 18 in topol.top and totalbox1.gro does not match
> > (H102 - HW2)
> > Warning: atom name 19 in topol.top and totalbox1.gro does not match (C45
> > - OW)
> > Warning: atom name 20 in topol.top and totalbox1.gro does not match
> > (H101 - HW1)
>
> Your topology is out of order with respect to the coordinates. The order
> of the [molecules] section in your .top must be identical to the order
> of the appearance of coordinates. This is not the case in your system,
> so you need to correct it. Do not use -maxwarn under any circumstances;


Dear Justin

1. For The above mentioned error is it advisable to manually edit the gro
file or top file?

2. What will the situation to use the flag “-maxwarn” ?


> you will get a physically invalid system.
>
> -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.
>
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] question

[Justin Lemkul]

On 12/30/17 1:39 AM, s.ghasemlou wrote:

Hello every one,

After using the command "g_grompp -f em.mdp -c totalbox1.gro -p
topol.top -o ions.tpr" I get the error:

ERROR 1 [file topol.top, line 863]:
   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.(my box vectors are 31.16343- 31.16343- 31.16343)


Check to be sure; it seems impossible to me that conventional cutoffs 
could trigger such an error with such a large box. Make sure that you're 
not thinking in A and trying to use nm (GROMACS convention).



I have tried different rlist, r columb and rvdw values. I have also
changed the box vector several times, but I still get the same error. I
don't know how to change them to fix the error.

There is also the below warning:

Warning: atom name 1 in topol.top and totalbox1.gro does not match (H55
- OW)
Warning: atom name 2 in topol.top and totalbox1.gro does not match (C2 -
HW1)
Warning: atom name 3 in topol.top and totalbox1.gro does not match (H53
- HW2)
Warning: atom name 4 in topol.top and totalbox1.gro does not match (H54
- OW)
Warning: atom name 5 in topol.top and totalbox1.gro does not match (C1 -
HW1)
Warning: atom name 6 in topol.top and totalbox1.gro does not match (H51
- HW2)
Warning: atom name 7 in topol.top and totalbox1.gro does not match (H52
- OW)
Warning: atom name 8 in topol.top and totalbox1.gro does not match (C50
- HW1)
Warning: atom name 9 in topol.top and totalbox1.gro does not match (H109
- HW2)
Warning: atom name 10 in topol.top and totalbox1.gro does not match
(H110 - OW)
Warning: atom name 11 in topol.top and totalbox1.gro does not match (O43
- HW1)
Warning: atom name 12 in topol.top and totalbox1.gro does not match (C42
- HW2)
Warning: atom name 13 in topol.top and totalbox1.gro does not match (C44
- OW)
Warning: atom name 14 in topol.top and totalbox1.gro does not match (C40
- HW1)
Warning: atom name 15 in topol.top and totalbox1.gro does not match (C41
- HW2)
Warning: atom name 16 in topol.top and totalbox1.gro does not match
(H100 - OW)
Warning: atom name 17 in topol.top and totalbox1.gro does not match (C46
- HW1)
Warning: atom name 18 in topol.top and totalbox1.gro does not match
(H102 - HW2)
Warning: atom name 19 in topol.top and totalbox1.gro does not match (C45
- OW)
Warning: atom name 20 in topol.top and totalbox1.gro does not match
(H101 - HW1)


Your topology is out of order with respect to the coordinates. The order 
of the [molecules] section in your .top must be identical to the order 
of the appearance of coordinates. This is not the case in your system, 
so you need to correct it. Do not use -maxwarn under any circumstances; 
you will get a physically invalid system.


-Justin

--
==

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

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

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

==

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Re: [gmx-users] question

[Nikhil Maroli]

Okay,

What forcefield are you using? it is not advised to change the parameters
such as r columb and rvdw. If the smallest box vector is less than 2 x
longest cut off then you are not satisfying the minimum image convention.
atom name mismatch may indicate that the order of the topology does not
match with the coordinate files, using maxwarn is not a good idea.So here
you can try to fix atom mismatch problem first.

If it is not yet solved post your coordinates and topology details.
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Re: [gmx-users] question

[s.ghasemlou]

در 2017-12-30 10:31، Nikhil Maroli نوشته است:

> Hello,
> 
> Read the previous posts and do a google search. maybe you can start from
> here :
> 
> http://www.gromacs.org/Documentation/Errors#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

Thank you dear Nikhil Maroli for your response. I have read the posts
before and also visited the site you introduced but it didn't help me.
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Re: [gmx-users] question

[s.ghasemlou]

در 2017-12-30 10:15، RAHUL SURESH نوشته است:

> On Sat, 30 Dec 2017 at 12:10 PM, s.ghasemlou  wrote: 
> thanks for your response 
> 
>> Hello every one,
>> 
>> After using the command "g_grompp -f em.mdp -c totalbox1.gro -p
>> topol.top -o ions.tpr" I get the error:
>> 
>> ERROR 1 [file topol.top, line 863]:
>> 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.(my box vectors are 31.16343- 31.16343- 31.16343)
> 
> What is the cut off scheme and value..? 
> 
> below is the em.mdp file content I have used 
> 
> ; LINES STARTING WITH ';' ARE COMMENTS
> title  = Minimization ; Title of run 
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep  ; Algorithm (steep = steepest descent minimization)
> emtol  = 1000.0   ; Stop minimization when the maximum force < 10.0 kJ/mol
> emstep  = 0.01  ; Energy step size
> nsteps  = 5; Maximum number of (minimization) steps to perform
> energygrps = system ; Which energy group(s) to write to disk 
> ; 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
> ns_type  = grid  ; Method to determine neighbor list (simple, grid)
> rlist  = 1.0  ; Cut-off for making neighbor list (short range forces)
> coulombtype = PME  ; Treatment of long range electrostatic interactions
> rcoulomb = 1.0  ; long range electrostatic cut-off
> rvdw  = 1.0  ; long range Van der Waals cut-off
> pbc = xyz   ; Periodic Boundary Conditions (yes/no) 
> 
>> I have tried different rlist, r columb and rvdw values. I have also
>> changed the box vector several times, but I still get the same error. I
>> don't know how to change them to fix the error.
>> 
>> There is also the below warning:
>> 
>> Warning: atom name 1 in topol.top and totalbox1.gro does not match (H55
>> - OW)
>> Warning: atom name 2 in topol.top and totalbox1.gro does not match (C2 -
>> HW1)
>> Warning: atom name 3 in topol.top and totalbox1.gro does not match (H53
>> - HW2)
>> Warning: atom name 4 in topol.top and totalbox1.gro does not match (H54
>> - OW)
>> Warning: atom name 5 in topol.top and totalbox1.gro does not match (C1 -
>> HW1)
>> Warning: atom name 6 in topol.top and totalbox1.gro does not match (H51
>> - HW2)
>> Warning: atom name 7 in topol.top and totalbox1.gro does not match (H52
>> - OW)
>> Warning: atom name 8 in topol.top and totalbox1.gro does not match (C50
>> - HW1)
>> Warning: atom name 9 in topol.top and totalbox1.gro does not match (H109
>> - HW2)
>> Warning: atom name 10 in topol.top and totalbox1.gro does not match
>> (H110 - OW)
>> Warning: atom name 11 in topol.top and totalbox1.gro does not match (O43
>> - HW1)
>> Warning: atom name 12 in topol.top and totalbox1.gro does not match (C42
>> - HW2)
>> Warning: atom name 13 in topol.top and totalbox1.gro does not match (C44
>> - OW)
>> Warning: atom name 14 in topol.top and totalbox1.gro does not match (C40
>> - HW1)
>> Warning: atom name 15 in topol.top and totalbox1.gro does not match (C41
>> - HW2)
>> Warning: atom name 16 in topol.top and totalbox1.gro does not match
>> (H100 - OW)
>> Warning: atom name 17 in topol.top and totalbox1.gro does not match (C46
>> - HW1)
>> Warning: atom name 18 in topol.top and totalbox1.gro does not match
>> (H102 - HW2)
>> Warning: atom name 19 in topol.top and totalbox1.gro does not match (C45
>> - OW)
>> Warning: atom name 20 in topol.top and totalbox1.gro does not match
>> (H101 - HW1)
>> (more than 20 non-matching atom names)
>> WARNING 1 [file topol.top, line 863]:
>> 32798 non-matching atom names
>> atom names from topol.top will be used
>> atom names from totalbox1.gro will be ignored
> 
> You can use maxwarn flag or change the cane in toolbox.gro 
> would you please tell me what the cane is in a .gro file? because using 
> maxwarn flag didn't fix it.
> 
>> As I checked both the .gro and topol.top contents, atom names are the
>> same but here atom names of solvent water are mixed with atom names of
>> the ligand I used.
> 
> Someone else would definitely help you in This.
> 
>> please help me on this. Thanks in advance.
>> --
>> 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.
> -- 
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
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* For (u

