Re: [gmx-users] energy minimization

[Dallas Warren]

 Gas phase simulations the inter-molecular interactions are smaller, and
intra-molecular interactions dominate. Therefore total energy will be
positive.

If it was filled with a solvent i.e. liquid phase, then inter-molecular
inteactions dominate and the total energy will be negative.

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 Tue, 14 Apr 2020 at 01:59, Afsane Farhadi 
wrote:

> hi friends I generated a box of mixed gas with gmx insert-moleculesI
> ran an energy minimizing.  the potential energy is 4.05e+07 and maximum
> force is 1.25e+03.I used different algorithm likes cg and steep for
> minimization. what do I have to do untill my system potential energy has
> negative value??I need a information about energy minimizing and potential
> energy. I know that positive value of potential energy means the
> intermolecular interaction  is weaker than intramolecular interaction but I
> don't know how I can control this matter. please help
>
> Sent from Yahoo Mail on Android
> --
> 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] semiisotropic pressure coupling.

[Miro Astore]

Hello all,

I am working with a rather large membrane bound protein. I was getting
an issue awhile ago where if the protein moved to the edge of the box
the box would elongate in the z direction. I fixed this in the short
term by setting my xy compressibility to 0 in my production mdp file
pcoupl  = Parrinello-Rahman
pcoupltype  = semiisotropic
tau_p   = 5.0

compressibility = 0  4.5e-5
ref_p   = 1.0 1.0
compressibility = 0  4.5e-5
ref_p   = 1.0 1.0

I have a few questions, why was it blowing up in the first place? I
would guess its to do with how the pressure is being calculated when
this large 'vacuum' is being created in the solvent when the protein
wraps around since my tc_grps is Protein non-Protein. The fact the
problem only occurs when the protein wraps seems to indicate this sort
of artifact, I can get into the hundreds of nano seconds before the
protein drifts if I'm lucky, this is all after a well equilibrated
system.

I could fix the protein in the center of the box but I fear that might
produce artifacts and I suspect there is a better way.

I want to start studying how this protein interacts with the lipids
and fixing the xy box size is not conducive to this so I'm wondering
how  I can let the lipids fluctuate while still maintaining sensible
system behavior.

Thank you for your time,

Best, Miro

mdp file can be found at
https://docs.google.com/document/d/16vsS4OOco9U3bUkarzSduN2OXohnBVVLedwLJanUi4w/edit?usp=sharing
--
Miro A. Astore   (he/him)
PhD Candidate | Computational Biophysics
Office 434 A28 School of Physics
University of Sydney
-- 
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] Replica exchange probabilities beyond version 2016

[Pritam Ganguly]

Hi Gül,

You are absolutely correct! I just checked this with tau_t=10, and it 
brought back the old behavior! Thank you so much for your suggestion!


Probabilities with tau_t=10, NH thermostat:

Repl 0    1    2    3    4    5    6    7    8    9   10 11   12   
13   14   15   16   17   18   19   20   21   22   23 24   25   26   27   
28   29   30   31   32   33   34   35   36 37   38   39   40   41   42   
43   44   45   46   47   48   49 50   51   52   53   54   55   56   57   
58   59   60   61   62 63
Repl  .29  .29  .30  .29  .30  .28  .31  .30  .29  .28  .29 .26  
.28  .29  .28  .27  .29  .26  .27  .28  .26  .26  .28  .27 .26  .27  
.26  .27  .26  .25  .26  .26  .23  .27  .26  .23  .24 .27  .23  .24  
.28  .27  .26  .25  .27  .24  .28  .24  .27  .27 .27  .27  .28  .25  
.27  .27  .26  .28  .26  .28  .27  .28  .30


Thanks again!

Regards,

Pritam

On 4/13/20 7:55 PM, Gül Zerze wrote:

Hi Pritam,

Did you check your energy fluctuations? Looks like you are using NH 
thermostat, you might be suffering from the interaction of NH 
thermostat oscillations with resonance modes in the system, which 
makes energy fluctuations substantially larger (compared to 
fluctuations with NH in older versions of Gromacs). As a result of 
amplified fluctuations, you have higher exchange probability. See here 
for a previous relevant exchange: 
https://redmine.gromacs.org/issues/2904 For my system, making tau_t=10 
helped to recover the old behavior.


Best,
Gül
*--*
*Gül H. Zerze*
Postdoctoral Research Associate

Chemical and Biological Engineering
Princeton University
http://pablonet.princeton.edu/



On Mon, Apr 13, 2020 at 8:01 PM Pritam Ganguly > wrote:


Hello,

I have noticed that the average exchange probability for a replica
exchange run increases significantly if I use Gromacs versions
2018, as
compared to versions 2016 or earlier. I have tested that by
simulating
the same system with versions 2016.4 and 2018.3 and the average
probabilities I find are:

Version 2016.4:

