Re: [gmx-users] GPU+Energy Groups

[Neda Rafiee]

Hi Mark,
Thanks a lot for your help. Actually, in my case tables are defined for 
non-bonded LJ interactions. Anyway, I need them since all we did were on 
defining those tables :)
Thanks again,
Neda


- Original Message -
From: Mark Abraham 
To: gmx-us...@gromacs.org
Sent: Fri, 06 Jul 2018 17:23:30 +0430 (IRDT)
Subject: Re: [gmx-users] GPU+Energy Groups

Hi,

You can't ever use a tabulated short-range interaction on a GPU in GROMACS
at this time.

Mark

On Fri, Jul 6, 2018 at 10:55 AM Neda Rafiee  wrote:

> Dear GMX-Users,
> I am going to use GPU acceleration for my simulations but since I have
> some energy tables for LJ interactions, and I am using cut-off scheme=group
> instead of Verlet, I receive these notes:
>
> "NOTE: GPU(s) found, but the current simulation can not use GPUs
>   To use a GPU, set the mdp option: cutoff-scheme = Verlet
> Multiple energy groups is not implemented for GPUs, falling back to the
> CPU. For better performance, run on the GPU without energy groups and then
> do gmx mdrun -rerun option on the trajectory with an energy group .tpr file.
> Using 1 MPI process"
>
> Is it reasonable to do my simulations using GPU and rerun it using
> energy-groups? How will those non-bonded interaction tables be taken into
> account in my first simulations with GPU?
> Thanks in advance.
> Neda
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Re: [gmx-users] Tacticity in polymer simulation

[Debadutta Prusty]

Sorry for posting the question here again. I cannot help but turn to this
forum since almost all papers I have read on tacticity in atomistic
simulations have used some kind of software package to build polymers with
desired tacticity. My university is banned from using Gaussian, which is
the most widely used package for generating such polymers. This prompted me
to  look for an algorithm that generates isotactic/syndiotactic/atactic
polymers. I have the pdb files for monomeric units (with two dangling bonds
to account for the bonds with neighbouring monomers). Now my polymer looks
like this: -CAH(R)-CBH2-CAH(R)-. I have a rough idea of how to go about
creating a polymer from a monomer. For example, if my program generates the
pdb file for the polymer by creating copies of the same monomer through the
translation of the CA atom along the x-axis keeping the relative
orientation of the other atoms (with respect to CA) the same for every
monomer, will I get an isotactic polymer ? If I flip the positions of R and
H for monomers adjacent to each other, will I get a syndiotactic polymer?
In my system, the adjacent monomeric units can be different (one charged,
another uncharged). How do I fix the angles that side groups make with the
plane containing the carbon atoms of the main chain.

Thanks,
Debadutta Prusty

On Thu, Jul 5, 2018 at 11:54 PM, Debadutta Prusty <
debaduttaprusty1.2...@u.northwestern.edu> wrote:

> Hi everyone,
>
> How does one go about preparing a polymer in a given state of tacticity?
> From what I understand about tacticity in polymers, it boils down to
> coefficients(C1,C2,C3,C4,C5,C6) in Ryckaert-Bellemans function. If the
> potential well is not deep enough, the polymer can easily transition from
> an isotactic state into a syndiotactic state. The above coefficients for
> dihedral angles are fixed for a particular force field. I found a few
> papers on the effect of tacticity on properties of PAA,PMAA polymers where
> the pattern is CA(R)-CB-CA(R'), where R is the acid group. They do not
> mention whether it is the initial configuration that sets the tacticity of
> a polymer.  I am not sure how to keep the relative orientations of two R
> groups constant since they do not appear simultaneously in a dihedral
> pattern (the dihedrals are R-CA-CB-CA or CA-CB-CA-R' ). Any help would be
> appreciated.
>
> Thanks,
> Debadutta Prusty
>
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Re: [gmx-users] Queries regarding temperature gradient

[Sabreen Farnaz]

Dear Dr. Lemkul,
Thank you for your answer. Can you please also advise how can I get the
temperature of a system as a function of distance using gromacs 5.1.5? gmx
energy plots the temperature of the centre of mass of energy groups against
time. gmx traj also does the same from velocity information.