Re: [gmx-users] question

[Nikhil Maroli]

Hello,

Read the previous posts and do a google search. maybe you can start from
here :

http://www.gromacs.org/Documentation/Errors#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
-- 
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Re: [gmx-users] question

[RAHUL SURESH]

On Sat, 30 Dec 2017 at 12:10 PM, s.ghasemlou  wrote:

> Hello every one,
>
> After using the command "g_grompp -f em.mdp -c totalbox1.gro -p
> topol.top -o ions.tpr" I get the error:
>
> ERROR 1 [file topol.top, line 863]:
>   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.(my box vectors are 31.16343- 31.16343- 31.16343)

What is the cut off scheme and value..?

>
>
> I have tried different rlist, r columb and rvdw values. I have also
> changed the box vector several times, but I still get the same error. I
> don't know how to change them to fix the error.
>
> There is also the below warning:
>
> Warning: atom name 1 in topol.top and totalbox1.gro does not match (H55
> - OW)
> Warning: atom name 2 in topol.top and totalbox1.gro does not match (C2 -
> HW1)
> Warning: atom name 3 in topol.top and totalbox1.gro does not match (H53
> - HW2)
> Warning: atom name 4 in topol.top and totalbox1.gro does not match (H54
> - OW)
> Warning: atom name 5 in topol.top and totalbox1.gro does not match (C1 -
> HW1)
> Warning: atom name 6 in topol.top and totalbox1.gro does not match (H51
> - HW2)
> Warning: atom name 7 in topol.top and totalbox1.gro does not match (H52
> - OW)
> Warning: atom name 8 in topol.top and totalbox1.gro does not match (C50
> - HW1)
> Warning: atom name 9 in topol.top and totalbox1.gro does not match (H109
> - HW2)
> Warning: atom name 10 in topol.top and totalbox1.gro does not match
> (H110 - OW)
> Warning: atom name 11 in topol.top and totalbox1.gro does not match (O43
> - HW1)
> Warning: atom name 12 in topol.top and totalbox1.gro does not match (C42
> - HW2)
> Warning: atom name 13 in topol.top and totalbox1.gro does not match (C44
> - OW)
> Warning: atom name 14 in topol.top and totalbox1.gro does not match (C40
> - HW1)
> Warning: atom name 15 in topol.top and totalbox1.gro does not match (C41
> - HW2)
> Warning: atom name 16 in topol.top and totalbox1.gro does not match
> (H100 - OW)
> Warning: atom name 17 in topol.top and totalbox1.gro does not match (C46
> - HW1)
> Warning: atom name 18 in topol.top and totalbox1.gro does not match
> (H102 - HW2)
> Warning: atom name 19 in topol.top and totalbox1.gro does not match (C45
> - OW)
> Warning: atom name 20 in topol.top and totalbox1.gro does not match
> (H101 - HW1)
> (more than 20 non-matching atom names)
> WARNING 1 [file topol.top, line 863]:
>   32798 non-matching atom names
>   atom names from topol.top will be used
>   atom names from totalbox1.gro will be ignored

You can use maxwarn flag or change the cane in toolbox.gro

>
>
> As I checked both the .gro and topol.top contents, atom names are the
> same but here atom names of solvent water are mixed with atom names of
> the ligand I used.

Someone else would definitely help you in This.

>
> please help me on this. Thanks in advance.
> --
> 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.
>
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] question of perturbing order in single topology FEP, gromacs

[asaffarhi]

Hi Peng,

You can compare the relative free energy with the other topology to  
see which order probably gives you the correct results. I don't know  
what is your project and for free energies associated with bonds where  
the atom (Carbon or Oxygen) is without nonbonded interactions there  
are analytic results


http://iopscience.iop.org/article/10.1088/1367-2630/18/2/023039/meta

Best,
Asaf

Quoting Peng He :


Hi, Asaf,

I totally agreed what you suggested, but I am considering the bonded energy
term changing in the free energy simulation in the single topology, I have
read the paper you suggested and it is using a dual topology method which
also works well in my case, in the single topology method, the bond
equilibrium length is changing according to lambda values. for example, in
ethane -> methanol case, the shrinking(changing the bonded lambdas) of cc
bond to co bond(the second carbon is changing to oxygen gradually and
shares one atom in the topology file) is gonna affect the 1,4 electrostatic
interaction of hydrogens connecting to carbon and carbon/oxygen center.
While in dual topology there is no such problem because the charge is only
disappearing and appearing with no position change. I am wondering if the
single topology method relies on the order of perturbation a lot and which
order is the most correct way.

Best
Peng

2017-11-30 9:27 GMT-05:00 :


Dear Peng,

There are several ways to do it.

The simplest way is to take each molecule and perturb it separately. You
have one Ethane molecule and one methanol molecule so you need a file
containing only Ethane and a file containing only methanol.

The different atoms between the molecules are CH3 in Ethane and OH in
methanol.
In each molecule you can remove the VDW and Coul terms of these atoms in
transformations. That's all. See Fig. 9.
The transformed systems should be identical in their remaining nonbonded
terms and bonded terms relating the common atoms so an additional minor
transformations may be needed.

There may be some issues related to changing the total charge in
transformations, which can cause artificial changes in the calculated free
energies.

Best regards,

Asaf


Quoting Peng He :

Hi, Asaf,


Thank you very much for your suggestions, I am not sure I understand it
correctly.

2017-11-29 13:22 GMT-05:00 :

Dear Peng,


You can transform each of the molecules seperately.



You can remove the nonbonded interactions of the atoms that are different


between the compared molecules.

Does it mean when going from A-B to A-C, decouple the B's nonbonded than

coupling the C's nonbonded interaction?

Then, if you have only one dihedral relating the different atoms to the

common atoms in each molecule it does not need to be removed. Also, the
bond angle and covalent bond terms do not need to be removed. This is
based
on NVT but may be also accurate for NPT.

In the Ethane -> methanol case, the C-C bond length decreases from 1.5 to

1.4 when perturbing to C-O bond, and the kappa for the bond also changes,
I
am not sure but I think we can use bonded lambdas to perturb the bond, I
did not remove any bond or angle in this case.
I think what you suggest is dual topology method which contains a dummy
CH3
group in Methanol and a dummy OH group in Ethane, in that case I don't
need
to change the bond length and angle, and it would not create such
different
free energy values. I really test it in dual topology method and there is
little effect from the order of perturbations.



