[gmx-users] Question about parameters for simulation annealing

[lazaro monteserin]

Dear Gromacs users,
I am trying to run a simulation annealing using Gromacs of a small
molecule. Does anybody knows if there is a protocol to set up the annealing
parameters for Gromacs; initial temperature, final temperature,
annealing-npoints, annealing-ntimes and the annealing-temp? My total
simulation time is 10ns and I collect frames every 200 fs.
   Kindly, Lazaro
-- 
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.

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

==

--
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
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 
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.

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
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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

==

--
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 
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.

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.
>
-- 
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.

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

* 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.

[gmx-users] Question on energygrps setting

[Lei Qian]

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?

Thanks!
Lei
-- 
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.

[gmx-users] question about how to analyze the free energy landscape generated with gmx sham

[lazaro monteserin]

Dear Gromacs users;

I have generated Gibbs free energy landscapes from the two first principal
components PC1 and PC2 obtained from Dihedral Principal Component analysis
performed using Gromacs.

So, now I have a file *"shamlog-1_2.log" *that contain a list of the bins
ordered by energy, for example :
Minima sorted after energy
Minimum 0 at index 40 energy  0.000
Minimum 1 at index 641 energy  0.146 (...)
and I have another file *bindex-1_2.ndx* that shows the frames contained in
each bin.
Now I do not know how to proceed from here. How do I select the best bins?
and then how do I select the best frames from those bins? Should I use all
the frames of the selected bins and obtain like an average structure?
Kindly, Lazaro
-- 
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.

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
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * 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
> > 

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
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For 

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!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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

[Sina Omrani]

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.

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
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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

==

--
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.

[gmx-users] Question on running gmx trjconv without 2 prompts

[Lei Qian]

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'.
Thanks!
Lei
-- 
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.

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
-- 
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.

[gmx-users] Question about gromacs mailing list and configurational entropy

[Amit Kumar]

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.

I have also asked previously this question and got a reply from David van
der Spoel too and after that, I am getting a value of schlitter's entropy
but getting only one value of schlitter's value while I want it for every
frame to plot time vs entropy graph.
So can you tell me what is happening and how to troubleshoot this?

Thank You
Amit Kumar
-- 
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.

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
> --
> 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.
>


-- 
Wanna help a great cause? Please:
https://www.raymondnicolettrust.com/events/2020/parismarathon
And many thanks!
Alan Silva ‍♂‍♂
-- 
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.

[gmx-users] question on dihedrals propers func 3 and impropers func 1

[Lei Qian]

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
-- 
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.

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
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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

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.

[gmx-users] Question about the SASA value per residue

[Pandya, Akash]

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?

Best wishes,

Akash
-- 
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.

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

==

--
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.

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

[gmx-users] question regarding gmx helix orientation

[SHAHEE ISLAM]

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.
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
-- 
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.

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

==

--
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.

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
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-requ...@gromacs.org.


-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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

==

--
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.

[gmx-users] Question: How to delete water

[변진영]

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

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
-- 
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.

[gmx-users] Question about implicit solvent and REMD

[Mohammad Madani]

Dear all
 I have 2 questions about REMD simulation with implicit solvent
1- when I want to run equilibration I have this error that when you use
sn-type = simple, DD does not support simple you should use grid or use one
thread.
I change the command to :
gmx mdrun -nt 1 -deffnm nvt
I confront with this error (segmentation fault)- core dumped.
I upload my .mdp file could you please help me what should I do? I use the
2018.8 version of gromacs.
2-when I want to run REMD simulation with implicit solvent-based on your
tutorial.
I run the equilibration section but when I see the result such as ener.edr
file the value of the temperature is (nan) in all directories. I do not
know what is the problem.
could you please help me what should I do? I really need to do this REMD
simulation with an implicit solvent.
please take a look at to my mdp file which I upload here.
Many thanks

[image: Mailtrack]

Sender
notified by
Mailtrack

12/04/19,
02:00:30 PM
include  = 
; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
define   = 

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.002
nsteps = = 5
; For exact run continuation or redoing part of a run
init-step= 0
; Part index is updated automatically on checkpointing (keeps files separate)
simulation-part  = 1
; mode for center of mass motion removal
comm-mode= Angular
; number of steps for center of mass motion removal
nstcomm  = 100
; group(s) for center of mass motion removal
comm-grps= 