Regards,
Neelima S.

On Sat, 7 Jul 2018, 00:01 Justin Lemkul,  wrote:

>
>
> On 7/6/18 1:07 PM, Sabreen Farnaz wrote:
> > Dear all,
> > This is in regard to my previous queries. The warning in NVT step can
> > possibly be ignored using -maxwarn but I am still not sure about the
> rest!
> > Can someone please help?
>
> tau_t = -1 means temperature coupling is not applied. Whether that's
> what you want or not is up to you, but in that case, your ensembles are
> not NVT or NPT, because T is no longer conserved.
>
> > Thanks,
> > Neelima S.
> >
> > On Fri, 6 Jul 2018, 01:56 Sabreen Farnaz, 
> wrote:
> >
> >> Dear all,
> >>
> >> I am setting up a system where I want the solute to be immersed in a
> >> solvent with a temperature gradient. I have defined two different
> >> temperature groups, two portions of the solvent, and want them to be at
> say
> >> T1 and T2 kelvins. The rest of the system will not be subjected to a
> >> thermostat  (tau_t=-1).
>
> Realize that with PBC, you're not likely to get what you want. I don't
> know how you're defining the T1 and T2 groups, but if they're in contact
> via PBC, the "gradient" really doesn't exist - you have a hot and cold
> bath directly in contact. See previous threads on temperature gradients
> for more discussion. If the T1 and T2 groups are capable of diffusing,
> then you definitely don't have a gradient.
>
> >> My questions are:
> >> 1. Should NVT and NPT mdp files also have the same t_ref and tau_t? A
> >> tau_t=-1 gives a warning in nvt grompp, can it be ignored?
> >> 2. I am generating velocities in nvt run and continuing npt with
> previous
> >> velocities. For production run, I only take the equilibrated structure
> and
> >> generate velocities again. (No continuation)
>
> If you're re-generating velocities, what was the point of the previous
> equilibration steps? You're just re-setting your system to a random state.
>
> >> Should gen_temp have the same temperature values in each of nvt and md
> mdp
> >> files?
>
> If you intend to model the same ensemble, yes, but again re-generating
> velocities after equilibrating doesn't make much sense to me.
>
> -Justin
>
> >>
> >> Please help.
> >> Thank you!
> >>
> >> Regards,
> >> Neelima S.
> >>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] umbrella sampling tutorial

[Justin Lemkul]

On 7/6/18 10:42 AM, hosein geraili wrote:

Dear all,
I have a question regarding the umbrella sampling tutorial. I am using the bash script to 
create the summary_distances.dat, but the problem is at first I would get the error 
"Unknown command-line option -o", then I used -oh instead of -o which worked, 
but the problem is the summary_distances.dat file is not correct, and it seems like:


-oh produces a histogram, not the distances themselves. Use -oall. I 
have fixed the script in the tutorial. Sorry for the typo.


-Justin


0 1 2 3 4 5 6 7 8 9 10 11 ...265 1000.000266 1000.000267 1000.000268 1000.000269 1000.000270 1000.000271 1000.000272 1000.000273 1000.000274 1000.000275 1000.000276 1000.000277 1000.000278 1000.000279 1000.000...10 tail -n 1 dist${i}.xvg | awk "{print 
$2}"11 tail -n 1 dist${i}.xvg | awk "{print $2}"12 tail -n 1 dist${i}.xvg | awk "{print $2}"13 tail -n 1 dist${i}.xvg | awk "{print $2}"14 tail -n 1 dist${i}.xvg | awk "{print $2}"15 tail -n 1 dist${i}.xvg | awk 
"{print $2}"16 tail -n 1 dist${i}.xvg | awk "{print $2}"17 tail -n 1 dist${i}.xvg | awk "{print $2}"18 tail -n 1 dist${i}.xvg | awk "{print $2}"19 tail -n 1 dist${i}.xvg | awk "{print $2}"20 tail -n 1 
dist${i}.xvg | awk "{print $2}"21 tail -n 1 dist${i}.xvg | awk "{print $2}"22 tail -n 1 dist${i}.xvg | awk "{print $2}"23 tail -n 1 dist${i}.xvg | awk "{print $2}"24 tail -n 1 dist${i}.xvg | awk "{print $2}"25 
tail -n 1 dist${i}.xvg | awk "{print $2}"26 tail -n 1 dist${i}.xvg | awk "{print $2}"27 tail -n 1 dist${i}.xvg | awk "{print $2}"...172 1000.000173 1000.000174 1000.000175 1000.000176 1000.000177 1000.000178 1000.000179 
1000.000180 1000.000181 1000.000182 1000.000183 1000.000184 1000.000185 1000.000...
What is the problem?Best