We also saw that the order of transforming matters but maybe you can try
without removing the bonded terms.




For more details you can read:

http://www.sciencedirect.com/science/article/pii/S0010465516303411

Best,
Asaf


Quoting Peng He :

HI, all,



I am recently doing some test FEP calculations to get familiar, I am
preparing a system of ethane -> methanol using Amber gaff force field
and
single topology method.

"  4 [ atomtypes ]
  5 ;name   bond_type mass charge   ptype   sigma
 epsilon
Amb
  6  c3   c3  0.0  0.0   A 3.39967e-01
4.57730e-01 ; 1.91  0.1094
  7  hc   hc  0.0  0.0   A 2.64953e-01
6.56888e-02 ; 1.49  0.0157
  8  oh   oh  0.0  0.0   A 3.06647e-01
8.80314e-01 ; 1.72  0.2104
  9  h1   h1  0.0  0.0   A 2.47135e-01
6.56888e-02 ; 1.39  0.0157
 10  dh   hc  0.0  0.0   A 0.0  0.0
 11  ho   ho  0.0  0.0   A 0.0e+00
 0.0e+00
 12 [ moleculetype ]
 13 ;namenrexcl
 14  UNK  3
 15
 16 [ atoms ]
 17 ;   nr  type  resi  res  atom  cgnr charge  mass   ;
qtot
bond_type
 18  1   c3 1   UNKC11-0.095100 12.01000   c3
 0.11670012.01000
 19  2   c3 1   UNKC22-0.095100 12.01000   oh
-0.59880112.01000
 20  3   hc 1   UNKH13 0.031700  1.00800   h1
 0.028700 1.00800
 21  4   hc 1

Re: [gmx-users] question of perturbing order in single topology FEP, gromacs

[Peng He]

Hi, Asaf,

I totally agreed what you suggested, but I am considering the bonded energy
term changing in the free energy simulation in the single topology, I have
read the paper you suggested and it is using a dual topology method which
also works well in my case, in the single topology method, the bond
equilibrium length is changing according to lambda values. for example, in
ethane -> methanol case, the shrinking(changing the bonded lambdas) of cc
bond to co bond(the second carbon is changing to oxygen gradually and
shares one atom in the topology file) is gonna affect the 1,4 electrostatic
interaction of hydrogens connecting to carbon and carbon/oxygen center.
While in dual topology there is no such problem because the charge is only
disappearing and appearing with no position change. I am wondering if the
single topology method relies on the order of perturbation a lot and which
order is the most correct way.

Best
Peng

2017-11-30 9:27 GMT-05:00 :

> Dear Peng,
>
> There are several ways to do it.
>
> The simplest way is to take each molecule and perturb it separately. You
> have one Ethane molecule and one methanol molecule so you need a file
> containing only Ethane and a file containing only methanol.
>
> The different atoms between the molecules are CH3 in Ethane and OH in
> methanol.
> In each molecule you can remove the VDW and Coul terms of these atoms in
> transformations. That's all. See Fig. 9.
> The transformed systems should be identical in their remaining nonbonded
> terms and bonded terms relating the common atoms so an additional minor
> transformations may be needed.
>
> There may be some issues related to changing the total charge in
> transformations, which can cause artificial changes in the calculated free
> energies.
>
> Best regards,
>
> Asaf
>
>
> Quoting Peng He :
>
> Hi, Asaf,
>>
>> Thank you very much for your suggestions, I am not sure I understand it
>> correctly.
>>
>> 2017-11-29 13:22 GMT-05:00 :
>>
>> Dear Peng,
>>>
>>> You can transform each of the molecules seperately.
>>>
>>
>> You can remove the nonbonded interactions of the atoms that are different
>>
>>> between the compared molecules.
>>>
>>> Does it mean when going from A-B to A-C, decouple the B's nonbonded than
>> coupling the C's nonbonded interaction?
>>
>> Then, if you have only one dihedral relating the different atoms to the
>>> common atoms in each molecule it does not need to be removed. Also, the
>>> bond angle and covalent bond terms do not need to be removed. This is
>>> based
>>> on NVT but may be also accurate for NPT.
>>>
>>> In the Ethane -> methanol case, the C-C bond length decreases from 1.5 to
>> 1.4 when perturbing to C-O bond, and the kappa for the bond also changes,
>> I
>> am not sure but I think we can use bonded lambdas to perturb the bond, I
>> did not remove any bond or angle in this case.
>> I think what you suggest is dual topology method which contains a dummy
>> CH3
>> group in Methanol and a dummy OH group in Ethane, in that case I don't
>> need
>> to change the bond length and angle, and it would not create such
>> different
>> free energy values. I really test it in dual topology method and there is
>> little effect from the order of perturbations.
>>
>>>
>>> We also saw that the order of transforming matters but maybe you can try
>>> without removing the bonded terms.
>>>
>>
>>
>> For more details you can read:
>>> http://www.sciencedirect.com/science/article/pii/S0010465516303411
>>>
>>> Best,
>>> Asaf
>>>
>>>
>>> Quoting Peng He :
>>>
>>> HI, all,
>>>

 I am recently doing some test FEP calculations to get familiar, I am
 preparing a system of ethane -> methanol using Amber gaff force field
 and
 single topology method.

 "  4 [ atomtypes ]
   5 ;name   bond_type mass charge   ptype   sigma
  epsilon
 Amb
   6  c3   c3  0.0  0.0   A 3.39967e-01
 4.57730e-01 ; 1.91  0.1094
   7  hc   hc  0.0  0.0   A 2.64953e-01
 6.56888e-02 ; 1.49  0.0157
   8  oh   oh  0.0  0.0   A 3.06647e-01
 8.80314e-01 ; 1.72  0.2104
   9  h1   h1  0.0  0.0   A 2.47135e-01
 6.56888e-02 ; 1.39  0.0157
  10  dh   hc  0.0  0.0   A 0.0  0.0
  11  ho   ho  0.0  0.0   A 0.0e+00
  0.0e+00
  12 [ moleculetype ]
  13 ;namenrexcl
  14  UNK  3
  15
  16 [ atoms ]
  17 ;   nr  type  resi  res  atom  cgnr charge  mass   ;
 qtot
 bond_type
  18  1   c3 1   UNKC11-0.095100 12.01000   c3
  0.11670012.01000
  19  2   c3 1   UNKC22-0.095100 12.01000   oh
 -0.59880112.01000
  20  3   hc 1   UNKH13 0.031700  1.00800   h1
  0.028700 1.00800
  21  4   hc 1   UNKH24 0.031700  

Re: [gmx-users] question of perturbing order in single topology FEP, gromacs

[asaffarhi]

Dear Peng,

There are several ways to do it.

The simplest way is to take each molecule and perturb it separately.  
You have one Ethane molecule and one methanol molecule so you need a  
file containing only Ethane and a file containing only methanol.


The different atoms between the molecules are CH3 in Ethane and OH in  
methanol.
In each molecule you can remove the VDW and Coul terms of these atoms  
in transformations. That's all. See Fig. 9.
The transformed systems should be identical in their remaining  
nonbonded terms and bonded terms relating the common atoms so an  
additional minor transformations may be needed.


There may be some issues related to changing the total charge in  
transformations, which can cause artificial changes in the calculated  
free energies.


Best regards,
Asaf


Quoting Peng He :


Hi, Asaf,

Thank you very much for your suggestions, I am not sure I understand it
correctly.