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric  = 0
ld-seed  = -1



; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 0
nstvout  = 0
nstfout  = 0
; Output frequency for energies to log file and energy file
nstlog   = 1000
nstcalcenergy= 100
nstenergy= 1000
; Output frequency and precision for .xtc file
nstxtcout= 0
xtc-precision= 1000
; This selects the subset of atoms for the .xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps = 
; Selection of energy groups
energygrps   = system

; NEIGHBORSEARCHING PARAMETERS
; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs)
cutoff-scheme= group
; nblist update frequency
nstlist  = 1
; ns algorithm (simple or grid)
ns-type  = simple
; Periodic boundary conditions: xyz, no, xy
pbc  = no
periodic-molecules   = no
; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist

; nblist cut-off
rlist= 0
; long-range cut-off for switched potentials


; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = cut-off
coulomb-modifier = none
rcoulomb-switch  = 0
rcoulomb = 0
; Relative dielectric constant for the medium and the reaction field
epsilon-r= 1
epsilon-rf   = 0
; Method for doing Van der Waals
vdw-type = Cut-off
vdw-modifier = none
; cut-off lengths   
rvdw-switch  = 0
rvdw = 0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Separate tables between energy group pairs
energygrp-table  = 

; FFT grid size, when a value is 0 fourierspacing will be used
fourier-nx   = 0
fourier-ny   = 0
fourier-nz   = 0
; EWALD/PME/PPPM parameters
pme-order= 4
epsilon-surface  = 0
optimize-fft = no

; IMPLICIT SOLVENT ALGORITHM
implicit-solvent = GBSA

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb-algorithm = OBC
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 0
; Dielectric coefficient of the implicit solvent
gb-epsilon-solvent   = 80
; Salt concentration in M for Generalized Born models
gb-saltconc  = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb-obc-alpha = 

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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

[Soomin Choi]

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
-- 
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.

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
-- 
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.

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

[gmx-users] Question about default auto setting of mdrun -pin

[aeszter]

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?

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.

A.

-- 
Ansgar Esztermann
Sysadmin Dep. Theoretical and Computational Biophysics
http://www.mpibpc.mpg.de/grubmueller/esztermann
-- 
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.

[gmx-users] Question about default auto setting of mdrun -pin

[Kutzner, Carsten]

Hi,

is it intended that the thread-MPI version of mdrun 2018 does pin to its core
if started with -nt 1 -pin auto?

Carsten

-- 
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.

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
> > --
> > 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.
> >
>
> - John
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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
> --
> 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.
>

- John


-- 
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.

[gmx-users] Question about gmx_wham

[Alexander Phillips]

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?)).

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?

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.

Thank You,
Alex
-- 
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.

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
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send
> > a mail to gmx-users-requ...@gromacs.org.
> >
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-requ...@gromacs.org.
>


-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

[gmx-users] question on system blow-up

[Lei Qian]

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?

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)"

Thank you!
-- 
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.

[gmx-users] question about tabulated force field

[Liu, Y.]

Hi there,
   I have a question about tabulated force field: what is the
difference when the tabulated potential and build-in potential are used in
Gromacs simulations? why they give different results?
   I simulate a DPPC membrane with Gromos force field. I use standard
gromos input parameters in the simulation, but the area per lipid (0.630
(0.008) nm2) is different from when I compute it with tabulated force
field(0.613 (0.007)nm2). This difference also exist when I use MARTINI
force field.
   I have use gmx dump -s *.tpr > comparison.xvg in two cases(build-in
and tabulated potential) to make sure that the only difference in two
scenarios is the tabulated potential. Here is the difference:
coulombtype= User
40,41c40,41
epsilon-rf = 1
>vdw-type   = User
164c164
tau-t:0.01 0.1   1
169c169
energygrp-flags[  0]: 2 1
   Then you may think my tabulated potential is problematic. However, I
have used Gromacs 4.* with -debug flag to output the tabulated potential.
Therefore, the tabulated potential should be correct.
   In the output .edr file, I also found that the tabulated potential
simulation cannot offer correct temperature for lipids as indicated in the
thermal stat. At least, with the same parameters, it works well in the
build-in potential simulation.
   I do not understand where is the problem and what is the difference
between the tabulated potential and build-in potential in Gromacs. Maybe it
use different engine to compute the force?
Looking forward to your reply. Thank you.
regards
Liuyang
-- 
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.