Replica exchange statistics
Repl  1666 attempts, 833 odd, 833 even
Repl  average probabilities:
Repl 0    1    2    3    4    5    6    7    8    9   10 11 12
13   14   15   16   17   18   19   20   21   22   23 24 25 26   27
28   29   30   31   32   33   34   35   36 37 38   39   40 41   42
43   44   45   46   47   48   49 50 51   52   53   54   55 56   57
58   59   60   61   62 63
Repl  .29  .33  .29  .30  .28  .30  .30  .29  .29  .29 .30 .26
.29  .30  .28  .29  .26  .26  .29  .28  .26  .27  .27  .27 .27  .28
.26  .27  .26  .25  .27  .25  .26  .27  .25  .24  .25 .26 .27  .25
.27  .26  .26  .26  .25  .26  .26  .24  .25  .27 .26  .27 .26  .25
.27  .27  .28  .26  .27  .26  .27  .27  .28


Version 2018.3:

Replica exchange statistics
Repl  1666 attempts, 833 odd, 833 even
Repl  average probabilities:
Repl 0    1    2    3    4    5    6    7    8    9   10 11 12
13   14   15   16   17   18   19   20   21   22   23 24 25 26   27
28   29   30   31   32   33   34   35   36 37 38   39   40 41   42
43   44   45   46   47   48   49 50 51   52   53   54   55 56   57
58   59   60   61   62 63
Repl  .39  .39  .37  .42  .38  .38  .39  .36  .36  .38 .40 .39
.40  .39  .37  .35  .40  .39  .35  .38  .40  .35  .38  .35 .36  .35
.36  .36  .38  .36  .37  .36  .35  .36  .36  .37  .35 .35 .35  .37
.37  .35  .37  .36  .37  .34  .36  .38  .38  .38 .35  .37 .36  .39
.36  .40  .38  .38  .40  .36  .37  .36  .33

These are test runs for 5 ns with exchange frequencies of 3 ps. I
have
used the same input parameters for both of these runs (mdp is
attached).
I actually observed this with many other systems and I was looking
for
any relevant gromacs release note for versions 2018 or beyond
related to
the replica exchange algorithm or the way the energies are
calculated,
but I could not figure it out.

Regards,

Pritam

-- 
Pritam Ganguly

Department of Chemistry and Biochemistry
University of California at Santa Barbara
Santa Barbara, CA, USA 93106

Office: PSBN 3606
Phone: +1-805-893-2767
http://people.chem.ucsb.edu/ganguly/pritam

-- 
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
.


--
Pritam Ganguly
Department of Chemistry and Biochemistry
University of California at Santa Barbara
Santa Barbara, CA, USA 93106

Office: PSBN 3606
Phone: +1-805-893-2767
http://people.chem.ucsb.edu/ganguly/pritam

--
Gromacs Users 

Re: [gmx-users] Velocities from the .gro file

[Eric Smoll]

My knowledge is a bit old.

Tpr files are binary so you cannot read them without a special tool.  In 
gromacs 2018, there was a tool that would spit out the contents of a tpr file 
in a readable format.  Execute 
“gmx dump -h” to learn more.

Justin is correct.  There is no tool or file that will allow you to add a 
constant velocity in the z direction to a set of atoms.  I would suggest 
writing a program to build a custom gro file from the start that has everything 
you want.  If that is not possible for you, you could use gen-vel and attempt 
to export a gro with the resulting velocities at some point afterward (e.g., 
use gen-vel tpr for a 1 step simulation writing coordinates and velocities to 
the trr at every step and then extract gro with velocities from the trr).  Then 
go through the gro file and add a constant z-velocity to all the atoms that 
need it.  Then read the edited gro file in again and proceed.