2017-11-29 13:22 GMT-05:00 :


Dear Peng,

You can transform each of the molecules seperately.


You can remove the nonbonded interactions of the atoms that are different

between the compared molecules.


Does it mean when going from A-B to A-C, decouple the B's nonbonded than
coupling the C's nonbonded interaction?


Then, if you have only one dihedral relating the different atoms to the
common atoms in each molecule it does not need to be removed. Also, the
bond angle and covalent bond terms do not need to be removed. This is based
on NVT but may be also accurate for NPT.


In the Ethane -> methanol case, the C-C bond length decreases from 1.5 to
1.4 when perturbing to C-O bond, and the kappa for the bond also changes, I
am not sure but I think we can use bonded lambdas to perturb the bond, I
did not remove any bond or angle in this case.
I think what you suggest is dual topology method which contains a dummy CH3
group in Methanol and a dummy OH group in Ethane, in that case I don't need
to change the bond length and angle, and it would not create such different
free energy values. I really test it in dual topology method and there is
little effect from the order of perturbations.


We also saw that the order of transforming matters but maybe you can try
without removing the bonded terms.




For more details you can read:
http://www.sciencedirect.com/science/article/pii/S0010465516303411

Best,
Asaf


Quoting Peng He :

HI, all,


I am recently doing some test FEP calculations to get familiar, I am
preparing a system of ethane -> methanol using Amber gaff force field and
single topology method.

"  4 [ atomtypes ]
  5 ;name   bond_type mass charge   ptype   sigma epsilon
Amb
  6  c3   c3  0.0  0.0   A 3.39967e-01
4.57730e-01 ; 1.91  0.1094
  7  hc   hc  0.0  0.0   A 2.64953e-01
6.56888e-02 ; 1.49  0.0157
  8  oh   oh  0.0  0.0   A 3.06647e-01
8.80314e-01 ; 1.72  0.2104
  9  h1   h1  0.0  0.0   A 2.47135e-01
6.56888e-02 ; 1.39  0.0157
 10  dh   hc  0.0  0.0   A 0.0  0.0
 11  ho   ho  0.0  0.0   A 0.0e+00
 0.0e+00
 12 [ moleculetype ]
 13 ;namenrexcl
 14  UNK  3
 15
 16 [ atoms ]
 17 ;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
bond_type
 18  1   c3 1   UNKC11-0.095100 12.01000   c3
 0.11670012.01000
 19  2   c3 1   UNKC22-0.095100 12.01000   oh
-0.59880112.01000
 20  3   hc 1   UNKH13 0.031700  1.00800   h1
 0.028700 1.00800
 21  4   hc 1   UNKH24 0.031700  1.00800   h1
 0.028700 1.00800
 22  5   hc 1   UNKH35 0.031700  1.00800   h1
 0.028700 1.00800
 23  6   hc 1   UNKH46 0.031700  1.00800   ho
 0.396000 1.00800
 24  7   hc 1   UNKH57 0.031700  1.00800   dh
 0.00 1.00800
 25  8   hc 1   UNKH68 0.031700  1.00800   dh
 0.00 1.00800
 26
 27 [ bonds ]
 28 ;   ai aj funct   r k
 29  1  2   11.5375e-012.5179e+05  1.4233e-01
2.6501e+05
 30  1  3   11.0969e-012.7665e+05  1.0969e-01
2.7665e+05
 31  1  4   11.0969e-012.7665e+05  1.0969e-01
2.7665e+05
 32  1  5   11.0969e-012.7665e+05  1.0969e-01
2.7665e+05
 33  2  6   11.0969e-012.7665e+05  9.7300e-02
3.1079e+05
 34  2  7   11.0969e-012.7665e+05  1.0969e-01
2.7665e+05
 35  2  8   11.0969e-012.7665e+05  1.0969e-01
2.7665e+05
...
..."

I know to perturbing from large molecule(ethane) to small(methanol), I
need
to perturb the electrostatic interaction first than vdw, But I don't know
where to perturb the bonded lambdas. I have tested different orders of
Bonded lambdas, and I have got a quite different answer which seems odd to
me. I have a table for that
stage1 stage2 stage3 dG

Re: [gmx-users] question of perturbing order in single topology FEP, gromacs

[Peng He]

Hi, Asaf,

Thank you very much for your suggestions, I am not sure I understand it
correctly.

2017-11-29 13:22 GMT-05:00 :

> Dear Peng,
>
> You can transform each of the molecules seperately.

You can remove the nonbonded interactions of the atoms that are different
> between the compared molecules.
>
Does it mean when going from A-B to A-C, decouple the B's nonbonded than
coupling the C's nonbonded interaction?

> Then, if you have only one dihedral relating the different atoms to the
> common atoms in each molecule it does not need to be removed. Also, the
> bond angle and covalent bond terms do not need to be removed. This is based
> on NVT but may be also accurate for NPT.
>
In the Ethane -> methanol case, the C-C bond length decreases from 1.5 to
1.4 when perturbing to C-O bond, and the kappa for the bond also changes, I
am not sure but I think we can use bonded lambdas to perturb the bond, I
did not remove any bond or angle in this case.
I think what you suggest is dual topology method which contains a dummy CH3
group in Methanol and a dummy OH group in Ethane, in that case I don't need
to change the bond length and angle, and it would not create such different
free energy values. I really test it in dual topology method and there is
little effect from the order of perturbations.
>
> We also saw that the order of transforming matters but maybe you can try
> without removing the bonded terms.


