Re: [gmx-users] definition electrical field in a special position

[Mark Abraham]

Hi,

No that cannot be done

Mark

On Mon, Feb 26, 2018, 05:22  wrote:

> Hi all
>
> when I use E_z, it applies an electric field in the z direction, but I
> want to apply that in special thickness in the z direction, not in all
> length, is there any way to do it?
>
> Thanks in advance
>
> Regards
>
> Azadeh
>
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[gmx-users] definition electrical field in a special position

[kordzadeh]

Hi all

when I use E_z, it applies an electric field in the z direction, but I want to 
apply that in special thickness in the z direction, not in all length, is there 
any way to do it?

Thanks in advance

Regards

Azadeh

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Re: [gmx-users] Inconsistent Shifts

[Justin Lemkul]

On 2/25/18 6:27 PM, Dallas Warren wrote:

Iman,

As I mentioned earlier, does the warning actually stop the simulation
from running/completing?  If not, then simply ignore it.

One of the developers will need to chime in here about the error itself.


It would be helpful to know what exactly was being done beyond "using 
some commands in gromacs" to help here.


If it was an analysis tool, then there's no significance to this 
message, given the fact that there are periodic molecules. If it was 
from trjconv, again, we would have to know the *exact* command being used.


-Justin


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 25 February 2018 at 20:34, Iman Ahmadabadi
 wrote:

Dear Dallas,

I have tried the 2016.5 version of gromacs that it has the same warning
about the inconsistent shifts. I don't know why it should arises as a
warning and what is the problem. Is there another way to fix this warning?

Sincerely
Iman

On Wed, Feb 21, 2018 at 11:26 AM, Iman Ahmadabadi <
imanahmadabad...@gmail.com> wrote:


Dear Dallas,

Yes, the system has periodic molecules (periodic-molecules = yes) and the
version of gromacs is 5.1.2. So, I should use for calculating the
properties of the system by gromacs 2016 and newer ones?

Respectfully,
Iman

On Tue, Feb 20, 2018 at 2:57 PM, Iman Ahmadabadi <
imanahmadabad...@gmail.com> wrote:


Dear Gromacs users,

In using some commands in gromacs, the sentence "There were 240
inconsistent shifts. Check your topology" come up on the screen and I don't
know what is wrong in my topology file, however it calculates correctly the
features of the system but I would like to know the reason of this warning.

Respectfully,
Iman




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Re: [gmx-users] Inconsistent Shifts

[Dallas Warren]

Iman,

As I mentioned earlier, does the warning actually stop the simulation
from running/completing?  If not, then simply ignore it.

One of the developers will need to chime in here about the error itself.
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 25 February 2018 at 20:34, Iman Ahmadabadi
 wrote:
> Dear Dallas,
>
> I have tried the 2016.5 version of gromacs that it has the same warning
> about the inconsistent shifts. I don't know why it should arises as a
> warning and what is the problem. Is there another way to fix this warning?
>
> Sincerely
> Iman
>
> On Wed, Feb 21, 2018 at 11:26 AM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com> wrote:
>
>> Dear Dallas,
>>
>> Yes, the system has periodic molecules (periodic-molecules = yes) and the
>> version of gromacs is 5.1.2. So, I should use for calculating the
>> properties of the system by gromacs 2016 and newer ones?
>>
>> Respectfully,
>> Iman
>>
>> On Tue, Feb 20, 2018 at 2:57 PM, Iman Ahmadabadi <
>> imanahmadabad...@gmail.com> wrote:
>>
>>> Dear Gromacs users,
>>>
>>> In using some commands in gromacs, the sentence "There were 240
>>> inconsistent shifts. Check your topology" come up on the screen and I don't
>>> know what is wrong in my topology file, however it calculates correctly the
>>> features of the system but I would like to know the reason of this warning.
>>>
>>> Respectfully,
>>> Iman
>>>
>>
>>
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Re: [gmx-users] Multiple runs for same system

[Justin Lemkul]

On 2/25/18 6:07 PM, Dr. Seema Mishra wrote:

Thanks Justin. Meaning I will simply set gen_seed as -1 instead of 173529. 
Right?


However you want to do it, either by specifying a seed or letting grompp 
generate one. Some prefer the former for reproducibility, but given all 
the things that can affect binary reproducibility, I don't think it's a 
big concern.



After this, how many runs will be performed? One? Then after the production run 
is finished, start it again with gen_seed=-1 for the second run?