-Eric

Sent from my iPhone

> On Apr 14, 2020, at 3:02 PM, Mohamed Abdelaal  wrote:
> 
> Many thanks Dr. Erik for your reply :)
> 
> 
>> On Tue, Apr 14, 2020 at 11:15 PM Eric Smoll  wrote:
>> 
>> No problem.
>> 
>> Now it is clear what you are trying to do.  The previous description of
>> your goals did not make much physical sense.  The initial velocities are
>> such that all three dimensions are sampled from the same 3D velocity
>> distribution (gaussian with the same width).  The difference is that there
>> is a constant velocity added in the z-direction so there is net motion in
>> the z-direction.
> 
> 
> 
>> One way to do this is to use gen-vel as usual and just add the constant to
>> the z-coordinate.
>> 
> 
> *Can you please tell me more details how to add the constant to the
> z-coordinate ? If I will generate the velocity from the .mdp file, in which
> file should I add the constant to the z-coordinate ?  *
> 
>> 
> 
> The velocities were probably read in.  By default, the velocities may not
>> be printed in the gro.  What matters is that they were loaded in the tpr.
>> Try a simulation to see if the molecule is moving as expected.
>> 
> 
> I will complete the simulation to the end to check whether or not the
> velocity was added from my .gro file.
> 
> 
>> Alternatively, dump the contents of the tpr and make sure the velocities
>> you created were read in.
>> 
>> Do you mean that I should manually edit the .tpr file ? I have tried to
> open it with text editor but it can't be open.
> 
> 
>> -Eric
>> 
>> On Tue, Apr 14, 2020 at 1:56 PM Mohamed Abdelaal 
>> wrote:
>> 
>>> Sorry for writing again in the same topic but I couldn't solve
>>> the velocity problem.
>>> 
>>> I am trying to reproduce a paper written by: Claire Tonnel + , Martin
>>> Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri,
>> Alpeshkumar
>>> K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and Benjamin J.
>>> Powell
>>> Title: Elucidating the Spatial Arrangement of Emitter Molecules in
>> Organic
>>> Light-Emitting Diode Films
>>> 
>>> It was mentioned in the paper that " The molecule was inserted into the
>>> system such that the x and y coordinates of the centre of mass were
>> sampled
>>> from a uniform distribution covering the entire box while the z
>> coordinate
>>> of the centre of mass was set to 2.0 nm above the current surface. The
>>> initial orientation of the molecule was randomised. *The velocities of
>> each
>>> atom within the inserted molecule in x and y were sampled from a Gaussian
>>> distribution with a mean of 0.0 nm/ps and a standard deviation
>> appropriate
>>> for the temperature constant (σ = sqrt(kT/m), where k B is Botzmann’s , T
>>> is the temperature and m is the mass of the atom). The velocities in z
>> were
>>> sampled from the distribution with the same standard deviation as x and y
>>> but with a mean of 0.05 nmps -1 , negative z velocities (molecule moving
>> in
>>> the direction opposite to the surface) were rectified by taking the
>>> absolute value. This ensured all molecules moved toward the surface.*
>>> 
>>> I have read the section 3.4.1 of the manual version 5.1.2 as recommended
>>> above and I have also read all the velocity related topics in the manual
>>> and user guide.
>>> 
>>> (After Dr. Justin and Dr. Eric replies)  I added velocity in my .gro file
>>> and then I inserted the molecule in a box using insert-molecules, However
>>> after the insertion process is completed I opened the output .gro file
>> but
>>> the velocity was not read. This means that I can only generate the
>> velocity
>>> through the .mdp file.
>>> 
>>> If I am going to generate the velocity using my .mdp file, is it possible
>>> to change the standard deviation and the mean ? if yes, how can I modify
>>> them ? (I can't find any way to modify the parameters of the Maxwell
>>> distribution)
>>> 
>>> I want to have velocity distributions with means equal to 0,0,0.5 nmps in
>>> the x,y,z directions respectively.
>>> 
>>> You wrote in your last email that, "A 3D Maxwell Boltzmann 

Re: [gmx-users] Velocities from the .gro file

[Mohamed Abdelaal]

Many thanks Dr. Erik for your reply :)


On Tue, Apr 14, 2020 at 11:15 PM Eric Smoll  wrote:

> No problem.
>
> Now it is clear what you are trying to do.  The previous description of
> your goals did not make much physical sense.  The initial velocities are
> such that all three dimensions are sampled from the same 3D velocity
> distribution (gaussian with the same width).  The difference is that there
> is a constant velocity added in the z-direction so there is net motion in
> the z-direction.



> One way to do this is to use gen-vel as usual and just add the constant to
> the z-coordinate.
>

*Can you please tell me more details how to add the constant to the
z-coordinate ? If I will generate the velocity from the .mdp file, in which
file should I add the constant to the z-coordinate ?  *

>

The velocities were probably read in.  By default, the velocities may not
> be printed in the gro.  What matters is that they were loaded in the tpr.
> Try a simulation to see if the molecule is moving as expected.
>

I will complete the simulation to the end to check whether or not the
velocity was added from my .gro file.


> Alternatively, dump the contents of the tpr and make sure the velocities
> you created were read in.
>
> Do you mean that I should manually edit the .tpr file ? I have tried to
open it with text editor but it can't be open.


> -Eric
>
> On Tue, Apr 14, 2020 at 1:56 PM Mohamed Abdelaal 
> wrote:
>
> > Sorry for writing again in the same topic but I couldn't solve
> > the velocity problem.
> >
> > I am trying to reproduce a paper written by: Claire Tonnel + , Martin
> > Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri,
> Alpeshkumar
> > K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and Benjamin J.
> > Powell
> > Title: Elucidating the Spatial Arrangement of Emitter Molecules in
> Organic
> > Light-Emitting Diode Films
> >
> > It was mentioned in the paper that " The molecule was inserted into the
> > system such that the x and y coordinates of the centre of mass were
> sampled
> > from a uniform distribution covering the entire box while the z
> coordinate
> > of the centre of mass was set to 2.0 nm above the current surface. The
> > initial orientation of the molecule was randomised. *The velocities of
> each
> > atom within the inserted molecule in x and y were sampled from a Gaussian
> > distribution with a mean of 0.0 nm/ps and a standard deviation
> appropriate
> > for the temperature constant (σ = sqrt(kT/m), where k B is Botzmann’s , T
> > is the temperature and m is the mass of the atom). The velocities in z
> were
> > sampled from the distribution with the same standard deviation as x and y
> > but with a mean of 0.05 nmps -1 , negative z velocities (molecule moving
> in
> > the direction opposite to the surface) were rectified by taking the
> > absolute value. This ensured all molecules moved toward the surface.*
> >
> > I have read the section 3.4.1 of the manual version 5.1.2 as recommended
> > above and I have also read all the velocity related topics in the manual
> > and user guide.
> >
> > (After Dr. Justin and Dr. Eric replies)  I added velocity in my .gro file
> > and then I inserted the molecule in a box using insert-molecules, However
> > after the insertion process is completed I opened the output .gro file
> but
> > the velocity was not read. This means that I can only generate the
> velocity
> > through the .mdp file.
> >
> > If I am going to generate the velocity using my .mdp file, is it possible
> > to change the standard deviation and the mean ? if yes, how can I modify
> > them ? (I can't find any way to modify the parameters of the Maxwell
> > distribution)
> >
> > I want to have velocity distributions with means equal to 0,0,0.5 nmps in
> > the x,y,z directions respectively.
> >
> > You wrote in your last email that, "A 3D Maxwell Boltzmann velocity
> > distribution corresponds to three identical gaussian speed distributions
> in
> > vx, vy, andvz centered at zero (mean should be zero for vx, vy, vz).
> Just
> > change the standard deviation of the velocity distribution sqrt(kT/m) for
> > each velocity component if you want them to be different.  If you don't
> > want the mean to be zero for whatever reason, add a constant."
> >
> > If the velocity will not be read from the .gro file where should I add
> the
> > constant to change the mean?
> >
> > Many thanks,
> > Mohamed
> >
> >
> > On Thu, Apr 9, 2020 at 5:00 AM Mohamed Abdelaal 
> > wrote:
> >
> > > Many thanks for your reply :)
> > >
> > > All your language assumptions are true and that is exactly what I
> wanted
> > > to communicate, next time I will try to be more precise and sorry for
> the
> > > confusion 
> > >
> > > I will read section 3.4.1 again carefully.
> > >
> > > Thanks again and sorry for the inconvenience.
> > >
> > > Mohamed
> > >
> > > On Thu, Apr 9, 2020 at 04:33 Eric Smoll  wrote:
> > >
> > >> On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal <
> 