> For more details you can read:
> http://www.sciencedirect.com/science/article/pii/S0010465516303411
>
> Best,
> Asaf
>
>
> Quoting Peng He :
>
> HI, all,
>>
>> I am recently doing some test FEP calculations to get familiar, I am
>> preparing a system of ethane -> methanol using Amber gaff force field and
>> single topology method.
>>
>> "  4 [ atomtypes ]
>>   5 ;name   bond_type mass charge   ptype   sigma epsilon
>> Amb
>>   6  c3   c3  0.0  0.0   A 3.39967e-01
>> 4.57730e-01 ; 1.91  0.1094
>>   7  hc   hc  0.0  0.0   A 2.64953e-01
>> 6.56888e-02 ; 1.49  0.0157
>>   8  oh   oh  0.0  0.0   A 3.06647e-01
>> 8.80314e-01 ; 1.72  0.2104
>>   9  h1   h1  0.0  0.0   A 2.47135e-01
>> 6.56888e-02 ; 1.39  0.0157
>>  10  dh   hc  0.0  0.0   A 0.0  0.0
>>  11  ho   ho  0.0  0.0   A 0.0e+00
>>  0.0e+00
>>  12 [ moleculetype ]
>>  13 ;namenrexcl
>>  14  UNK  3
>>  15
>>  16 [ atoms ]
>>  17 ;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
>> bond_type
>>  18  1   c3 1   UNKC11-0.095100 12.01000   c3
>>  0.11670012.01000
>>  19  2   c3 1   UNKC22-0.095100 12.01000   oh
>> -0.59880112.01000
>>  20  3   hc 1   UNKH13 0.031700  1.00800   h1
>>  0.028700 1.00800
>>  21  4   hc 1   UNKH24 0.031700  1.00800   h1
>>  0.028700 1.00800
>>  22  5   hc 1   UNKH35 0.031700  1.00800   h1
>>  0.028700 1.00800
>>  23  6   hc 1   UNKH46 0.031700  1.00800   ho
>>  0.396000 1.00800
>>  24  7   hc 1   UNKH57 0.031700  1.00800   dh
>>  0.00 1.00800
>>  25  8   hc 1   UNKH68 0.031700  1.00800   dh
>>  0.00 1.00800
>>  26
>>  27 [ bonds ]
>>  28 ;   ai aj funct   r k
>>  29  1  2   11.5375e-012.5179e+05  1.4233e-01
>> 2.6501e+05
>>  30  1  3   11.0969e-012.7665e+05  1.0969e-01
>> 2.7665e+05
>>  31  1  4   11.0969e-012.7665e+05  1.0969e-01
>> 2.7665e+05
>>  32  1  5   11.0969e-012.7665e+05  1.0969e-01
>> 2.7665e+05
>>  33  2  6   11.0969e-012.7665e+05  9.7300e-02
>> 3.1079e+05
>>  34  2  7   11.0969e-012.7665e+05  1.0969e-01
>> 2.7665e+05
>>  35  2  8   11.0969e-012.7665e+05  1.0969e-01
>> 2.7665e+05
>> ...
>> ..."
>>
>> I know to perturbing from large molecule(ethane) to small(methanol), I
>> need
>> to perturb the electrostatic interaction first than vdw, But I don't know
>> where to perturb the bonded lambdas. I have tested different orders of
>> Bonded lambdas, and I have got a quite different answer which seems odd to
>> me. I have a table for that
>> stage1 stage2 stage3 dG(kj) dG(kcal)
>> single topology solv q/bonded/vdw -14.36 -3.43
>> bonded q vdw -13.79 -3.30
>> bonded/q vdw -14.91 -3.56
>> q bonded vdw -17.13 -4.09
>> q bonded/vdw -20.22 -4.83
>> q vdw bonded -25.2 -6.02
>> single topology vac q/bonded/vdw 10.32 2.47
>> bonded q vdw 9.53 2.28
>> bonded/q vdw 9.1 2.17
>> q bonded vdw 8.71 2.08
>> q bonded/vdw 9.64 2.30
>> q vdw bonded 9.84 2.35
>> The desolvation free energy of ethane is -2.48 and methanol 3.48kcal.
>> The best result which close the cyclo for ethane,vac -> ethane, solv ->
>> methanol, solv -> methanol,vac -> ethane,vac is perturbing all thr

Re: [gmx-users] question of perturbing order in single topology FEP, gromacs

[asaffarhi]

Dear Peng,

You can transform each of the molecules seperately.
You can remove the nonbonded interactions of the atoms that are  
different between the compared molecules.
Then, if you have only one dihedral relating the different atoms to  
the common atoms in each molecule it does not need to be removed.  
Also, the bond angle and covalent bond terms do not need to be  
removed. This is based on NVT but may be also accurate for NPT.
We also saw that the order of transforming matters but maybe you can  
try without removing the bonded terms.


For more details you can read:
http://www.sciencedirect.com/science/article/pii/S0010465516303411

Best,
Asaf


Quoting Peng He :


HI, all,

I am recently doing some test FEP calculations to get familiar, I am
preparing a system of ethane -> methanol using Amber gaff force field and
single topology method.

"  4 [ atomtypes ]
  5 ;name   bond_type mass charge   ptype   sigma epsilon
Amb
  6  c3   c3  0.0  0.0   A 3.39967e-01
4.57730e-01 ; 1.91  0.1094
  7  hc   hc  0.0  0.0   A 2.64953e-01
6.56888e-02 ; 1.49  0.0157
  8  oh   oh  0.0  0.0   A 3.06647e-01
8.80314e-01 ; 1.72  0.2104
  9  h1   h1  0.0  0.0   A 2.47135e-01
6.56888e-02 ; 1.39  0.0157
 10  dh   hc  0.0  0.0   A 0.0  0.0
 11  ho   ho  0.0  0.0   A 0.0e+00   0.0e+00
 12 [ moleculetype ]
 13 ;namenrexcl
 14  UNK  3
 15
 16 [ atoms ]
 17 ;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
bond_type
 18  1   c3 1   UNKC11-0.095100 12.01000   c3
 0.11670012.01000
 19  2   c3 1   UNKC22-0.095100 12.01000   oh
-0.59880112.01000
 20  3   hc 1   UNKH13 0.031700  1.00800   h1
 0.028700 1.00800
 21  4   hc 1   UNKH24 0.031700  1.00800   h1
 0.028700 1.00800
 22  5   hc 1   UNKH35 0.031700  1.00800   h1
 0.028700 1.00800
 23  6   hc 1   UNKH46 0.031700  1.00800   ho
 0.396000 1.00800
 24  7   hc 1   UNKH57 0.031700  1.00800   dh
 0.00 1.00800
 25  8   hc 1   UNKH68 0.031700  1.00800   dh
 0.00 1.00800
 26
 27 [ bonds ]
 28 ;   ai aj funct   r k
 29  1  2   11.5375e-012.5179e+05  1.4233e-012.6501e+05
 30  1  3   11.0969e-012.7665e+05  1.0969e-012.7665e+05
 31  1  4   11.0969e-012.7665e+05  1.0969e-012.7665e+05
 32  1  5   11.0969e-012.7665e+05  1.0969e-012.7665e+05
 33  2  6   11.0969e-012.7665e+05  9.7300e-023.1079e+05
 34  2  7   11.0969e-012.7665e+05  1.0969e-012.7665e+05
 35  2  8   11.0969e-012.7665e+05  1.0969e-012.7665e+05
...
..."

I know to perturbing from large molecule(ethane) to small(methanol), I need
to perturb the electrostatic interaction first than vdw, But I don't know
where to perturb the bonded lambdas. I have tested different orders of
Bonded lambdas, and I have got a quite different answer which seems odd to
me. I have a table for that
stage1 stage2 stage3 dG(kj) dG(kcal)
single topology solv q/bonded/vdw -14.36 -3.43
bonded q vdw -13.79 -3.30
bonded/q vdw -14.91 -3.56
q bonded vdw -17.13 -4.09
q bonded/vdw -20.22 -4.83
q vdw bonded -25.2 -6.02
single topology vac q/bonded/vdw 10.32 2.47
bonded q vdw 9.53 2.28
bonded/q vdw 9.1 2.17
q bonded vdw 8.71 2.08
q bonded/vdw 9.64 2.30
q vdw bonded 9.84 2.35
The desolvation free energy of ethane is -2.48 and methanol 3.48kcal.
The best result which close the cyclo for ethane,vac -> ethane, solv ->
methanol, solv -> methanol,vac -> ethane,vac is perturbing all three
together(q/bonded/vdw) followed by perturbing bonded/q together then vdw.
The worst is to decouple bonded lambdas the last. When I try dual topology
method, there is no such difference where to place the bonded lambdas...

 I am confused that which one should used and why others are not OK?

Thank you
Best
Peng
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Re: [gmx-users] Question about "gmx traj" command

[Mark Abraham]

Hi,

Force is a vector, yes. And its units are not kcal/mol nm in GROMACS. See
chapter 2 of the reference manual.