[gmx-users] Question about the pulling code

[Tingguang.S]

Dear All,


I want to pulling a ligand out of the binding pocket using Gromacs 2019. The 
pulling code was:
pull= yes
pull_ncoords= 1 

pull_coord1_type= umbrella
pull_coord1_geometry= direction
pull_ngroups= 1
pull_group1_name= Ligand
pull_coord1_dim = Y N N
pull-coord1-vec = 1 0 0

pull_coord1_rate= 0.0005 
pull_coord1_k   = 830



I think the reaction coordinate had been defined by COM of the pulling group 
(i.e the ligand) and the pulling direction vector (i.e 1 0 0), but why still 
need to provide two groups for pull_coord1_groups ? If provided, then the 
reaction coordinate was also defined by the COM of the two groups, is this 
right?


How should I set up my pulling code with "pull_coord1_geometry= direction". 
Any suggestion would be appreciated!


Best regards
Sting








-- 
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.

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

==

--
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.

[gmx-users] Question about distance restraints

[Tanos Franca]

    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?


    Bests,

    Tanos França.


---
Este email foi escaneado pelo Avast antivírus.
https://www.avast.com/antivirus

--
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.

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

==

--
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.

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
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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

--
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.

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

==

--
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.

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!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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

==

--
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.

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!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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

==

--
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.

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
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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

==

--
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.

[gmx-users] question on ffG43a1p force field

[Lei Qian]

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?
Thanks
lei
-- 
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.

[gmx-users] Question about center of mass definition in RDF tool (gromacs 5.11)

[Sergio Garay]

Hi all

My name is Sergio Garay, and I've simulated a micelle formed by 30
molecules (Anphiphile Peptide) in water. Each of my molecules are made up
of 5 residues and I want to calculate the RDF of each residue around the
micelle center of
mass. I've use rdf tool from gromacs_5.11 to do the calculation, but I'm
not sure if I've done the correct selection of the reference:

*-selrpos whole_mol_com* --> (and I selected a group with all molecules as
reference)
it will select the com of all molecules as reference?

What about if I want to use the com of a group of particular atoms as
reference?
What it would be the correct option? Is this: "part_res_com"?

Thank you for your time
Sergio

-- 








*Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs.
BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 -
Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54
(342) 4575-221 *
-- 
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.

[gmx-users] Question about center of mass definition in RDF tool (gromacs 5.11)

[Sergio Garay]

Hi all

My name is Sergio Garay, and I've simulated a micelle formed by 30
molecules in water. Each of my molecules are made up of 5 residues and I
want to calculate the RDF of each residue around the micelle center of
mass. I've use rdf tool from gromacs_5.11 to do the calculation, but I'm
not sure if I've done the correct selection of the reference:

*-selrpos whole_mol_com* --> (and I select a group with all molecules as
reference)
it will select the com of all molecules as reference?

What about if I want to use the com of a group of particular atoms as
reference?
What it would be the correct option? Is this: "part_res_com"?

Thank you for your time
Sergio





-- 








*Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs.
BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 -
Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54
(342) 4575-221 *
-- 
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.

[gmx-users] Question of constraining bonds

[Dong Woo Kang]

Dear all gromacs users,I'm new to gromacs, and I have some questions about bond 
constraints.Now I have a system with methane, hydrogen, and TIP4P/Ew water. In 
special, topology of hydrogen molecule is including [ constraints ], for 
constructing a virtual site in the center of hydrogen molecule.By including 
"constraint-algorithm = lincs" and "constraints = h-bonds", I found that all 
bonds including H were constrained.So I changed *.mdp file with 
"constraint-algorithm = lincs" and "constraints = none", and I found that LINCS 
are applied to hydrogen, but it seemed that SETTLE is applied to water instead 
of LINCS.If I want to apply LINCS both on hydrogen molecules and waters, and 
not on methane or other hydrocarbons including hydrogen atoms, how can I do 
that?Any advices will be very helpful.Dong Woo Kang
-- 
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.