--
==

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

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

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

==


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Re: [gmx-users] Queries regarding temperature gradient

[Justin Lemkul]

On 7/6/18 1:07 PM, Sabreen Farnaz wrote:

Dear all,
This is in regard to my previous queries. The warning in NVT step can
possibly be ignored using -maxwarn but I am still not sure about the rest!
Can someone please help?


tau_t = -1 means temperature coupling is not applied. Whether that's 
what you want or not is up to you, but in that case, your ensembles are 
not NVT or NPT, because T is no longer conserved.



Thanks,
Neelima S.

On Fri, 6 Jul 2018, 01:56 Sabreen Farnaz,  wrote:


Dear all,

I am setting up a system where I want the solute to be immersed in a
solvent with a temperature gradient. I have defined two different
temperature groups, two portions of the solvent, and want them to be at say
T1 and T2 kelvins. The rest of the system will not be subjected to a
thermostat  (tau_t=-1).


Realize that with PBC, you're not likely to get what you want. I don't 
know how you're defining the T1 and T2 groups, but if they're in contact 
via PBC, the "gradient" really doesn't exist - you have a hot and cold 
bath directly in contact. See previous threads on temperature gradients 
for more discussion. If the T1 and T2 groups are capable of diffusing, 
then you definitely don't have a gradient.



My questions are:
1. Should NVT and NPT mdp files also have the same t_ref and tau_t? A
tau_t=-1 gives a warning in nvt grompp, can it be ignored?
2. I am generating velocities in nvt run and continuing npt with previous
velocities. For production run, I only take the equilibrated structure and
generate velocities again. (No continuation)


If you're re-generating velocities, what was the point of the previous 
equilibration steps? You're just re-setting your system to a random state.



Should gen_temp have the same temperature values in each of nvt and md mdp
files?


If you intend to model the same ensemble, yes, but again re-generating 
velocities after equilibrating doesn't make much sense to me.


-Justin



Please help.
Thank you!

Regards,
Neelima S.



--
==

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

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

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

==

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Re: [gmx-users] gmx convert-tpr tool is not found but tpbconv_mpi is present in gromacs 5.0.4

[Justin Lemkul]

On 7/6/18 11:58 AM, Santanu Santra wrote:

Hi all,
  I have installed gromacs 5.0.4 in a parallel cluster. While I was
serching for gmx convert-tpr tool to extend my simulation that has been run
previously upto 15 ns (I want to continue the simulation upto 100 ns).
According to gromacs documentation tpbconv_mpi tool is removed from gromacs
5.0. version and this is replaced by gmx convert-tpr tool. But in my
bin directory there is nothing in the name of  gmx convert-tpr or in
similar name, but I found tpbconv_mpi . I also tried with that tool to
extend but it is showing error .