Mark

On Tue, Oct 17, 2017 at 9:00 AM Chang Woon Jang 
wrote:

> Dear Justin,
>
> Thank you for your help. One more question is that there are positive
> and negative values. Does this mean that the forces are written as
> vector values? For example, the value of -40 means negative Z direction
> with 40 kcal/mol nm ?
>
> Thank you.
>
> Best regards,
> Changwoon Jang
>
> On Mon, Oct 16, 2017 at 10:38 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 10/16/17 9:36 AM, Chang Woon Jang wrote:
> >
> >> Dear Gromacs Users,
> >>
> >>  I have a question about the gmx traj in order to calculate the
> force
> >> components.
> >>
> >> I used the following command. > gmx traj -f topol_new.trr -s
> topol_new.tpr
> >> -af force_all_z_l9.xvg -z yes
> >>
> >> It produced "force_all_z_l9.xvg" file. In the file, there are four
> >> columns.
> >> The first column should be the atom ID.
> >>
> >> My question is what is the rest of columns? For example, some of the
> >> values
> >> are negative and the other values are positive.
> >>
> >> -z yes means the plot of Z-component in the manual. I do not know what
> the
> >> exact meaning of three columns. Would you please give me a comment on
> >> that?
> >>
> >
> > You're getting (x,y,z) because you haven't turned them off (note from the
> > help info that all dimensions are on by default).
> >
> > All you need is:
> >
> > gmx traj ... -nox -noy -z
> >
> > -Justin
> >
> >
> > Thank you.
> >>
> >>
> >> # This file was created Mon Oct 16 21:53:33 2017
> >> # Created by:
> >> #:-) GROMACS - gmx traj, 2016.4-dev-20170620-8d2584c-unknown (-:
> >> #
> >> # Executable:  /home/chang/Packages/votca/bin/gmx
> >> # Data prefix:  /home/chang/Packages/votca
> >> # Working dir:  /home/chang/2017_NU_PROJECT/1_
> >> FIRST_PROJECT/1_Less_5Million/
> >> 5_REVERSED_ATOMISTIC_TEST/1_Lambda_9/1_TENSION/1_SR10e8_l9_
> >> 300K/ANALYSIS/7_Force_Component
> >> # Command line:
> >> #  gmx traj -f topol_new.trr -s topol_new.tpr -af force_all_z_l9.xvg -z
> >> yes
> >> # gmx traj is part of G R O M A C S:
> >> #
> >> # Gromacs Runs One Microsecond At Cannonball Speeds
> >> #
> >> @title "average force"
> >> @xaxis  label "Atom"
> >> @yaxis  label "Spatial component"
> >> @TYPE xy
> >> 1-11.866  42.002  29.565
> >> 2  22.660-11.028-21.749
> >> 3  -0.232  -3.681  4.181
> >> 4  -9.308-31.931-22.545
> >> 5-27.221-21.572  7.099
> >> 6  11.648  4.523  -8.757
> >> 7  32.491  0.888  17.891
> >>
> >>
> >> Best regards,
> >> Changwoon Jang
> >>
> >
> > --
> > ==
> >
> > 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.
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Re: [gmx-users] Question about "gmx traj" command

[Chang Woon Jang]

Dear Justin,

Thank you for your help. One more question is that there are positive
and negative values. Does this mean that the forces are written as
vector values? For example, the value of -40 means negative Z direction
with 40 kcal/mol nm ?

Thank you.

Best regards,
Changwoon Jang

On Mon, Oct 16, 2017 at 10:38 PM, Justin Lemkul  wrote:

>
>
> On 10/16/17 9:36 AM, Chang Woon Jang wrote:
>
>> Dear Gromacs Users,
>>
>>  I have a question about the gmx traj in order to calculate the force
>> components.
>>
>> I used the following command. > gmx traj -f topol_new.trr -s topol_new.tpr
>> -af force_all_z_l9.xvg -z yes
>>
>> It produced "force_all_z_l9.xvg" file. In the file, there are four
>> columns.
>> The first column should be the atom ID.
>>
>> My question is what is the rest of columns? For example, some of the
>> values
>> are negative and the other values are positive.
>>
>> -z yes means the plot of Z-component in the manual. I do not know what the
>> exact meaning of three columns. Would you please give me a comment on
>> that?
>>
>
> You're getting (x,y,z) because you haven't turned them off (note from the
> help info that all dimensions are on by default).
>
> All you need is:
>
> gmx traj ... -nox -noy -z
>
> -Justin
>
>
> Thank you.
>>
>>
>> # This file was created Mon Oct 16 21:53:33 2017
>> # Created by:
>> #:-) GROMACS - gmx traj, 2016.4-dev-20170620-8d2584c-unknown (-:
>> #
>> # Executable:  /home/chang/Packages/votca/bin/gmx
>> # Data prefix:  /home/chang/Packages/votca
>> # Working dir:  /home/chang/2017_NU_PROJECT/1_
>> FIRST_PROJECT/1_Less_5Million/
>> 5_REVERSED_ATOMISTIC_TEST/1_Lambda_9/1_TENSION/1_SR10e8_l9_
>> 300K/ANALYSIS/7_Force_Component
>> # Command line:
>> #  gmx traj -f topol_new.trr -s topol_new.tpr -af force_all_z_l9.xvg -z
>> yes
>> # gmx traj is part of G R O M A C S:
>> #
>> # Gromacs Runs One Microsecond At Cannonball Speeds
>> #
>> @title "average force"
>> @xaxis  label "Atom"
>> @yaxis  label "Spatial component"
>> @TYPE xy
>> 1-11.866  42.002  29.565
>> 2  22.660-11.028-21.749
>> 3  -0.232  -3.681  4.181
>> 4  -9.308-31.931-22.545
>> 5-27.221-21.572  7.099
>> 6  11.648  4.523  -8.757
>> 7  32.491  0.888  17.891
>>
>>
>> Best regards,
>> Changwoon Jang
>>
>
> --
> ==
>
> 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.
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Re: [gmx-users] Question about "gmx traj" command

[Justin Lemkul]

On 10/16/17 9:36 AM, Chang Woon Jang wrote:

Dear Gromacs Users,

 I have a question about the gmx traj in order to calculate the force
components.

I used the following command. > gmx traj -f topol_new.trr -s topol_new.tpr
-af force_all_z_l9.xvg -z yes

It produced "force_all_z_l9.xvg" file. In the file, there are four columns.
The first column should be the atom ID.

My question is what is the rest of columns? For example, some of the values
are negative and the other values are positive.

-z yes means the plot of Z-component in the manual. I do not know what the
exact meaning of three columns. Would you please give me a comment on that?


You're getting (x,y,z) because you haven't turned them off (note from 
the help info that all dimensions are on by default).


All you need is:

gmx traj ... -nox -noy -z

-Justin


Thank you.


# This file was created Mon Oct 16 21:53:33 2017
# Created by:
#:-) GROMACS - gmx traj, 2016.4-dev-20170620-8d2584c-unknown (-:
#
# Executable:  /home/chang/Packages/votca/bin/gmx
# Data prefix:  /home/chang/Packages/votca
# Working dir:  /home/chang/2017_NU_PROJECT/1_FIRST_PROJECT/1_Less_5Million/
5_REVERSED_ATOMISTIC_TEST/1_Lambda_9/1_TENSION/1_SR10e8_l9_
300K/ANALYSIS/7_Force_Component
# Command line:
#  gmx traj -f topol_new.trr -s topol_new.tpr -af force_all_z_l9.xvg -z yes
# gmx traj is part of G R O M A C S:
#
# Gromacs Runs One Microsecond At Cannonball Speeds
#
@title "average force"
@xaxis  label "Atom"
@yaxis  label "Spatial component"
@TYPE xy
1-11.866  42.002  29.565
2  22.660-11.028-21.749
3  -0.232  -3.681  4.181
4  -9.308-31.931-22.545
5-27.221-21.572  7.099
6  11.648  4.523  -8.757
7  32.491  0.888  17.891


Best regards,
Changwoon Jang


--
==

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] Question regarding nrexcl and gen-pairs for angle terms with incomplete bonds (ClayFF)

[Thomas Underwood]

Hi Matt, thanks a bunch for your response.

