Re: [gmx-users] Pressure coupling in expanded ensemble simulations

[Gregory Man Kai Poon]

Hi Michael,

I am just following up on your thoughts on how carrying out expanded ensemble 
at NVT and converting back to NPT on the mailing list.  Again I appreciate your 
advice in this area.

Best wishes,

Gregory


On 5/8/2019 12:01 PM, Michael Shirts wrote:

Yeah, this is an unfortunately place in the code where not all combinations
work - very long story.  Hopefully this will be working better in 2020.

What I would recommend is, if possible, performing the expanded ensemble
simulation at NVT.  Everything should work fine there (paper coming out
hopefully soon comparing a bunch of free energy methods).  Once can always
correct the free energy at lambda=1 from NVT to NPT.  I Can fill in the
details.

You do NOT want to do Berendsen for NPT when running expanded ensemble.
The results will be incorrect (as I have learned by sad experience_

On Wed, May 8, 2019 at 8:14 AM Gregory Man Kai Poon 
 wrote:



Hi all:

We are interested to do expanded ensemble simulations (such as simulated
tempering) on GROMACS.  Extensive fiddling with the settings and
googling on other people's experience suggests that these simulations
must use the md-vv integrator, which in turn is compatible with
Berendsen or MTTK coupling for pressure.  However, MTTK does not work
with constraints, which are needed for the forcefields.  Berendsen can
handle constraints but is not recommended for preserving thermodynamic
ensembles.  Any ideas on how one should proceed?

Many thanks for your thoughts.

Gregory


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Re: [gmx-users] water mediated Hbond

[spss4]

 Thank you for your kind reply.
- Message from Bratin Kumar Das <177cy500.bra...@nitk.edu.in> -
    Date: Fri, 17 May 2019 13:33:30 +0530
    From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] water mediated Hbond
      To: gmx-us...@gromacs.org


Hi,
   There are two types of hydrogen bond from dynamic point of view. 1)
intermittent and 2) continuous. Between two type of hydrogen bond
continuous h-bond autocorrelation will give you proper lifetime ...not
intermittent. In gmx h-bond if we give the ACF of intermittent h-bond.
Therefore it's better to go for md-analysis..there you find code for
continuous h-bond ACF which you give proper h-bond life time in which area
you want to calculate.

On Fri 17 May, 2019, 11:00 AM ,  wrote:


Hi
In gmx hbond command there is a flag -ac -contact which gives hbond
autocorrelation function with respect to time. Can I use that to get
idea about lifetime of a Hbond? Because integration of the
autocorrelation function will give the lifetime. Is there anything
wrong?

- Message from Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
-
    Date: Tue, 14 May 2019 19:21:19 +0530
    From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] water mediated Hbond
      To: gmx-us...@gromacs.org

Hi
    In md analysis you can calculate continuous h-bond. That will give you
proper lifetime.

On Tue 14 May, 2019, 11:58 AM Bratin Kumar Das, <
177cy500.bra...@nitk.edu.in>
wrote:

In gromacs you can not calculate h-bond life time. You can use
mdanalysis
tool for calculating h-bond lifetime.

On Tue 14 May, 2019, 11:56 AM ,  wrote:

Then what is the right way to calculate lifetime of a hydrogen bond?
- Message from Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
-
     Date: Mon, 13 May 2019 22:24:51 +0530
     From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] water mediated Hbond
       To: gmx-us...@gromacs.org

The lifetime of the h-bond can be calculated by calculating the
autocorrelation of continuous h-bonds. I don't think gmx h-bond is
suitable
for continuous hydrogen ACF. It can give the intermittent h-bond ACF
which
can be helpful for calculating the structural relaxation.

On Mon 13 May, 2019, 8:51 PM ,  wrote:

Hii
Thank you for your reply. So as u suggest I have to calculate 2 Hbond
separately. But for how long that water mediated Hbond is stable; for
that can I use Hbond number with time? For how many frames both the
bonds appearing together. Is this right? One more thing is that I want
to calculate lifetime of the Hbond. I have used gmx hbond -ac -contact
command. Then I am getting a time dependent autocorrelation function.
Integration of the C(t) will give me lifetime of the Hbond. Is this a
right way to proceed?