Each .tpr specifies one initial set of conditions for a simulation. If 
you want another simulation, generate another .tpr that specifies a 
different set of conditions.


-Justin


This is to be done for 3 independent runs for same protein-ligand system.

Seema
  


 On Monday, 26 February 2018 4:16 AM, Justin Lemkul  wrote:
  

  
Multiple runs are typically initiated simply by changing gen_seed when

generating velocities at the outset of equilibration.

As for clustering, you'll have to explain what you mean. Clustering
ligand poses? Protein? What? Does a Google search for "GROMACS
clustering" or the help information for gmx cluster point you to
anything useful

-Justin

On 2/25/18 4:11 PM, Dr. Seema Mishra wrote:

Or just direct me to the steps written anywhere

       On Saturday, 24 February 2018 3:51 PM, Dr. Seema Mishra 
 wrote:
   


   Hi, Can anyone tell me the steps and commands for performing multiple runs 
of 50 ns for same protein-ligand system? Also the clustering for further 
analyses. Thanks.


 


--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

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

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

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Re: [gmx-users] Multiple runs for same system

[Dr. Seema Mishra]

Thanks Justin. Meaning I will simply set gen_seed as -1 instead of 173529. 
Right?
After this, how many runs will be performed? One? Then after the production run 
is finished, start it again with gen_seed=-1 for the second run?

This is to be done for 3 independent runs for same protein-ligand system.

Seema
 

On Monday, 26 February 2018 4:16 AM, Justin Lemkul  wrote:
 

 
Multiple runs are typically initiated simply by changing gen_seed when 
generating velocities at the outset of equilibration.

As for clustering, you'll have to explain what you mean. Clustering 
ligand poses? Protein? What? Does a Google search for "GROMACS 
clustering" or the help information for gmx cluster point you to 
anything useful

-Justin

On 2/25/18 4:11 PM, Dr. Seema Mishra wrote:
> Or just direct me to the steps written anywhere
>
>      On Saturday, 24 February 2018 3:51 PM, Dr. Seema Mishra 
> wrote:
>  
>
>  Hi, Can anyone tell me the steps and commands for performing multiple runs 
>of 50 ns for same protein-ligand system? Also the clustering for further 
>analyses. Thanks.
>
>
>    

-- 
==

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

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

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

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Re: [gmx-users] Multiple runs for same system

[Justin Lemkul]

Multiple runs are typically initiated simply by changing gen_seed when 
generating velocities at the outset of equilibration.


As for clustering, you'll have to explain what you mean. Clustering 
ligand poses? Protein? What? Does a Google search for "GROMACS 
clustering" or the help information for gmx cluster point you to 
anything useful


-Justin

On 2/25/18 4:11 PM, Dr. Seema Mishra wrote:

Or just direct me to the steps written anywhere

 On Saturday, 24 February 2018 3:51 PM, Dr. Seema Mishra 
 wrote:
  


  Hi, Can anyone tell me the steps and commands for performing multiple runs of 
50 ns for same protein-ligand system? Also the clustering for further analyses. 
Thanks.





--
==

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

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

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

==

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Re: [gmx-users] Multiple runs for same system

[Dr. Seema Mishra]

Or just direct me to the steps written anywhere 

On Saturday, 24 February 2018 3:51 PM, Dr. Seema Mishra 
 wrote:
 

 Hi, Can anyone tell me the steps and commands for performing multiple runs of 
50 ns for same protein-ligand system? Also the clustering for further analyses. 
Thanks. 


   
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Re: [gmx-users] UNL residue error

[Justin Lemkul]

On 2/25/18 11:53 AM, Radhika Arora wrote:

Hello,


I face an error in PDB file of cellulose to run GROMACS. I want to know
what should I write in place of UNL residue.


ATOM   1700  C   UNL 1  29.680 -48.720 -19.563  0.00 -0.02
.177 C

ATOM   1701  C   UNL 1  13.970 -44.542 -17.378  0.00 -0.02
.177 C

ATOM   1702  C   UNL 1   6.116 -42.453 -16.285  0.00 -0.02
.177 C

ATOM   1703  C   UNL 1  -1.739 -40.364 -15.193  0.00 -0.02
.177 C

ATOM   1704  C   UNL 1  -9.594 -38.274 -14.101  0.00 -0.02
.177 C

ATOM   1705  C   UNL 1  21.826 -46.631 -18.470  0.00 -0.02
.177 C

ATOM   1706  C   UNL 1  43.915  -4.197   5.342 -0.01 -0.05
.178 C

ATOM   1707  C   UNL 1  47.803  -0.833   8.026 -0.01 -0.05
.178 C

ATOM   1708  C   UNL 1  46.897   4.435  10.275 -0.00 -0.05
.178 C

ATOM   1709  C   UNL 1  50.785   7.800  12.959  0.00 -0.05
.178 C
ATOM   1710  C   UNL 1  49.879  13.068  15.208  0.00 -0.04
.178 C




http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

Your coordinate file is also not suitable because it does not use unique 
atom names.