[gmx-users] question about polar.mdp file in MMPBSA

[mmousivand93]

Dear all 

I RUN MOLECULAR SIMULATION FOR  DNA-SMALL MOLECULE COMPLEX (50 NS), I
WANT TO ANALYSIS USING MMPBSA, FOR  POLAR SOLVATION ENERGY CALCULATION ,
I USED THE  MMPBSA.MDP [1] OBTAINED FROM 
HTTPS://RASHMIKUMARI.GITHUB.IO/G_MMPBSA/HOW-TO-RUN.HTML.  

 I THINK THERE IS SOME PROBLEM, BECAUSE AFTER RUN THIS COMMAND"g_mmpbsa
-f traj.xtc -s topol.tpr -i mmpbsa.mdp -n index.ndx -nomme -pbsa -decomp
-apol apolar.xvg -apcon contrib_apol.dat" , THE ANALYSIS WAS SO SLOWLY,
HOWEVER THERE ARE SPECIAL ITEM IN MMPBSA.MDP [1] AS FALLOW: 

"MAXIMUM MEMORY (IN MB) AVAILABLE PER-PROCESSOR FOR A CALCULATION. 
GMEMCEIL = 4000" 

IF I CHANGE THE ITEM IN MDP FILE, THE ANALYSIS MAY BE PERFORMED FASTER ?


Best Regards 

   

Links:
--
[1]
https://github.com/RashmiKumari/g_mmpbsa/blob/master/test/sasa_orig/mmpbsa.mdp
-- 
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.

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

==

--
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.

[gmx-users] Question from new gromacs user

[Nabil Abid]

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

Nabil Abid, PhD Assistant professor Bioinformatic,Molecular Biology, Virology  
High Institute of BiotechnologySidi Thabet  University ManoubaTunisia 
Tel:(+216)93541940   

 

-- 
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.

[gmx-users] question regarding coulomb potential output

[Ali Khodayari]

Dear all,

 

I have a question regarding the output of the Coulombic energy from the edr
file.

I am looking at the interactions between two molecules, and trying to
analyse the contribution of different interaction types between these two. 

Since hydrogen bonds are formed based on the charge differences between
donors and acceptors, I am wondering whether the coulomb potential which I
get from the edr file also contains the hydrogen bond energies.

Thank you for your kind responses.

Kind regards,

Ali

-- 
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.

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

==

--
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.

[gmx-users] question about convert Ryckaert-Bellemans dihendral to dihendral type 9

[张敏华]

Dear all:
I am trying use antichamber to generate an tpr file for a special 
residue. When I got the converted tpr file, I noticed that the "func" in 
[dihendral] is 3, that means it is a Rychaert-Bellemans dihendral. But the 
Amber03 forcefield use dihendral type 9(func 9). So does anyone knows how to 
convert Rychaert-Bellemans dihendral to dihendral type 9? I calculated the 
charge of this special residule by gaussian and fitted into RESP charge, then 
converted it to topology file in Amber forcefield.  I have encountered an fatal 
error when I using pdb2gmx, which tells me that residues in one molecule have a 
different 'dihendrals' type: 9 and 3. 
I would appreciate any advice!
Best,


Minhua Zhang
Institute of Plant Physiology and Ecology, SIBS, CAS
mhzhan...@sibs.ac.cn
-- 
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.

[gmx-users] Question on generating hydrogens

[tca1]

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.


Thanks,
Tom Allen


--
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.

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?*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

[gmx-users] question

[m mar]

*hello*

*How can I position restraint cofactor and ligand **together?*
-- 
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.

[gmx-users] question

[m mar]

*hello*

*How can I position restraint cofactor and ligand **together?*
-- 
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.

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
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

[gmx-users] question about make_ndx

[Carlos Navarro]

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
-- 
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.

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

[gmx-users] Question about gmx order ...

[Sergio Garay]

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
-- 
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.

[gmx-users] question about the QM/MM calcuation in Gromacs/ORCA interface

[Mahnaz Tehrani]

Dear all,

I am going to use Gromacs/ORCA interface for QM/MM calculation in the
metalloenzyme model. I have done some QMMM calculations with other
interface (AMBER/TURBOMOLE)  I am also familiar with QM in ORCA but new
user of Gromacs!