- Message from Justin Lemkul  -
      Date: Mon, 13 May 2019 09:10:41 -0400
      From: Justin Lemkul 
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] water mediated Hbond
        To: gmx-us...@gromacs.org

On 5/13/19 8:48 AM, Bratin Kumar Das wrote:
Hi,
        You can make a ndx file containing the residue of interest and
the
SOL. In gmx h-bond command use the index file. It will give you water
mediated hbond

That's not what a water-mediated hydrogen bond is. That's when a
water molecule simultaneously participates in hydrogen bonds with
two other species. GROMACS does not have the ability to do such
calculations easily. It would require one calculation of H-bonds
between species A and water, saving those waters into index groups
per frame, and then computing the H-bonds of those waters with
species B in a separate calculation. Only then do you get the number
of water-mediated (not direct) hydrogen bonds.

-Justin

On Tue 7 May, 2019, 12:40 PM ,  wrote:

Dear all
I want to determine the water mediated hydrogen between DNA bases and
small molecule. What extra flag should I use in gmx hbond command? Is
there any other option to capture the water mediated Hbonds? Please
suggest something.
Sunipa Sarkar
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Re: [gmx-users] Umbrella sampling PMF using pull-geometry=direction

[Pradyumn Sharma]

I am sorry I forgot to give the link in the last mail.

https://indianinstituteofscience-my.sharepoint.com/:f:/g/personal/pradyumn_iisc_ac_in/EkAdkzcZsepHvbE1UDJPS5UBg2mENMYsRC2S0Z2DDWS9xQ?e=3GeICo

On Fri, May 17, 2019 at 5:03 PM Pradyumn Sharma <
cherpradyumnsha...@gmail.com> wrote:

> Dear all
> I am trying to get a PMF for a small molecule translocation through an
> asymmetric membrane. I am doing it using pull-geometry= direction to do
> umbrella sampling at each window. I am getting a profile in which PMF of
> molecule in the bulk water at one side of the membrane is different from
> the one in bulk water on the other side, which should not be the case
> because it is bulk water on both sides. I saw the trajectory, as well as my
> density map, both shows that windows at either end are corresponding to the
> position of molecule in bulk water.
> I am giving a link for files related including:
>
> a. MDP file - for one window
> b. Density map for water along the z-direction, where 0 represents my
> membrane centre
> c. PMF profile
>
> Am I interpreting this correctly? if some mistake is there in parameters
> or my interpretation kindly let me know.
>
> Additional details:
> 1. I am using gromacs-2018.2.
> 2. I got the initial system. from CHARMMGUI.
> 3. Proper overlapping is there I checked my histograms, also if that was
> the case than PMF would not have been so smooth.
> 3. I already did US simulations for symmetric membrane with
> pull-geometry=distance, also I have reproduced results in the literature
> already.
> --
> Regards
> Pradyumn Sharma
> PhD Student
> Department of Chemical Engineering
> Indian Institute Of Science (IISc)
>


-- 
Regards
Pradyumn Sharma
PhD Student
Department of Chemical Engineering
Indian Institute Of Science (IISc)
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[gmx-users] Umbrella sampling PMF using pull-geometry=direction

[Pradyumn Sharma]

Dear all
I am trying to get a PMF for a small molecule translocation through an
asymmetric membrane. I am doing it using pull-geometry= direction to do
umbrella sampling at each window. I am getting a profile in which PMF of
molecule in the bulk water at one side of the membrane is different from
the one in bulk water on the other side, which should not be the case
because it is bulk water on both sides. I saw the trajectory, as well as my
density map, both shows that windows at either end are corresponding to the
position of molecule in bulk water.
I am giving a link for files related including:

a. MDP file - for one window
b. Density map for water along the z-direction, where 0 represents my
membrane centre
c. PMF profile

Am I interpreting this correctly? if some mistake is there in parameters or
my interpretation kindly let me know.

Additional details:
1. I am using gromacs-2018.2.
2. I got the initial system. from CHARMMGUI.
3. Proper overlapping is there I checked my histograms, also if that was
the case than PMF would not have been so smooth.
3. I already did US simulations for symmetric membrane with
pull-geometry=distance, also I have reproduced results in the literature
already.
-- 
Regards
Pradyumn Sharma
PhD Student
Department of Chemical Engineering
Indian Institute Of Science (IISc)
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Re: [gmx-users] select an atom for "only" residue with make_ndx [ Resolved ]

[ABEL Stephane]

Thanks Justin it worked. 