-Justin

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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Re: [gmx-users] Positive potential energy

[Justin Lemkul]

On 2/25/18 10:15 AM, Mahsa wrote:

Dear Justin,

Thank you for your reply!

In general, is it a good approach to first use steep algorithm for EM and
then to further minimize do EM with cg algorithm, on the output structure?


I usually don't find multiple steps of EM needed in most cases, but 
occasionally. The purpose of EM is to find a plausible starting point 
for the simulation - you can never know if you're in the global minimum 
so it's a bit of working in the dark, anyway. But the gradient (max 
force) reports on that.



Could you please comment on my question about the mdp files and pbc as
well? Actually, you mentioned here:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
/2017-February/111219.html

that for one chain of polymer in vacuum, pbc should not be considered. So,
for my simulation, in the first step I have one chain in vaccum and
eventually I want to pack the whole box with polymer chains and ions,
should I use pbc or not and which of the mdp files in my first post is
correct?


If you're working in the condensed phase, you need finite cutoffs, PME, 
and PBC.


-Justin


Regards,
Mahsa

On Sun, Feb 25, 2018 at 3:39 PM, Justin Lemkul  wrote:



On 2/25/18 9:26 AM, Mahsa wrote:


Dear Mark,

Thank you for your reply. However, this is not clear for me yet since I
read this in the tutorial from Justin:

"There are two very important factors to evaluate and determine if EM was
successful. The first is the potential energy (printed at the end of the
EM
process, even without -v). Epot should be negative. The second important
feature is the maximum force, Fmax, the target for which was set in
minim.mdp - "emtol = 1000.0" - indicating a target Fmax of no greater than
1000 kJ mol-1 nm-1."

So I don't know whether it is correct to continue a simulation which gives
positive potential energy after the energy minimisation or not?

And also as I mentioned in my first post (the two different mdp files), I
don't know if I should consider pbc or not, in my simulation.

Unfortunately, I didn't understand your answer to my previous questions.
Do
you mean that the steep integrator is not good to do energy minimization
for this type of simulation?

Would you please help me to fix these problems?


There is no problem. You're just comparing apples and oranges.

The tutorial system is a simple protein solvated by lots of water. The
potential energy function is the sum of bonded and nonbonded terms. In an
aqueous protein system, the nonbonded terms (particularly water-water
electrostatics) dominate the potential energy via favorable hydrogen bond
interactions. The internal (bonded) parameters for all the other species
are small in magnitude, by comparison, so the nonbonded terms dominate and
you get a negative potential energy.

In your case, you have comparatively weak nonbonded terms and larger
bonded terms, such that the potential energy function is dominated by
internal energy, which is by definition, positive.

This is not an indication that anything is wrong with the algorithms used.

-Justin


Regards,

Mahsa

On Sat, Feb 24, 2018 at 8:54 AM, Mark Abraham 
wrote:

Hi,

Even if there are minima on the surface that have negative energy (which
will depend how the model was developed, which you should look into)
there's no reason to expect an arbitrary starting configuration will find
one after a steepest descent search. A tangled pile of strings will stay
tangled.

Mark

On Fri, Feb 23, 2018, 23:28 Mahsa E  wrote:

Hello,

I want to simulate a box of polymer (32 chains) with salt. I started
with
one chain of the polymer in the box. However, after the energy
minimisation, the energy is still positive. I found the discussion in
the
link below very similar to the problem I have:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
/2017-February/111219.html

and tried the tips from Justin in the link but I still get positive


energy.


This is my first MDP file:

define   =
integrator   = steep
nsteps   = -1
nstcgsteep   = 10
constraints  = none
lincs_order  = 8
emtol= 20
emstep   = 0.01
comm-mode= Linear
nstcomm  = 1
nstcalcenergy= 1
; Output frequency for energies to log file and energy file
nstlog   = 1
nstenergy= 1
ns_type  = grid
cutoff-scheme= verlet
coulombtype  = PME
nstlist  = 10
rlist= 1.0
rcoulomb = 1.0
rvdw = 1.0
Tcoupl   = no
Pcoupl   = no
gen_vel  = no
nstxout  = 1
pbc  = xyz

and this is the second one which I tried to follow the tips from the
link
mentioned  above:

define   =
integrator   = 

[gmx-users] UNL residue error

[Radhika Arora]

Hello,


I face an error in PDB file of cellulose to run GROMACS. I want to know
what should I write in place of UNL residue.