I tried the command==
tpbconv_mpi -s md_nvt -o md_nvt_25.tpr -extend 1

I got 
GROMACS:  gmx tpbconv, VERSION 5.0.4
Executable:   /opt/gromacs-5.0.4/bin/gmx_mpi
Library dir:  /opt/gromacs-5.0.4/share/gromacs/top
Command line:
   tpbconv_mpi -s md_nvt -o md_nvt_25.tpr -extend 1

This tool has been removed from Gromacs 5.0. Please see
   http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0
for ideas how to perform the same tasks with the new tools.
===

I am confused with two contrary statements.
(1) If tpbconv_mpi tool is removed from gromacs 5.0.X version, then how it
is present in my bin directory and also it is not working


Version 5.0 was a transitional version between "old" and "new" command 
syntax. If a user attempts to run tpbconv, they are greeted with this 
message, which tells them they need to update the scripts. You will note 
that the contents of your bin directory are all symlinks to the gmx 
binary, rather than standalone executables, like they once were.



(2) why  gmx convert-tpr tool is absent in my bin directory. As all other
tools are available in my bin directory.


You won't see anything named "convert-tpr," but you will see a binary 
called "gmx" (or maybe "gmx_mpi," as it appears your entire set of tools 
was compiled with MPI). Then invoke gmx convert-tpr, as the error 
message states.


-Justin

--
==

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

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

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

==

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Re: [gmx-users] Queries regarding temperature gradient

[Sabreen Farnaz]

Dear all,
This is in regard to my previous queries. The warning in NVT step can
possibly be ignored using -maxwarn but I am still not sure about the rest!
Can someone please help?

Thanks,
Neelima S.

On Fri, 6 Jul 2018, 01:56 Sabreen Farnaz,  wrote:

> Dear all,
>
> I am setting up a system where I want the solute to be immersed in a
> solvent with a temperature gradient. I have defined two different
> temperature groups, two portions of the solvent, and want them to be at say
> T1 and T2 kelvins. The rest of the system will not be subjected to a
> thermostat  (tau_t=-1).
> My questions are:
> 1. Should NVT and NPT mdp files also have the same t_ref and tau_t? A
> tau_t=-1 gives a warning in nvt grompp, can it be ignored?
> 2. I am generating velocities in nvt run and continuing npt with previous
> velocities. For production run, I only take the equilibrated structure and
> generate velocities again. (No continuation)
> Should gen_temp have the same temperature values in each of nvt and md mdp
> files?
>
> Please help.
> Thank you!
>
> Regards,
> Neelima S.
>
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[gmx-users] gmx convert-tpr tool is not found but tpbconv_mpi is present in gromacs 5.0.4

[Santanu Santra]

Hi all,
 I have installed gromacs 5.0.4 in a parallel cluster. While I was
serching for gmx convert-tpr tool to extend my simulation that has been run
previously upto 15 ns (I want to continue the simulation upto 100 ns).
According to gromacs documentation tpbconv_mpi tool is removed from gromacs
5.0. version and this is replaced by gmx convert-tpr tool. But in my
bin directory there is nothing in the name of  gmx convert-tpr or in
similar name, but I found tpbconv_mpi . I also tried with that tool to
extend but it is showing error .

I tried the command==
tpbconv_mpi -s md_nvt -o md_nvt_25.tpr -extend 1

I got 
GROMACS:  gmx tpbconv, VERSION 5.0.4
Executable:   /opt/gromacs-5.0.4/bin/gmx_mpi
Library dir:  /opt/gromacs-5.0.4/share/gromacs/top
Command line:
  tpbconv_mpi -s md_nvt -o md_nvt_25.tpr -extend 1

This tool has been removed from Gromacs 5.0. Please see
  http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0
for ideas how to perform the same tasks with the new tools.
===

I am confused with two contrary statements.
(1) If tpbconv_mpi tool is removed from gromacs 5.0.X version, then how it
is present in my bin directory and also it is not working
(2) why  gmx convert-tpr tool is absent in my bin directory. As all other
tools are available in my bin directory.