For the record, I have also found that 

27 & a C31 C32 C33 is equivalent to a C31 | aC32 | aC33  &  rLIPIDC or aC31 | 
aC32 | aC33  &  27. 

Note For the two latter commands  the order of "r27 or rLIPIDC" is important

Thanks again 

On 5/16/19 5:44 AM, ABEL Stephane wrote:
> Thanks Justin
>
> but it does not work either
>
> LIPIDC is indeed in a group (#27)
>
> So I when typed with GMX5.1.4 or GMX2018.2
>
> LIPIDC & a C31 | a C32 | a C33  ---> Syntax error: "LIPIDC & a C31 | a C32 | 
> a C33"
> 27 & a C31 | a C32 | a C33  ---> the command works  but I selected "all" the 
> C31, C32 and C33 atoms and not only those in the LIPIDC group

Sorry, the correct syntax is:

27 & a C31 C32 C33

-Justin

> St?phane
>
> On 5/15/19 11:03 AM, ABEL Stephane wrote:
>> Hello all,
>>
>> I am currently doing simulations of a model of membranes with different 
>> types of lipids (LIPIDA, LIPIDB and LIPIDC)  and I would like to select a 
>> group of  atoms for only the same lipid with make_ndx. Below an example
>>
>> Three different lipids : LIPIDA, LIPIDB and LIPIDC contain few atoms with 
>> the same name (C31, C32 and C33). With make_ndx I would like to have the 
>> atoms C33 and C32 for "only" the LIPIDC
>>
>> So If I do
>>
>> rLIPIDC & aC32 | aC33 ---> I have the indices of the C32 and C33 of the 3 
>> lipid types.
>> So what is the exact command
> Each different [moleculetype] already has its own default group, so
> choosing atoms in LIPIDC should be as simple as:
>
> N & a C31 | a C32 | a C33
>
> where N is the group corresponding to LIPIDC.
>
> -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
>
> ==
>
>

--
==

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

==



--

Message: 5
Date: Thu, 16 May 2019 13:55:33 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Charmm 36m
Message-ID: <5a0fe974-b580-dff7-74a3-98ccd6365...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 5/15/19 3:54 PM, Coire Gavin-Hanner wrote:
> Dear Gromacs users,
>
> I am trying to use the charmm36m forcefield to simulate a protein. The most 
> recent release of charmm36 includes 36m and the ability to toggle between the 
> two. Is 36m the default state?

Yes, though it is possible to use the old C36 parameters with the
(hopefully very clear) define statement:

define = -DUSE_OLD_C36

Otherwise, the parameters used are C36m.

-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

==



--

Message: 6
Date: Thu, 16 May 2019 18:13:34 + (UTC)
From: mary ko 
To: Discussion List for GROMACS Users

Subject: [gmx-users] number of coordinates in coordinate file does not
match   topology
Message-ID: <172035957.1411431.1558030414...@mail.yahoo.com>
Content-Type: text/plain; charset=UTF-8

Hello all
I want to run a simulation of a protein from PDB data bank with a ligand. It 
has two chains and I need only chain A. when I delete chain B in CHIMERA and 
try to run the simulation, it stops at the gmx_mpi grompp -f ions.mdp -c 
solve.pdb -p topol.top -o ions.tpr step with the error of number of coordinates 
in the solve.pdb (143982) does not match the topol.top (143983). I checked the 
.pdb file and it starts from residue 13. Do I get the error because of that 
residues not being sorted from 1, since I use the same method for the sorted 
files and they run without errors.Thank you

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End of gromacs.org_gmx-users Digest, Vol 181, Issue 39
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Re: [gmx-users] Rupture force definition

[Rakesh Mishra]

Dear Justin

After long time again I want to ask one question.
If suppose I want to repeat the same production
simulation ( final md simulation) for different seeds,
then how to do. Because as from the knowledge of
gromacs there is no manual way to put different seeds
in the .mdp files.