ATOM   1700  C   UNL 1  29.680 -48.720 -19.563  0.00 -0.02
.177 C

ATOM   1701  C   UNL 1  13.970 -44.542 -17.378  0.00 -0.02
.177 C

ATOM   1702  C   UNL 1   6.116 -42.453 -16.285  0.00 -0.02
.177 C

ATOM   1703  C   UNL 1  -1.739 -40.364 -15.193  0.00 -0.02
.177 C

ATOM   1704  C   UNL 1  -9.594 -38.274 -14.101  0.00 -0.02
.177 C

ATOM   1705  C   UNL 1  21.826 -46.631 -18.470  0.00 -0.02
.177 C

ATOM   1706  C   UNL 1  43.915  -4.197   5.342 -0.01 -0.05
.178 C

ATOM   1707  C   UNL 1  47.803  -0.833   8.026 -0.01 -0.05
.178 C

ATOM   1708  C   UNL 1  46.897   4.435  10.275 -0.00 -0.05
.178 C

ATOM   1709  C   UNL 1  50.785   7.800  12.959  0.00 -0.05
.178 C
ATOM   1710  C   UNL 1  49.879  13.068  15.208  0.00 -0.04
.178 C



‌
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Re: [gmx-users] Positive potential energy

[Mahsa]

Dear Justin,

Thank you for your reply!

In general, is it a good approach to first use steep algorithm for EM and
then to further minimize do EM with cg algorithm, on the output structure?

Could you please comment on my question about the mdp files and pbc as
well? Actually, you mentioned here:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
/2017-February/111219.html

that for one chain of polymer in vacuum, pbc should not be considered. So,
for my simulation, in the first step I have one chain in vaccum and
eventually I want to pack the whole box with polymer chains and ions,
should I use pbc or not and which of the mdp files in my first post is
correct?

Regards,
Mahsa

On Sun, Feb 25, 2018 at 3:39 PM, Justin Lemkul  wrote:

>
>
> On 2/25/18 9:26 AM, Mahsa wrote:
>
>> Dear Mark,
>>
>> Thank you for your reply. However, this is not clear for me yet since I
>> read this in the tutorial from Justin:
>>
>> "There are two very important factors to evaluate and determine if EM was
>> successful. The first is the potential energy (printed at the end of the
>> EM
>> process, even without -v). Epot should be negative. The second important
>> feature is the maximum force, Fmax, the target for which was set in
>> minim.mdp - "emtol = 1000.0" - indicating a target Fmax of no greater than
>> 1000 kJ mol-1 nm-1."
>>
>> So I don't know whether it is correct to continue a simulation which gives
>> positive potential energy after the energy minimisation or not?
>>
>> And also as I mentioned in my first post (the two different mdp files), I
>> don't know if I should consider pbc or not, in my simulation.
>>
>> Unfortunately, I didn't understand your answer to my previous questions.
>> Do
>> you mean that the steep integrator is not good to do energy minimization
>> for this type of simulation?
>>
>> Would you please help me to fix these problems?
>>
>
> There is no problem. You're just comparing apples and oranges.
>
> The tutorial system is a simple protein solvated by lots of water. The
> potential energy function is the sum of bonded and nonbonded terms. In an
> aqueous protein system, the nonbonded terms (particularly water-water
> electrostatics) dominate the potential energy via favorable hydrogen bond
> interactions. The internal (bonded) parameters for all the other species
> are small in magnitude, by comparison, so the nonbonded terms dominate and
> you get a negative potential energy.
>
> In your case, you have comparatively weak nonbonded terms and larger
> bonded terms, such that the potential energy function is dominated by
> internal energy, which is by definition, positive.
>
> This is not an indication that anything is wrong with the algorithms used.
>
> -Justin
>
>
> Regards,
>> Mahsa
>>
>> On Sat, Feb 24, 2018 at 8:54 AM, Mark Abraham 
>> wrote:
>>
>> Hi,
>>>
>>> Even if there are minima on the surface that have negative energy (which
>>> will depend how the model was developed, which you should look into)
>>> there's no reason to expect an arbitrary starting configuration will find
>>> one after a steepest descent search. A tangled pile of strings will stay
>>> tangled.
>>>
>>> Mark
>>>
>>> On Fri, Feb 23, 2018, 23:28 Mahsa E  wrote:
>>>
>>> Hello,