I could get general overview how this feature works in Gromacs (from 2
provided tutorial examples and also Q/A of users in the mailing list) but
that would be great to have a successful sample model to reproduce data
before running the real model.

I was going to test "Thymine dimer splitting" as given example with MOPAC
interface (http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/tutorial.html)
and using provided files from the website then use ORCA interface for QM
part but it was not successful. so can you please someone share the example
with me (inputs/output). Any help would be really appreciated!

Regards,

Zahra


-- 

Zahra Aliakbar Tehrani

Ph.D. in Physical Organic Chemistry
Post-Doctoral Researcher, Institute of Organic Chemistry & Biochemistry
AS CR, v.v.i. (IOCB), 166 10 Praha 6

E-mail: zahra.aliakbar_tehr...@uochb.cas.cz
-- 
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.

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!
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

Re: [gmx-users] Question on gmx editconf, pbc and NPT (Sebastian Muraru)

[Sebastian Muraru]

> Sunipa
> - End message from SHAHEE ISLAM  -
> --
> 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.


--

Message: 3
Date: Thu, 27 Dec 2018 13:12:46 +0200 (EET)
From: Sebastian Muraru 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Question on gmx editconf, pbc and NPT
Message-ID:
<1457525096.48541545909166873.javamail.r...@webmail.chim.upb.ro>
Content-Type: text/plain; charset=utf-8

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!


--

Message: 4
Date: Thu, 27 Dec 2018 16:47:39 +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:
<20181227164739.horde.cg717yibka2pua0otamy...@mailweb.iacs.res.in>
Content-Type: text/plain; charset=UTF-8; format=flowed; DelSp=Yes

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

> 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  -
>> --
>> 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
>&

[gmx-users] Question on gmx editconf, pbc and NPT

[Sebastian Muraru]

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!
-- 
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.

[gmx-users] Question on pressure coupling

[Mohsen Ramezanpour]

Dear Gromacs users,

Inverted hexagonal phases are usually simulated (and should be) using a
triclinic box with either semi-isotropic or anisotropic pressure couplings.

I am not sure what a semi-isotropic and anisotropic means in a "Triclinic"
box, exactly?
The .log files look the same for the Triclinic box and rectangular box.


Here is an example:
Semi-isotropic (.mdp file):

compressibility = 4.5e-5  4.6e-5
ref_p   = 1.5 1.6

The .log file looks like:
compressibility (3x3):
  compressibility[0]={ 4.5e-05,  0.0e+00,  0.0e+00}
  compressibility[1]={ 0.0e+00,  4.5e-05,  0.0e+00}
  compressibility[2]={ 0.0e+00,  0.0e+00,  4.6e-05}
   ref-p (3x3):
  ref-p[0]={ 1.5e+00,  0.0e+00,  0.0e+00}
  ref-p[1]={ 0.0e+00,  1.5e+00,  0.0e+00}
  ref-p[2]={ 0.0e+00,  0.0e+00,  1.6e+00}



and for Anisotropic (.mdp file)

compressibility = 4.5e-5  4.6e-5  4.7e-5  4.8e-5   4.9e-5   4.1e-5
ref_p   = 1.5 1.6 1.7 1.8  1.9  1.1

The .log file looks like:

compressibility (3x3):
  compressibility[0]={ 4.5e-05,  4.8e-05,  4.9e-05}
  compressibility[1]={ 4.8e-05,  4.6e-05,  4.1e-05}
  compressibility[2]={ 4.9e-05,  4.1e-05,  4.7e-05}
   ref-p (3x3):
  ref-p[0]={ 1.5e+00,  1.8e+00,  1.9e+00}
  ref-p[1]={ 1.8e+00,  1.6e+00,  1.1e+00}
  ref-p[2]={ 1.9e+00,  1.1e+00,  1.7e+00}

How the scaling is done differently for Triclinic and rectangular boxes?
(The question is also valid for isotropic coupling, but for semi and
aniso is more confusing)
Or, is there any difference in the implementation of pressure coupling for
different PBC types at all?