On Mon, Jun 25, 2018 at 7:27 PM Justin Lemkul  wrote:

>
>
> On 6/25/18 8:48 AM, Rakesh Mishra wrote:
> > Dear Justin.
> >
> > I have observed one thing that during pulling (Constant velocity pulling
> )
> > of dsDNA/dsRNA ( globally say Nucleic acid ) along helical direction, we
> > observe that in the force/time .xvg file, some time force value  is +ve
> and
> > some time force value is -ve. So why it happens. In my thinking it should
> > always be +ve.
>
> Free energy surfaces are rugged. Some intermediate conformations may
> result in local free energy wells.
>
> -Justin
>
> > On Mon, Jun 11, 2018 at 5:37 PM, Justin Lemkul  wrote:
> >
> >>
> >> On 6/8/18 2:52 AM, Rakesh Mishra wrote:
> >>
> >>> Dear Justin .
> >>> I have  two query
> >>>
> >>> 1-What can be the optimized value of rate can be taken
> >>> for pulling of  dsDNA/dsRNA using gromacs format where solvent is
> aqua.
> >>>   From your umbrella sampling manual,  rate is very high like (0.01
> nm/ps),
> >>> which is equal to 0.0001Angstrom/fs.
> >>>
> >> You'll note in the SI we tested lower values and achieved the same
> >> outcome, so you need to test a few to be sure that whatever pull rate
> you
> >> impose does not introduce artifacts. There is no way, a priori, to know
> >> what an "optimized" rate would be. That term also has multiple
> >> interpretations.
> >>
> >> 2- In pulling mdp file no random seed is discussed. But if we want to
> >>> obtain 2 or 3 different trajectory during
> >>>pulling ( of the same system ) for  different seed, then how to
> give
> >>> different seed in pulling  mdp file.
> >>>
> >>> Note -  In my thinking in gromacs, gen_seed  = -1 is default value.
> And
> >>> it
> >>> comes , when NVT is applied ( where
> >>>velocity generation is allowed, to achieve required
> >>> temperature through maxwell distribution ). But in case of pulling,
> where
> >>> no velocity
> >>>generation is allowed . Then how to calculate different
> >>> pulling simulation of the same system for different seeds.
> >>>
> >> One does not supply a new random seed when doing a continuation of a
> run.
> >> If you want to start new simulations in each window or in multiple
> >> replicates of a run, then use "gen_seed = -1" to get a completely random
> >> seed based on the process ID.
> >>
> >>
> >> -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!
> >>
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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.
> >>
> >
> >
>
> --
> ==
>
> 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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> send a mail to gmx-users-requ...@gromacs.org.
>


-- 

*With Best-Rakesh Kumar Mishra  (RA)*

*Dr. D. S. Kothari Fellow.School of Computational *
*& Integrative Sciences, JNU.*
*Phone n. +91 9473662491, +918777496532*
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Re: [gmx-users] water mediated Hbond

[Bratin Kumar Das]

Hi,
There are two types of hydrogen bond from dynamic point of view. 1)
intermittent and 2) continuous. Between two type of hydrogen bond
continuous h-bond autocorrelation will give you proper lifetime ...not
intermittent. In gmx h-bond if we give the ACF of intermittent h-bond.
Therefore it's better to go for md-analysis..there you find code for
continuous h-bond ACF which you give proper h-bond life time in which area
you want to calculate.

On Fri 17 May, 2019, 11:00 AM ,  wrote:

>   Hi
> In gmx hbond command there is a flag -ac -contact which gives hbond
> autocorrelation function with respect to time. Can I use that to get
> idea about lifetime of a Hbond? Because integration of the
> autocorrelation function will give the lifetime. Is there anything
> wrong?
>
> - Message from Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
> -
> Date: Tue, 14 May 2019 19:21:19 +0530
> From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
> Reply-To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] water mediated Hbond
>   To: gmx-us...@gromacs.org
>
> > Hi
> >In md analysis you can calculate continuous h-bond. That will give you
> > proper lifetime.
> >
> > On Tue 14 May, 2019, 11:58 AM Bratin Kumar Das, <
> 177cy500.bra...@nitk.edu.in>
> > wrote:
> >
> >> In gromacs you can not calculate h-bond life time. You can use
> mdanalysis
> >> tool for calculating h-bond lifetime.
> >>
> >> On Tue 14 May, 2019, 11:56 AM ,  wrote:
> >>
> >>> Then what is the right way to calculate lifetime of a hydrogen bond?
> >>> - Message from Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
> >>> -
> >>> Date: Mon, 13 May 2019 22:24:51 +0530
> >>> From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
> >>> Reply-To: gmx-us...@gromacs.org
> >>> Subject: Re: [gmx-users] water mediated Hbond
> >>>   To: gmx-us...@gromacs.org
> >>>
> >>> The lifetime of the h-bond can be calculated by calculating the
> >>> autocorrelation of continuous h-bonds. I don't think gmx h-bond is
> >>> suitable
> >>> for continuous hydrogen ACF. It can give the intermittent h-bond ACF
> >>> which
> >>> can be helpful for calculating the structural relaxation.
> >>>
> >>> On Mon 13 May, 2019, 8:51 PM ,  wrote:
> >>>
> >>> Hii
> >>> Thank you for your reply. So as u suggest I have to calculate 2 Hbond
> >>> separately. But for how long that water mediated Hbond is stable; for
> >>> that can I use Hbond number with time? For how many frames both the
> >>> bonds appearing together. Is this right? One more thing is that I want
> >>> to calculate lifetime of the Hbond. I have used gmx hbond -ac -contact
> >>> command. Then I am getting a time dependent autocorrelation function.
> >>> Integration of the C(t) will give me lifetime of the Hbond. Is this a
> >>> right way to proceed?
> >>>
> >>> - Message from Justin Lemkul  -
> >>>  Date: Mon, 13 May 2019 09:10:41 -0400
> >>>  From: Justin Lemkul 
> >>> Reply-To: gmx-us...@gromacs.org
> >>> Subject: Re: [gmx-users] water mediated Hbond
> >>>To: gmx-us...@gromacs.org
> >>>
> >>> On 5/13/19 8:48 AM, Bratin Kumar Das wrote:
> >>> Hi,
> >>>You can make a ndx file containing the residue of interest and
> >>> the
> >>> SOL. In gmx h-bond command use the index file. It will give you water
> >>> mediated hbond
> >>>
> >>> That's not what a water-mediated hydrogen bond is. That's when a
> >>> water molecule simultaneously participates in hydrogen bonds with
> >>> two other species. GROMACS does not have the ability to do such
> >>> calculations easily. It would require one calculation of H-bonds
> >>> between species A and water, saving those waters into index groups
> >>> per frame, and then computing the H-bonds of those waters with
> >>> species B in a separate calculation. Only then do you get the number
> >>> of water-mediated (not direct) hydrogen bonds.
> >>>
> >>> -Justin
> >>>
> >>> On Tue 7 May, 2019, 12:40 PM ,  wrote:
> >>>
> >>> Dear all
> >>> I want to determine the water mediated hydrogen between DNA bases and
> >>> small molecule. What extra flag should I use in gmx hbond command? Is
> >>> there any other option to capture the water mediated Hbonds? Please
> >>> suggest something.
> >>> Sunipa Sarkar
> >>> --
> >>> 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
> >>>
> >>> 

Re: [gmx-users] control parameter on the Lennard-Jones interactions

[Omkar Singh]

I have protein MD simulation file I want to find out protein water rdf with
coordination number. Can anyone help regarding this?

Thanks


On Thu, May 16, 2019, 10:55  wrote:

>
> Dear gromacs members,
>
> I would ask you if in gromacs is possible to add a control parameter on
> the Lennard-Jones interactions.
> For example we have two atoms A and B and the corresponding parameters;
> sigma(A), eps(A),  sigma(B), esp(B); then for the A-B interactions we have
> the parameters obtained with the Lorentz-Berthelot or with the geometrical
> average.
>
> I would like to have a standard interaction between A or B with the other
> atoms of the system.  In the same time I would like to add a control
> parameter C on the interaction between A and B to have the following
> potential:
> V(r(AB))=4*eps(AB)*[(sigma(AB)/r(AB))^(12)-C*(sigma(AB)/r(AB))^(6)]
>
> Is it possible? How can I manage this calculation?
>
>
> Many thanks,
>
>
> Anna
>
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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