Re: [gmx-users] How to prevent velocity generation for my position restrained molecules ?

[Justin Lemkul]

On 4/14/20 5:48 PM, Mohamed Abdelaal wrote:

Hello everybody,

I am simulating the evaporation process for different atoms on a graphene
sheet and the z-coordinate of each graphene carbon atom was restrained
(using position restrain).

The energy minimization was successfully done without any errors

Then I started the equilibration, I have done the NVT. My nvt.mdp file
is written below. I have added the -DPOSRES to enable the position
restrain and I added temperature

  coupling for both the GRM (the graphene sheet molecules) and the G8LE
(The residue molecules; the molecules I am evaporating) then I wrote
generate velocity = yes.

After finishing the NVT  equilibration, I checked the nvt.gro file and
the problem now is that, I have velocity for both the graphene
molecules (which supposed to be position

restrained) and for the residue. How can I generate velocity for the
residue only (G8LE) and make sure that the graphene sheet is
restrained.



Applying restraints does not prevent dynamics; your restrained atoms 
will have velocities. There will be a "Position Rest." term written to 
the .log and .edr files that is a clear signal your restraints were on 
and working.


If you want the group completely frozen (no position or velocity 
updates), that's what freezegrps is for, but freezing anything is highly 
artificial.


-Justin


title   =  NVT equilibration
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.0005 ; 0.5 fs
; Output control
nstxout = 500   ; save coordinates every 1.0 ps
nstvout = 500   ; save velocities every 1.0 ps
nstenergy   = 500   ; save energies every 1.0 ps
nstlog  = 500   ; update log file every 1.0 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm= lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Nonbonded settings all-angles
cutoff-scheme   = Verlet; Buffered neighbor searching
ns_type = grid  ; search neighboring grid cells
nstlist = 10; 20 fs, largely irrelevant with Verlet
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Electrostatics
coulombtype = cut-off   ; Particle Mesh Ewald for
long-range electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = G8LE GRM  ; two coupling groups - more accurate
tau_t   = 0.1   0.1  ; time constant, in ps
ref_t   = 300   300 ; reference temperature, one for
each group, in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed
periodic_molecules = yes


Many thanks,

Mohamed


--
==

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] Velocities from the .gro file

[Mohamed Abdelaal]

Many thanks for your quick reply :)

On Tue, Apr 14, 2020 at 11:09 PM Justin Lemkul  wrote:

>
>
> On 4/14/20 4:55 PM, Mohamed Abdelaal wrote:
> > Sorry for writing again in the same topic but I couldn't solve
> > the velocity problem.
> >
> > I am trying to reproduce a paper written by: Claire Tonnel + , Martin
> > Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri,
> Alpeshkumar
> > K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and Benjamin J.
> > Powell
> > Title: Elucidating the Spatial Arrangement of Emitter Molecules in
> Organic
> > Light-Emitting Diode Films
> >
> > It was mentioned in the paper that " The molecule was inserted into the
> > system such that the x and y coordinates of the centre of mass were
> sampled
> > from a uniform distribution covering the entire box while the z
> coordinate
> > of the centre of mass was set to 2.0 nm above the current surface. The
> > initial orientation of the molecule was randomised. *The velocities of
> each
> > atom within the inserted molecule in x and y were sampled from a Gaussian
> > distribution with a mean of 0.0 nm/ps and a standard deviation
> appropriate
> > for the temperature constant (σ = sqrt(kT/m), where k B is Botzmann’s , T
> > is the temperature and m is the mass of the atom). The velocities in z
> were
> > sampled from the distribution with the same standard deviation as x and y
> > but with a mean of 0.05 nmps -1 , negative z velocities (molecule moving
> in
> > the direction opposite to the surface) were rectified by taking the
> > absolute value. This ensured all molecules moved toward the surface.*
>
> Presumably the authors used different software; GROMACS does not allow
> such granular control of velocities.
>
> > I have read the section 3.4.1 of the manual version 5.1.2 as recommended
> > above and I have also read all the velocity related topics in the manual
> > and user guide.
> >
> > (After Dr. Justin and Dr. Eric replies)  I added velocity in my .gro file
> > and then I inserted the molecule in a box using insert-molecules, However
> > after the insertion process is completed I opened the output .gro file
> but
> > the velocity was not read. This means that I can only generate the
> velocity
> > through the .mdp file.
>
> That's not true. If you know what velocities you want to assign, do so
> *after* building the whole system by writing the velocities to the .gro
> file (you will need your own code/script to do this). Then do not
> generate velocities in the .mdp file and they will be read from the .gro
> file.
>
> > If I am going to generate the velocity using my .mdp file, is it possible
> > to change the standard deviation and the mean ? if yes, how can I modify
> > them ? (I can't find any way to modify the parameters of the Maxwell
> > distribution)
>
> No, GROMACS has no such capability.
>
> -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] Velocities from the .gro file

[Justin Lemkul]

On 4/14/20 4:55 PM, Mohamed Abdelaal wrote:

Sorry for writing again in the same topic but I couldn't solve
the velocity problem.

I am trying to reproduce a paper written by: Claire Tonnel + , Martin
Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, Alpeshkumar
K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and Benjamin J.
Powell
Title: Elucidating the Spatial Arrangement of Emitter Molecules in Organic
Light-Emitting Diode Films

It was mentioned in the paper that " The molecule was inserted into the
system such that the x and y coordinates of the centre of mass were sampled
from a uniform distribution covering the entire box while the z coordinate
of the centre of mass was set to 2.0 nm above the current surface. The
initial orientation of the molecule was randomised. *The velocities of each
atom within the inserted molecule in x and y were sampled from a Gaussian
distribution with a mean of 0.0 nm/ps and a standard deviation appropriate
for the temperature constant (σ = sqrt(kT/m), where k B is Botzmann’s , T
is the temperature and m is the mass of the atom). The velocities in z were
sampled from the distribution with the same standard deviation as x and y
but with a mean of 0.05 nmps -1 , negative z velocities (molecule moving in
the direction opposite to the surface) were rectified by taking the
absolute value. This ensured all molecules moved toward the surface.*


Presumably the authors used different software; GROMACS does not allow 
such granular control of velocities.



I have read the section 3.4.1 of the manual version 5.1.2 as recommended
above and I have also read all the velocity related topics in the manual
and user guide.

(After Dr. Justin and Dr. Eric replies)  I added velocity in my .gro file
and then I inserted the molecule in a box using insert-molecules, However
after the insertion process is completed I opened the output .gro file but
the velocity was not read. This means that I can only generate the velocity
through the .mdp file.


That's not true. If you know what velocities you want to assign, do so 
*after* building the whole system by writing the velocities to the .gro 
file (you will need your own code/script to do this). Then do not 
generate velocities in the .mdp file and they will be read from the .gro 
file.



If I am going to generate the velocity using my .mdp file, is it possible
to change the standard deviation and the mean ? if yes, how can I modify
them ? (I can't find any way to modify the parameters of the Maxwell
distribution)


No, GROMACS has no such capability.

-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] Velocities from the .gro file

[Mohamed Abdelaal]

Sorry for writing again in the same topic but I couldn't solve
the velocity problem.

I am trying to reproduce a paper written by: Claire Tonnel + , Martin
Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, Alpeshkumar
K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and Benjamin J.
Powell
Title: Elucidating the Spatial Arrangement of Emitter Molecules in Organic
Light-Emitting Diode Films

It was mentioned in the paper that " The molecule was inserted into the
system such that the x and y coordinates of the centre of mass were sampled
from a uniform distribution covering the entire box while the z coordinate
of the centre of mass was set to 2.0 nm above the current surface. The
initial orientation of the molecule was randomised. *The velocities of each
atom within the inserted molecule in x and y were sampled from a Gaussian
distribution with a mean of 0.0 nm/ps and a standard deviation appropriate
for the temperature constant (σ = sqrt(kT/m), where k B is Botzmann’s , T
is the temperature and m is the mass of the atom). The velocities in z were
sampled from the distribution with the same standard deviation as x and y
but with a mean of 0.05 nmps -1 , negative z velocities (molecule moving in
the direction opposite to the surface) were rectified by taking the
absolute value. This ensured all molecules moved toward the surface.*

I have read the section 3.4.1 of the manual version 5.1.2 as recommended
above and I have also read all the velocity related topics in the manual
and user guide.

(After Dr. Justin and Dr. Eric replies)  I added velocity in my .gro file
and then I inserted the molecule in a box using insert-molecules, However
after the insertion process is completed I opened the output .gro file but
the velocity was not read. This means that I can only generate the velocity
through the .mdp file.