I'm still slightly unsure that this would work as you describe it. If I set 
nrexcl = 0, then the non bonded interactions between all neighbours will be 
included. (Though, the fudge factors = 0 then cancel this out?)

The problem comes from the fact that I don't want the non bonded interactions 
between hydroxyl atoms in my simulations, but I do need the other nearest 
neighbour interactions included.

In my example, I have the triplet {i,j,k}. Let's say that i is my hydrogen, j 
is my oxygen, and k is my metal (Al/Mg) atom.
I need the non bonded interactions between my metal atom and the oxygen atom 
included in my simulation (j & k), as well as the non bonded interaction 
between the metal and the hydrogen (i & k). I need to exclude the non bonded 
interaction between the hydrogen and the oxygen (i & j).

So far, I've assumed that if I declare a bond between my hydrogen and oxygen, 
but not between the oxygen and metal atom, then my non bonded interaction 
between oxygen and metal remain included in the simulations.
I suppose the key question is... does the inclusion of the angle term change 
the non-bonded interactions between atoms i and k, even though I don't have a 
bond defined between atoms j and k.
Is the nearest neighbour list build up exclusively from bonds, or does gromacs 
use angles (and dihedrals) to also build up its neighbour list.

Cheers,

Tom

On 2 Oct 2017, 18:10 -0400, Thompson, Matthew White 
, wrote:
The normal use (nrexcl = 3 and fudgeQQ & fudgeLJ > 0) results in GROMACS 
removing 1-2, 1-3, and 1-4 non-bonded interactions and then adding back scaled 
to the numbers given. In ClayFF, as I understand it, there is no such exclusion 
of these 1-x interactions and therefore no 1-4 scaling. If you want 1-2 
non-bonded interactions to be included, which it seems you do, you can set to 
set nrexcl = 0. In this case, it is still possible for there to be bonded 
interactions between the 1-2 pair independent of whether or not the non-bonded 
interactions are included. But I don't think you want any pairs, as you're not 
"adding back" any scaled 1-4 or other interactions, so you would want to set 
fudgeQQ and fudgeLJ = 0. Otherwise some interactions will be double-counted (or 
1.5x counted). I have used nrexcl = 0 and fudge = 0 for a similar system based 
on ClayFF and found that was the only way to get data to agree with other 
simulation engines, whereas other setups would cause the system to
crash. I'm pretty sure any other combination will cause interactions to be 
counted incorrectly with respect to ClayFF.

Matt


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Thomas 
Underwood [thomas.underw...@princeton.edu]
Sent: Monday, October 02, 2017 3:02 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Question regarding nrexcl and gen-pairs for angle terms 
with incomplete bonds (ClayFF)

Dear GMX'ers,

I have a brief question regarding the use of nrexcl and gen-pairs when used 
with a non-bonded forcefield, such as ClayFF. I've had a brief look through 
previous posts but haven't found a completely satisfactory answer.

Currently, I have a system that is entirely non-bonded. The exception to this 
is hydroxyl groups.
In addition, there is an angle term between the hydroxyl group and an adjacent 
metal atom.
I'm wondering what implications this angle term has on the nonbonded 
interactions of my system.

Let's say I have a triplet of atoms: {i,j,k}.
I define a bond between atoms i and j; I have an angle defined between i, j, 
and k; but I have NO angle defined between j and k.

Now, if I set nrexcl = 1, will the nonbonded interaction between j and k still 
be present in my simulation? I.e. does the angle term at all affect the outcome 
of my pair interactions?

Overall, I need nonbonded interactions between atoms {i,k} and {j,k} in this 
setup.

Further, gen-pairs is typically used for 1-4 interactions. However, when I set 
nrexcl less than 3, does this also generate 1-3 interactions, such as the one 
between i and k above?

Thanks in advance,

Tom

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Re: [gmx-users] Question regarding nrexcl and gen-pairs for angle terms with incomplete bonds (ClayFF)

[Thompson, Matthew White]

The normal use (nrexcl = 3 and fudgeQQ & fudgeLJ > 0) results in GROMACS 
removing 1-2, 1-3, and 1-4 non-bonded interactions and then adding back scaled 
to the numbers given. In ClayFF, as I understand it, there is no such exclusion 
of these 1-x interactions and therefore no 1-4 scaling. If you want 1-2 
non-bonded interactions to be included, which it seems you do, you can set to 
set nrexcl = 0. In this case, it is still possible for there to be bonded 
interactions between the 1-2 pair independent of whether or not the non-bonded 
interactions are included. But I don't think you want any pairs, as you're not 
"adding back" any scaled 1-4 or other interactions, so you would want to set 
fudgeQQ and fudgeLJ = 0. Otherwise some interactions will be double-counted (or 
1.5x counted). I have used nrexcl = 0 and fudge = 0 for a similar system based 
on ClayFF and found that was the only way to get data to agree with other 
simulation engines, whereas other setups would cause the system to
  crash. I'm pretty sure any other combination will cause interactions to be 
counted incorrectly with respect to ClayFF.

Matt


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Thomas 
Underwood [thomas.underw...@princeton.edu]
Sent: Monday, October 02, 2017 3:02 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Question regarding nrexcl and gen-pairs for angle terms 
with incomplete bonds (ClayFF)

Dear GMX'ers,

I have a brief question regarding the use of nrexcl and gen-pairs when used 
with a non-bonded forcefield, such as ClayFF. I've had a brief look through 
previous posts but haven't found a completely satisfactory answer.

Currently, I have a system that is entirely non-bonded. The exception to this 
is hydroxyl groups.
In addition, there is an angle term between the hydroxyl group and an adjacent 
metal atom.
I'm wondering what implications this angle term has on the nonbonded 
interactions of my system.

Let's say I have a triplet of atoms: {i,j,k}.
I define a bond between atoms i and j; I have an angle defined between i, j, 
and k; but I have NO angle defined between j and k.

Now, if I set nrexcl = 1, will the nonbonded interaction between j and k still 
be present in my simulation? I.e. does the angle term at all affect the outcome 
of my pair interactions?

Overall, I need nonbonded interactions between atoms {i,k} and {j,k} in this 
setup.

Further, gen-pairs is typically used for 1-4 interactions. However, when I set 
nrexcl less than 3, does this also generate 1-3 interactions, such as the one 
between i and k above?

Thanks in advance,

Tom

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Re: [gmx-users] Question about the No chi1 & chi2 angle problem with gmx Chi

[Justin Lemkul]

On 8/19/17 1:21 PM, Xingcheng Lin wrote:

Hi,

I am using Gromacs function gmx chi to calculate the X1 and X2 angle based
on my pdbs. However, it prompts this warnning:

WARNING: not all dihedrals found in topology (only 317 out of 496)!
No chi1 & chi2 angle for VAL7
No chi1 & chi2 angle for ALA13
...

However, the output seems to be complete for these indicated residues
where, for example, ramaPhiPsiVAL7.xvg has all X1 and X2 dihedrals I wanted.

I am wondering if this is a redundant output from gmx Chi or is it
something I need to pay attention to?



It's reminding you of basic amino acid structure.  Valine has chi1 but not chi2, 
alanine has neither, etc.


-Justin

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==

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Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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Re: [gmx-users] question about gmx do_dssp

[Justin Lemkul]

On 8/5/17 8:12 PM, Mark Abraham wrote:

Hi,

I'd start by checking if that last residue is a normal one...