Any help or suggestion is highly accepted. Thanks in advance.
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[gmx-users] umbrella sampling tutorial

[hosein geraili]

Dear all,
I have a question regarding the umbrella sampling tutorial. I am using the bash 
script to create the summary_distances.dat, but the problem is at first I would 
get the error "Unknown command-line option -o", then I used -oh instead of -o 
which worked, but the problem is the summary_distances.dat file is not correct, 
and it seems like:
0 1 2 3 4 5 6 7 8 9 10 11 ...265 1000.000266 1000.000267 1000.000268 
1000.000269 1000.000270 1000.000271 1000.000272 1000.000273 1000.000274 
1000.000275 1000.000276 1000.000277 1000.000278 1000.000279 1000.000...10 tail 
-n 1 dist${i}.xvg | awk "{print $2}"11 tail -n 1 dist${i}.xvg | awk "{print 
$2}"12 tail -n 1 dist${i}.xvg | awk "{print $2}"13 tail -n 1 dist${i}.xvg | awk 
"{print $2}"14 tail -n 1 dist${i}.xvg | awk "{print $2}"15 tail -n 1 
dist${i}.xvg | awk "{print $2}"16 tail -n 1 dist${i}.xvg | awk "{print $2}"17 
tail -n 1 dist${i}.xvg | awk "{print $2}"18 tail -n 1 dist${i}.xvg | awk 
"{print $2}"19 tail -n 1 dist${i}.xvg | awk "{print $2}"20 tail -n 1 
dist${i}.xvg | awk "{print $2}"21 tail -n 1 dist${i}.xvg | awk "{print $2}"22 
tail -n 1 dist${i}.xvg | awk "{print $2}"23 tail -n 1 dist${i}.xvg | awk 
"{print $2}"24 tail -n 1 dist${i}.xvg | awk "{print $2}"25 tail -n 1 
dist${i}.xvg | awk "{print $2}"26 tail -n 1 dist${i}.xvg | awk "{print $2}"27 
tail -n 1 dist${i}.xvg | awk "{print $2}"...172 1000.000173 1000.000174 
1000.000175 1000.000176 1000.000177 1000.000178 1000.000179 1000.000180 
1000.000181 1000.000182 1000.000183 1000.000184 1000.000185 1000.000...
What is the problem?Best
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Re: [gmx-users] GPU+Energy Groups

[Mark Abraham]

Hi,

You can't ever use a tabulated short-range interaction on a GPU in GROMACS
at this time.

Mark

On Fri, Jul 6, 2018 at 10:55 AM Neda Rafiee  wrote:

> Dear GMX-Users,
> I am going to use GPU acceleration for my simulations but since I have
> some energy tables for LJ interactions, and I am using cut-off scheme=group
> instead of Verlet, I receive these notes:
>
> "NOTE: GPU(s) found, but the current simulation can not use GPUs
>   To use a GPU, set the mdp option: cutoff-scheme = Verlet
> Multiple energy groups is not implemented for GPUs, falling back to the
> CPU. For better performance, run on the GPU without energy groups and then
> do gmx mdrun -rerun option on the trajectory with an energy group .tpr file.
> Using 1 MPI process"
>
> Is it reasonable to do my simulations using GPU and rerun it using
> energy-groups? How will those non-bonded interaction tables be taken into
> account in my first simulations with GPU?
> Thanks in advance.
> Neda
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Re: [gmx-users] question regarding high temperature simulation in Gromacs

[Mark Abraham]

Hi,

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

Mark

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

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

[Justin Lemkul]

On 7/6/18 8:44 AM, Srinivasa Ramisetti wrote:

Thanks Justin for the info. I understand that gmx distance -oh will produce the 
histogram for single pair of molecules. Since I want to generate histogram for 
several other combinations (96 in total) then I may have to call gmx distance 
several times which can be done through scripting. But I would like to know if 
there is any other approach like using gmx pairdist to generate the histogram 
for all pairs in one call.


You can probably post-process the output with gmx analyze -dist, which 
produces a histogram from whatever data you pass to it.