Thanks for your comments in advance,
Cheers,
Mohsen
-- 
*Rewards work better than punishment ...*
-- 
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.

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).
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

[gmx-users] Question about nsttcouple

[minky son]

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).
-- 
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.

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

--
==

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

==

--
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.

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.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

[gmx-users] Question about nsttcouple

[minky son]

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.
-- 
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.

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




--
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!

* 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.

[gmx-users] Question about Entropy Calculation

[kai . exner]

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.


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).


I would be thankful for any help!

With my best regards,
Kai

--
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.

[gmx-users] Question about integrator md-vv and associated documentation

[James]

Hi,

There is a long-standing typo in the description of md-vv. It says:

"*The* the kinetic energy, which is determined from the whole step
velocities and is therefore slightly too high."


Should that be "*There *the kinetic energy..."?

The docs then go on to say:

"The advantage of this integrator is more accurate, reversible Nose-Hoover
and Parrinello-Rahman coupling integration based on Trotter expansion, as
well as (*slightly too small*) full step velocity output."


Can anyone quantify "slightly too small"? I am using double precision
gromacs with Verlet cutoffs and the md-vv integrator, on 5.0.4, no
thermostat. I am trying to watch potential energy be converted into
friction/temperature. I am seeing temperature go down slightly on runs
where I would expect it to go up slightly, and wondering if the "slightly
too small" velocity output is the reason. (I cannot use md-vv-avek -- I
assume it is not implemented for Verlet cutoffs, at least in 5.0.4).

I know most people don't need this level of accuracy, but for my models,
I've compared single and double precision, and md versus md-vv, and double
precision with md-vv substantially reduces total energy drift. I'm just
trying to figure out if I can improve it further because it is still a
little off, and the drift is always negative (again, going back to whether
this is because of the "slightly too small" issue).

Sincerely,
James Ryley
-- 
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.

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
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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

==

--
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.

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
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

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

==

--
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.

[gmx-users] Question regarding dihedral angle parameters

[Upendra N]

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.

Thank you.

Upendra N
-- 
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.

[gmx-users] Question about relation among couple-moltype , couple-lambda0 and couple-lambda1 parameter in free energy calculation.

[김현준]

Hello, Thank you for your reading.I am trying free energy 
calculation about base pair mutation(G * T -> G_enol * T). Actually,
 I explicitly mention a both state A and B in topology file(Atom type, 
charge, any parameter related). So, I didn't use couple-moltype option 
because i already made B state.My initial state is wobble G*T 
base pair and B state is G_enol * T state. I use couple-lambda0 = vdw-q 
and couple-lambda1=none. Is it wrong?? Should i use couple-lambda1=vdw-q or 
there are no effect? Thank you.

-- 
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.

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at https://na01.safelinks.
> protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%
> 2FSupport%2FMailing_Lists%2FGMX-Users_Listdata=02%
> 7C01%7Ckevin.boyd%40uconn.edu%7C3aa7ca6a980e4192de0308d5f9342caf%
> 7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636688924848859602
> sdata=%2FYvf3bt64HrV9DcUC4n8okZFcAeZxLWCci4glwEXsrk%3Dreserved=0
> before posting!
>
> * Can't post? Read https://na01.safelinks.protection.outlook.com/?url=
> http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists
> data=02%7C01%7Ckevin.boyd%40uconn.edu%7C3aa7ca6a980e4192de0308d5f9342caf%
> 7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636688924848859602
> sdata=TOia5O%2FTldeyGFIcNJi6ro5hUVSp4gbnU5Shm6uBiuE%3Dreserved=0
>
> * For (un)subscribe requests visit
> https://na01.safelinks.protection.outlook.com/?url=
> https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%
> 2Fgromacs.org_gmx-usersdata=02%7C01%7Ckevin.boyd%40uconn.edu%
> 7C3aa7ca6a980e4192de0308d5f9342caf%7C17f1a87e2a254eaab9df9d439034
> b080%7C0%7C1%7C636688924848859602sdata=KKiOEB3FiwyvnlxqKNxAN7gQ2%
> 2FKXyA68yqzfb4o0Uc4%3Dreserved=0 or send a mail to
> gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

[gmx-users] Question about water insertion

[G R]

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
-- 
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.