The check_oo() function in gmx_do_dssp.cpp looks like it will not work correclty 
for CHARMM, because it does not identify CHARMM termini, thereby ignoring the 
C-terminus.  It looks for O, O1, or OC1 (which actually doesn't appear to be 
used by any force field).  CHARMM uses OT1/OT2 for COO- termini, so a check for 
OT1 needs to be added.


-Justin

--
==

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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.
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Re: [gmx-users] question about gmx do_dssp

[Mark Abraham]

Hi,

I'd start by checking if that last residue is a normal one...

Mark

On Sat, Aug 5, 2017 at 2:02 PM YanhuaOuyang <15901283...@163.com> wrote:

>
>
> Dear Mark,
>
>Thank you, I have figure out the problem, but to my surprise, the
> output xpm file lack the information of the last residue for the CHARMM27
> force file (charmm's trajectory is good), but not for other force field. I
> wonder whether the DSSP program in the gromacs ignore the last residue of
> structures generated by CHARMM27 force field.
>
> Best regards,
> Ouyang
>
>
>
>
>
>
>
>
> At 2017-08-04 22:32:25, "Mark Abraham"  wrote:
> >Hi,
> >
> >Isn't that figure what is in the xpm file?
> >
> >Mark
> >
> >On Fri, Aug 4, 2017 at 4:20 PM YanhuaOuyang <15901283...@163.com> wrote:
> >
> >> Hi,
> >>I have run a MD simulation and used gmx do_dssp to calculate the
> >> secondary structure content. The output files are md_dssp.xpm and
> >> scount.xvg. I want to know that each residue  belongs to what kind of
> >> secondary structure for each frame. But the scount.xvg output file only
> >> have the number of residues with each secondary structure and the total
> >> secondary structure count as a function of time. So,  can I get the
> >> information on "each residue belongs to which kind of secondary
> structure
> >> for each frame" to draw a figure of " amino acid vs secondary
> structure" ?
> >>
> >> Best regards,
> >> Ouyang
> >> --
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Re: [gmx-users] question about gmx do_dssp

[YanhuaOuyang]

Dear Mark,

   Thank you, I have figure out the problem, but to my surprise, the output xpm 
file lack the information of the last residue for the CHARMM27 force file 
(charmm's trajectory is good), but not for other force field. I wonder whether 
the DSSP program in the gromacs ignore the last residue of structures generated 
by CHARMM27 force field.

Best regards,
Ouyang








At 2017-08-04 22:32:25, "Mark Abraham"  wrote:
>Hi,
>
>Isn't that figure what is in the xpm file?
>
>Mark
>
>On Fri, Aug 4, 2017 at 4:20 PM YanhuaOuyang <15901283...@163.com> wrote:
>
>> Hi,
>>I have run a MD simulation and used gmx do_dssp to calculate the
>> secondary structure content. The output files are md_dssp.xpm and
>> scount.xvg. I want to know that each residue  belongs to what kind of
>> secondary structure for each frame. But the scount.xvg output file only
>> have the number of residues with each secondary structure and the total
>> secondary structure count as a function of time. So,  can I get the
>> information on "each residue belongs to which kind of secondary structure
>> for each frame" to draw a figure of " amino acid vs secondary structure" ?
>>
>> Best regards,
>> Ouyang
>> --
>> 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
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>>
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Re: [gmx-users] question about gmx do_dssp

[Mark Abraham]

Hi,

Isn't that figure what is in the xpm file?

Mark

On Fri, Aug 4, 2017 at 4:20 PM YanhuaOuyang <15901283...@163.com> wrote:

> Hi,
>I have run a MD simulation and used gmx do_dssp to calculate the
> secondary structure content. The output files are md_dssp.xpm and
> scount.xvg. I want to know that each residue  belongs to what kind of
> secondary structure for each frame. But the scount.xvg output file only
> have the number of residues with each secondary structure and the total
> secondary structure count as a function of time. So,  can I get the
> information on "each residue belongs to which kind of secondary structure
> for each frame" to draw a figure of " amino acid vs secondary structure" ?
>
> Best regards,
> Ouyang
> --
> 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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Re: [gmx-users] Question on Umbrella Sampling with varied ionic strength.

[Justin Lemkul]

On 7/31/17 5:19 PM, Yuanchao Liu (MSU) wrote:

Hi all

I have a question on umbrella sampling results under varied ionic strength.
I have just done some regular umbrella sampling on the system of glucose
6-phosphate (small ligand molecule) on oligopeptide with LYS side chains. I
mostly follow the tutorial by Justin
.
I use explicit ions to represent the ionic strength level.

There is hardly any difference between my calculated adsorption energy (by
PMF) under different ionic strengths (0, 20, 40, 70, 120 mM). However, we
did observe apparent difference on surface retention time in regular MD
simulations, which indicated a weaker surface interaction. During my
simulation, the sampling time is 10 ns for each window, and I am wondering
if the effect of explicit ions need longer simulation time to be reflected
on results.

Here is some detail of my simulation:
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.evernote.com_l_AAMCVXRkp3tPYrhq-5F4oRHdtfnRb1VJo71U0_&d=DwIFaQ&c=nE__W8dFE-shTxStwXtp0A&r=gCy395jfSTIKIGBjdJ8SwSg8yN7wywRqF0ilx8ZoefpMNPZKIUY0jXzHKcFUwcQV&m=wjjoIomb4xozoyp9lqY4_wEzyhxGWILHcyUjAvXhess&s=B67nP5cwU6r5g_KBORUyrzAardEsfEzcojVKVZFomfU&e=

I will appreciate it if anybody with relevant experience can give me some
suggestion on this. Thank you.



It will be difficult to determine any real, meaningful difference with such 
small changes in ionic strength.  Your histogram overlap looks good, so I doubt 
that more sampling will improve the result.  Is the observed difference in 
retention time reproducible?  How did you determine it, and over what time 
scale?  Is it possible that those simulations simply got stuck in a local 
minimum (common in MD simulations) rather than actually reflecting a real 
physical difference?  Additionally, if the retention times are not substantially 
different, then the energy differences may not be large enough to resolve via 
umbrella sampling.


-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] Question on force field

[YanhuaOuyang]

Dear Justin,  Thank you very much. I get it now.Best 
regards,Ouyang
At 2017-07-31 10:46:10, "Justin Lemkul"  wrote:
>
>
>On 7/30/17 8:58 PM, YanhuaOuyang wrote:
>> Hi,
>>   I have run a protein MD simulation and choose a force field "8: CHARMM27 
>> all-atom force field (CHARM22 plus CMAP for proteins) ". I wonder that 
>> whether the CHARMM27 all-atom force field here is equal to the CHARMM22/CMAP
>> 
>
>Well, not "equal" but it means that the "CHARMM27" files include C22/CMAP for 
>proteins.  There is no such thing as a CHARMM27 protein force field.  The C27 
>nucleic acid and lipid parameters came out at the same time as the C22/CMAP 
>protein force field, and got somewhat unfortunately lumped together in 
>nomenclature.
>
>-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] Question on force field

[Justin Lemkul]

On 7/30/17 8:58 PM, YanhuaOuyang wrote:

Hi,
  I have run a protein MD simulation and choose a force field "8: CHARMM27 all-atom 
force field (CHARM22 plus CMAP for proteins) ". I wonder that whether the CHARMM27 
all-atom force field here is equal to the CHARMM22/CMAP



Well, not "equal" but it means that the "CHARMM27" files include C22/CMAP for 
proteins.  There is no such thing as a CHARMM27 protein force field.  The C27 
nucleic acid and lipid parameters came out at the same time as the C22/CMAP 
protein force field, and got somewhat unfortunately lumped together in nomenclature.


-Justin

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==

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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