-Justin



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

Sent: 06 July 2018 12:47:21
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] histogram of distance between similar molecules



On 7/6/18 4:30 AM, Srinivasa Ramisetti wrote:

Dear Gromacs users,


I would like to know which tool (gmx distance or gmx pairdist) can be used to 
get a histogram (showing probability distribution function) of the centre of 
mass distance between similar molecules (14 molecules in total) for a range of 
time steps.

gmx distance -oh

-Justin

--
==

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

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

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

==

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==

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

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

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

==

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Re: [gmx-users] histogram of distance between similar molecules

[Srinivasa Ramisetti]

Thanks Justin for the info. I understand that gmx distance -oh will produce the 
histogram for single pair of molecules. Since I want to generate histogram for 
several other combinations (96 in total) then I may have to call gmx distance 
several times which can be done through scripting. But I would like to know if 
there is any other approach like using gmx pairdist to generate the histogram 
for all pairs in one call.


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

Sent: 06 July 2018 12:47:21
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] histogram of distance between similar molecules



On 7/6/18 4:30 AM, Srinivasa Ramisetti wrote:
> Dear Gromacs users,
>
>
> I would like to know which tool (gmx distance or gmx pairdist) can be used to 
> get a histogram (showing probability distribution function) of the centre of 
> mass distance between similar molecules (14 molecules in total) for a range 
> of time steps.

gmx distance -oh

-Justin

--
==

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

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

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

==

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Re: [gmx-users] How to change to heavyh in an equilibrated system

[Justin Lemkul]

On 7/6/18 4:52 AM, Ramon Crehuet wrote:

Dear all,
For testing reasons, I would like to compare a system that I have setup using 
heavy hydrogens (-heavyh option in pdb2gmx) to exactly the same system without 
using heavy hydrogens.
I could redo all the system setup starting from the pdb2gmx, but I would like 
to avoid that. That setup was tedious and I would like to start from the 
exactly the same coordinate file.
I could write a script to change the atom masses in the .itp files, but again, 
this doesn't seem the easiest way.
Is there a way to generate a new topology from the equilibrated .gro or .tpr 
file? (when simply feeding these files to pdb2gmx the ions are not recognized).


If you only want to introduce a difference in the topology, re-process 
the starting coordinates (protein or whatever) with pdb2gmx and then 
just update the .top to match the contents of the non-heavy H system. 
The coordinates will be the same but the topology will be different.


-Justin

--
==

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

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

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

==

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Re: [gmx-users] histogram of distance between similar molecules

[Justin Lemkul]

On 7/6/18 4:30 AM, Srinivasa Ramisetti wrote:

Dear Gromacs users,


I would like to know which tool (gmx distance or gmx pairdist) can be used to 
get a histogram (showing probability distribution function) of the centre of 
mass distance between similar molecules (14 molecules in total) for a range of 
time steps.


gmx distance -oh

-Justin

--
==

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

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

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

==

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Re: [gmx-users] ZnO Parameters

[ali akgün]

Hi,

You can fınd parameters on solid state books(for example kittel)

Thank you.


6 Tem 2018 Cum 13:09 tarihinde  şunu yazdı:

> Dear Gromacs Users
>
> Can anyone provide me the parameters for Zinc Oxide (ZnO)?
>
> Thank You
>
> Regards
> Zaved Hazarika
> PhD Scholar
> Dept.of Molecular Biology and Biotechnology
> Tezpur University
> India
>
>
>
> * * * D I S C L A I M E R * * *
> This e-mail may contain privileged information and is intended solely for
> the individual named. If you are not the named addressee you should not
> disseminate, distribute or copy this e-mail. Please notify the sender
> immediately by e-mail if you have received this e-mail in error and destroy
> it from your system. Though considerable effort has been made to deliver
> error free e-mail messages but it can not be guaranteed to be secure or
> error-free as information could be intercepted, corrupted, lost, destroyed,
> delayed, or may contain viruses. The recipient must verify the integrity of
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> --
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Re: [gmx-users] question regarding high temperature simulation in Gromacs

[Dr. Puspita Halder]

Hi Mark,

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

Thanks

Puspita

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

Hi,

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

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

Mark

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

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

[zaved]

Dear Gromacs Users

Can anyone provide me the parameters for Zinc Oxide (ZnO)?