If I am going to generate the velocity using my .mdp file, is it possible
to change the standard deviation and the mean ? if yes, how can I modify
them ? (I can't find any way to modify the parameters of the Maxwell
distribution)

I want to have velocity distributions with means equal to 0,0,0.5 nmps in
the x,y,z directions respectively.

You wrote in your last email that, "A 3D Maxwell Boltzmann velocity
distribution corresponds to three identical gaussian speed distributions in
vx, vy, andvz centered at zero (mean should be zero for vx, vy, vz).  Just
change the standard deviation of the velocity distribution sqrt(kT/m) for
each velocity component if you want them to be different.  If you don't
want the mean to be zero for whatever reason, add a constant."

If the velocity will not be read from the .gro file where should I add the
constant to change the mean?

Many thanks,
Mohamed


On Thu, Apr 9, 2020 at 5:00 AM Mohamed Abdelaal 
wrote:

> Many thanks for your reply :)
>
> All your language assumptions are true and that is exactly what I wanted
> to communicate, next time I will try to be more precise and sorry for the
> confusion 
>
> I will read section 3.4.1 again carefully.
>
> Thanks again and sorry for the inconvenience.
>
> Mohamed
>
> On Thu, Apr 9, 2020 at 04:33 Eric Smoll  wrote:
>
>> On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal 
>> wrote:
>>
>> > Many thanks for your reply 
>> >
>> > The limitation in the generate velocity using the .mdp file, is that
>> while
>> > I can generate the velocity from Maxwell distribution,  I will have the
>> > same velocities in the x, y and z directions.
>> >
>>
>> I think you mean "same velocity *distributions* in the x, y, and z
>> directions."  The distributions will be approximately the same but each
>> atom will have a different velocity.
>>
>> >
>> > On the other hand, generating the velocity from the .gro file will let
>> me
>> > specify different velocities in the x,y and z directions but they will
>> be
>> > the same velocities for all the atoms (will not be taken from a maxwell
>> > distribution with variation in the atoms velocities).
>> >
>>
>> I think you mean "specify different velocity *distributions* in the x, y,
>> and z directions"
>>
>> >
>> > Is it possible to generate different velocities in the x,y and z
>> directions
>> >
>>
>> I think you mean "generate different velocity *distributions* in the x, y,
>> and z directions."  If so, the answer is obviously yes. Because you can
>> type in each individual vxi, vyi, and vzi for every atom i, you can
>> generate different velocity distributions in the x, y, and z directions.
>>
>>
>> > from a maxwell distribution ?
>>
>>
>> I am not sure what this part of the sentence means.  If you do what you
>> are
>> suggesting, you will not be working with a maxwell distribution because
>> all
>> three directions should have identical distributions.  See comment below.
>> If there is another misunderstanding, you need to spend more time crafting
>> precise sentences to communicate what you are after.
>>
>>
>> > (for example the velocities to be taken from
>> > a maxwell 

Re: [gmx-users] Basic question about command line

[shubhadip das]

In Bob I'm _ bk no ññllkmjk mm lll look okk jul ki o ki olk by hmm j by by
he

On Tue, 14 Apr 2020, 6:33 pm Justin Lemkul,  wrote:

>
>
> On 4/13/20 10:03 PM, Mohammad Madani wrote:
> > Dear all
> > Hi,
> > I have a basic question about the using the gromacs.
> > I want to use gmx cluster for clustering. I use the cluster hpc.
> > When I run the this command:
> > gmx cluster -f *.trr -s *.gro -g *.log -clid *.xvg
> > I receive the error that I should select the group for least rmsd.
> > Could you please help me how can I add this part to the command line?
> > Can I do this??
>
> 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] Basic question about command line

[Justin Lemkul]

On 4/13/20 10:03 PM, Mohammad Madani wrote:

Dear all
Hi,
I have a basic question about the using the gromacs.
I want to use gmx cluster for clustering. I use the cluster hpc.
When I run the this command:
gmx cluster -f *.trr -s *.gro -g *.log -clid *.xvg
I receive the error that I should select the group for least rmsd.
Could you please help me how can I add this part to the command line?
Can I do this??


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.

Re: [gmx-users] gromacs 2020, bug? high total energy

[Tamas Hegedus]

Hi,

It was not gromacs 2020, but my fault and mixing up various tools 
(grompp, mdrun) from 2019 and 2020 versions.

I am sorry.

Bests,
Tamas

On 4/14/20 4:44 PM, Tamas Hegedus wrote:

Hi,

There might be some bug(?) in gromacs 2020. I can not decide.

I just installed 2020.1 today using the same script (and libraries) 
what I have used for gromacs 2019.

After energy minimization, in the nvt equilibration run, it stops:
Fatal error:
Step 0: The total potential energy is 1.99295e+23, which is extremely 
high.
The LJ and electrostatic contributions to the energy are 73028.7 and 
-712615,

respectively. A very high potential energy can be caused by overlapping
interactions in bonded interactions or very large coordinate values. 
Usually

this is caused by a badly- or non-equilibrated initial configuration,
incorrect interactions or parameters in the topology.

I tried two different systems (two different soluble proteins, ff 
charmm-36m).