Thank You

Regards
Zaved Hazarika
PhD Scholar
Dept.of Molecular Biology and Biotechnology
Tezpur University
India



* * * D I S C L A I M E R * * *
This e-mail may contain privileged information and is intended solely for the 
individual named. If you are not the named addressee you should not 
disseminate, distribute or copy this e-mail. Please notify the sender 
immediately by e-mail if you have received this e-mail in error and destroy it 
from your system. Though considerable effort has been made to deliver error 
free e-mail messages but it can not be guaranteed to be secure or error-free as 
information could be intercepted, corrupted, lost, destroyed, delayed, or may 
contain viruses. The recipient must verify the integrity of this e-mail message.
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[gmx-users] Coarse graining carbon nanotubes and MARTINI

[Raman Preet Singh]

Dear All,


I want to run a CG simulation of carbon nanotubes (CNTs) and different 
proteins. I have a few questions for which I request help:

  1.
Several groups have used CG models of CNTs, mapping 2, 2.5 or 3 carbons per CG 
bead. I am a novice in CG models. Any help on creating CG models or reference 
to a tutorial/website/paper/script will be appreciated.
  2.
VMD offers a residue-based CG which can convert the atomistic to CG structure 
of proteins. Will it be OK to use this CG model of protein with CG model of 
CNTs and perform simulation using MARTINI force field.


Thank you in advance.


Regards,

Raman



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[gmx-users] How to change to heavyh in an equilibrated system

[Ramon Crehuet]

Dear all, 
For testing reasons, I would like to compare a system that I have setup using 
heavy hydrogens (-heavyh option in pdb2gmx) to exactly the same system without 
using heavy hydrogens. 
I could redo all the system setup starting from the pdb2gmx, but I would like 
to avoid that. That setup was tedious and I would like to start from the 
exactly the same coordinate file. 
I could write a script to change the atom masses in the .itp files, but again, 
this doesn't seem the easiest way. 
Is there a way to generate a new topology from the equilibrated .gro or .tpr 
file? (when simply feeding these files to pdb2gmx the ions are not recognized). 
Thanks! 
Ramon 

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[gmx-users] GPU+Energy Groups

[Neda Rafiee]

Dear GMX-Users,
I am going to use GPU acceleration for my simulations but since I have some 
energy tables for LJ interactions, and I am using cut-off scheme=group instead 
of Verlet, I receive these notes:

"NOTE: GPU(s) found, but the current simulation can not use GPUs
  To use a GPU, set the mdp option: cutoff-scheme = Verlet
Multiple energy groups is not implemented for GPUs, falling back to the CPU. 
For better performance, run on the GPU without energy groups and then do gmx 
mdrun -rerun option on the trajectory with an energy group .tpr file.
Using 1 MPI process"

Is it reasonable to do my simulations using GPU and rerun it using 
energy-groups? How will those non-bonded interaction tables be taken into 
account in my first simulations with GPU?
Thanks in advance.
Neda
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[gmx-users] Thermal gradient in a system

[Sabreen Farnaz]

Dear all,

How can I get the temperature of a system as a function of distance using
gromacs 5.1.5? gmx energy plots the temperature of the centre of mass of
energy groups against time. gmx traj also does the same from velocity
information.
Please help!

Regards,
Neelima S.
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[gmx-users] histogram of distance between similar molecules

[Srinivasa Ramisetti]

Dear Gromacs users,


I would like to know which tool (gmx distance or gmx pairdist) can be used to 
get a histogram (showing probability distribution function) of the centre of 
mass distance between similar molecules (14 molecules in total) for a range of 
time steps.


Regards,

Srinivasa

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

[Mark Abraham]

Hi,

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

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

Mark

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

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

[Dr. Puspita Halder]

Hi All,

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

Thanks for your help.

Puspita Halder

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

Hi All,

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

Thanks for your help in advance.

Regards
Puspita Halder
-- 
Gromacs Users mailing list

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

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