However, if I start the simulations with 2019.4, there is no problem 
at all.


Have a nice day,
Tamas



--
Tamas Hegedus, PhD
Senior Research Fellow
Department of Biophysics and Radiation Biology
Semmelweis University | phone: (36) 1-459 1500/60233
Tuzolto utca 37-47| mailto:ta...@hegelab.org
Budapest, 1094, Hungary   | http://www.hegelab.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] gromacs 2020, bug? high total energy

[Tamas Hegedus]

Hi,

There might be some bug(?) in gromacs 2020. I can not decide.

I just installed 2020.1 today using the same script (and libraries) what 
I have used for gromacs 2019.

After energy minimization, in the nvt equilibration run, it stops:
Fatal error:
Step 0: The total potential energy is 1.99295e+23, which is extremely high.
The LJ and electrostatic contributions to the energy are 73028.7 and 
-712615,

respectively. A very high potential energy can be caused by overlapping
interactions in bonded interactions or very large coordinate values. Usually
this is caused by a badly- or non-equilibrated initial configuration,
incorrect interactions or parameters in the topology.

I tried two different systems (two different soluble proteins, ff 
charmm-36m).


However, if I start the simulations with 2019.4, there is no problem at all.

Have a nice day,
Tamas

--
Tamas Hegedus, PhD
Senior Research Fellow
Department of Biophysics and Radiation Biology
Semmelweis University | phone: (36) 1-459 1500/60233
Tuzolto utca 37-47| mailto:ta...@hegelab.org
Budapest, 1094, Hungary   | http://www.hegelab.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] Basic question about command line (Mohammad Madani)

[Teslim Olayiwola]

Hi Mohammed Madani,

Your command is missing the group as mentioned in the error message. While
correct for periodic error, you should ensure that you extract (that's if
your top/file has more than one groups) the appropriate group (not system)
from the production file (xtc) by using trjconv option. After extracting
with trj, you can regenerate the tpr file for the select groups. After
doing this, you can then use the following command

gmxi clustsize -f file.nojump.mol.xtc -n group.ndx -s group.tpr -mol yes
-cut 0.35 -pbc yes

On Tue, 14 Apr 2020 at 11:09, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se
>
> You can reach the person managing the list at
> gromacs.org_gmx-users-ow...@maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. Basic question about command line (Mohammad Madani)
>2. Basic question about command line (Mohammad Madani)
>3. Re: Replica exchange probabilities beyond version 2016 (G?l Zerze)
>4. How to solve the "LINCS WARNING" problem (???)
>5. Re: How to solve the "LINCS WARNING" problem (Yu Du)
>
>
> --
>
> Message: 1
> Date: Mon, 13 Apr 2020 22:03:07 -0400
> From: Mohammad Madani 
> To: "gmx-us...@gromacs.org" ,
> "gromacs.org_gmx-users@maillist.sys.kth.se"
> 
> Subject: [gmx-users] Basic question about command line
> Message-ID:
> <
> cabarwomj3av7nfpr4cjnbqthweebl9wgbrmhwtau2yejoxx...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear all
> Hi,
> I have a basic question about the using the gromacs.
> I want to use gmx cluster for clustering. I use the cluster hpc.
> When I run the this command:
> gmx cluster -f *.trr -s *.gro -g *.log -clid *.xvg
> I receive the error that I should select the group for least rmsd.
> Could you please help me how can I add this part to the command line?
> Can I do this??
>
> Many thanks
>
>
> --
>
> Message: 2
> Date: Mon, 13 Apr 2020 22:03:07 -0400
> From: Mohammad Madani 
> To: "gmx-us...@gromacs.org" ,
> "gromacs.org_gmx-users@maillist.sys.kth.se"
> 
> Subject: [gmx-users] Basic question about command line
> Message-ID:
> <
> cabarwomj3av7nfpr4cjnbqthweebl9wgbrmhwtau2yejoxx...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear all
> Hi,
> I have a basic question about the using the gromacs.
> I want to use gmx cluster for clustering. I use the cluster hpc.
> When I run the this command:
> gmx cluster -f *.trr -s *.gro -g *.log -clid *.xvg
> I receive the error that I should select the group for least rmsd.
> Could you please help me how can I add this part to the command line?
> Can I do this??
>
> Many thanks
>
>
> --
>
> Message: 3
> Date: Mon, 13 Apr 2020 22:55:35 -0400
> From: G?l Zerze 
> To: gmx-us...@gromacs.org, pgang...@chem.ucsb.edu
> Subject: Re: [gmx-users] Replica exchange probabilities beyond version
> 2016
> Message-ID:
>  6t8zvbhhpgn_w1...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Pritam,
>
> Did you check your energy fluctuations? Looks like you are using NH
> thermostat, you might be suffering from the interaction of NH thermostat
> oscillations with resonance modes in the system, which makes energy
> fluctuations substantially larger (compared to fluctuations with NH in
> older versions of Gromacs). As a result of amplified fluctuations, you have
> higher exchange probability. See here for a previous relevant exchange:
> https://redmine.gromacs.org/issues/2904 For my system, making tau_t=10
> helped to recover the old behavior.
>
> Best,
> G?l
> *--*
> *G?l H. Zerze*
> Postdoctoral Research Associate
>
> Chemical and Biological Engineering
> Princeton University
> http://pablonet.princeton.edu/
>
>
>
> On Mon, Apr 13, 2020 at 8:01 PM Pritam Ganguly 
> wrote:
>
> > Hello,
> >
> > I have noticed that the average exchange probability for a replica
> > exchange run increases significantly if I use Gromacs versions 2018, as
> > compared to versions 2016 or earlier. I have tested that by simulating
> > the same system with versions 2016.4 and 2018.3 and the average
> > probabilities I find are:
> >
> > Version 2016.4:
> >
> > Replica exchange statistics
> > Repl  1666 attempts, 833 odd, 833 even
> > Repl  average probabilities:
> > Repl 0123456789   10 11 12
> > 13   14   15   16   17   18   19   20   21   22   23 24 25   26 

Re: [gmx-users] How to solve the "LINCS WARNING" problem

[Yu Du]

Hi Jinyoung,

I guess that the LINCS WARNING you encountered maybe came from hiden errors in 
the configuration of either protein or ligand OR more directly from the 
ligand's topology. You need to carefully check the configuration of protein and 
ligand, e.g. side chain goes through benzene ring.

After a careful check, If you want more suggestion, you need to provide some 
details of the generation of ligand's topology.

Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China.
Zip: 200032, Tel: (86) 021 5492 5275

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

Sent: Tuesday, April 14, 2020 14:32
To: gmx-us...@gromacs.org 
Subject: [gmx-users] How to solve the "LINCS WARNING" problem

Dear GROMACS users,

Since I have run the nvt  and npt processes for the protein-ligand interaction, 
I met the the warning messages below

Step 231785, time 463.57 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000176, max 0.003912 (between atoms 3035 and 3037)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   3035   3036   34.00.1090   0.1087  0.1090

….

Step 231825, time 463.65 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   3024   3025   90.00.1090   0.1236  0.1090
   3026   3027  100.80.1090   6.6242  0.1090
   3028   3029  162.51.7683 5245.4102  0.1090
   3033   3034  106.70.1090 426.5654  0.1090
   3035   3037   90.00.3851   0.7991  0.1090
   3038   3039   90.00.6045   0.4497  0.1090
   3038   3040   90.00.1123   0.2833  0.1090
   3041   3042   59.00.1020   0.1020  0.1020
Wrote pdb files with previous and current coordinates

Step 231826, time 463.652 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 191384000.00, max 4098777344.00 (between atoms 3033 and 3034)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   1423   1424  140.40.1000 503.9983  0.1000
   3024   3025   61.10.1236 223337872.  0.1090
   3026   3027  168.86.6242 149263.5000  0.1090
   3028   3029  165.8  5245.4102 263929.4375  0.1090
   3031   3032  116.20.1090 223428336.  0.1090
   3033   3034  179.9  426.5654 446766720.  0.1090
   3035   3036   35.3   29.6105 831.0708  0.1090
   3035   3037  102.90.7991 775.3371  0.1090
   3038   3039   90.00.4497   0.6355  0.1090
   3038   3040   47.70.2833   0.  0.1090
step 231826: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

So I checked the my input configuration. the 3035, 3028, 3035 atoms are ligand 
C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms.
Why does the LINCS warning  occurs? and How I solve this problem?

Many Thanks

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.
-- 
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] How to solve the "LINCS WARNING" problem

[변진영]

Dear GROMACS users,

Since I have run the nvt  and npt processes for the protein-ligand interaction, 
I met the the warning messages below

Step 231785, time 463.57 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000176, max 0.003912 (between atoms 3035 and 3037)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   3035   3036   34.00.1090   0.1087  0.1090

….

Step 231825, time 463.65 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   3024   3025   90.00.1090   0.1236  0.1090
   3026   3027  100.80.1090   6.6242  0.1090
   3028   3029  162.51.7683 5245.4102  0.1090
   3033   3034  106.70.1090 426.5654  0.1090
   3035   3037   90.00.3851   0.7991  0.1090
   3038   3039   90.00.6045   0.4497  0.1090
   3038   3040   90.00.1123   0.2833  0.1090
   3041   3042   59.00.1020   0.1020  0.1020
Wrote pdb files with previous and current coordinates

Step 231826, time 463.652 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 191384000.00, max 4098777344.00 (between atoms 3033 and 3034)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   1423   1424  140.40.1000 503.9983  0.1000
   3024   3025   61.10.1236 223337872.  0.1090
   3026   3027  168.86.6242 149263.5000  0.1090
   3028   3029  165.8  5245.4102 263929.4375  0.1090
   3031   3032  116.20.1090 223428336.  0.1090
   3033   3034  179.9  426.5654 446766720.  0.1090
   3035   3036   35.3   29.6105 831.0708  0.1090
   3035   3037  102.90.7991 775.3371  0.1090
   3038   3039   90.00.4497   0.6355  0.1090
   3038   3040   47.70.2833   0.  0.1090
step 231826: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

So I checked the my input configuration. the 3035, 3028, 3035 atoms are ligand 
C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms. 
Why does the LINCS warning  occurs? and How I solve this problem? 

Many Thanks 

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.