 I want to simulate a box of polymer (32 chains) with salt. I started
 with
 one chain of the polymer in the box. However, after the energy
 minimisation, the energy is still positive. I found the discussion in
 the
 link below very similar to the problem I have:

 https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
 /2017-February/111219.html

 and tried the tips from Justin in the link but I still get positive

>>> energy.
>>>
 This is my first MDP file:

 define   =
 integrator   = steep
 nsteps   = -1
 nstcgsteep   = 10
 constraints  = none
 lincs_order  = 8
 emtol= 20
 emstep   = 0.01
 comm-mode= Linear
 nstcomm  = 1
 nstcalcenergy= 1
 ; Output frequency for energies to log file and energy file
 nstlog   = 1
 nstenergy= 1
 ns_type  = grid
 cutoff-scheme= verlet
 coulombtype  = PME
 nstlist  = 10
 rlist= 1.0
 rcoulomb = 1.0
 rvdw = 1.0
 Tcoupl   = no
 Pcoupl   = no
 gen_vel  = no
 nstxout  = 1
 pbc  = xyz

 and this is the second one which I tried to follow the tips from the
 link
 mentioned  above:

 define   =
 integrator   = steep
 nsteps   = 

Re: [gmx-users] Removal of Waters in Hydrophobic Core

[Justin Lemkul]

On 2/22/18 1:33 PM, Smith, Iris wrote:

Hi Justin,

In a previous post (Nov 2016) between Chris Neal and Saint Rahman 
regarding removal of waters in hydrophobic core you mentioned the 
bilayer_seperator.pl script would be useful in conjunction with gmx traj.


I am trying to determine the upperz and lowers coordinate values of my 
bilayer to remove a lot of water in hydrophobic core. How does one 
determine the z(reference) > z(middle) -> top in the invocation:


perl bilayer_seperator.pl –in bilayer.gro *–ref 011* *–middle C50* -v



Just define the last carbon in one chain for -middle (as that will 
approximately define the center of the bilayer along the normal) and 
some upper boundary for -ref (in the example, O11 is in the glycerol 
region of DPPC).


-Justin

--
==

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

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

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

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Re: [gmx-users] Protein protein complex molecular dynamic simulation

[Justin Lemkul]

On 2/24/18 7:06 AM, SHYANTANI MAITI wrote:

Can molecular dynamic simulation be performed over protein-protein
complexes using gromacs?


Yes. This scenario is functionally no different than a single protein. 
pdb2gmx can write a topology for any multi-chain system, provided the 
input coordinate file explicitly includes chain breaks (TER) or 
different chain identifiers.


-Justin

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

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

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Re: [gmx-users] cut-off length error

[Justin Lemkul]

On 2/23/18 1:03 PM, Mahmood Naderan wrote:

Hi,

I downloaded a water benchmark from gromacs web site
and tried to run a sample. However it fails with a cut-off
length error while there is no such parameter in topol.top



mahmood@orca:~/gromacs-2018/bench/water-cut1.0_GMX50_bare/.65$ ls
conf.gro  mdout.mdp  pme.mdp  rf.mdp  topol.top
mahmood@orca:~/gromacs-2018/bench/water-cut1.0_GMX50_bare/.65$ gmx grompp 
-f pme.mdp -c conf.gro -p topol.top -o wa.tpr
    :-) GROMACS - gmx grompp, 2018 (-:

     GROMACS is written by:
  Emile Apol  Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar
  Aldert van Buuren   Rudi van Drunen Anton Feenstra    Gerrit Groenhof
  Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios Karkoulis
     Peter Kasson    Jiri Kraus  Carsten Kutzner  Per Larsson
   Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg   Pieter Meulenhoff
    Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
    Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
    Peter Tieleman    Teemu Virolainen  Christian Wennberg    Maarten Wolf
    and the project leaders:
     Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2017, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx grompp, version 2018
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/mahmood/gromacs-2018/bench/water-cut1.0_GMX50_bare/.65
Command line:
   gmx grompp -f pme.mdp -c conf.gro -p topol.top -o wa.tpr

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
Setting the LD random seed to 2025508713
Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...

ERROR 1 [file topol.top, line 37]:
   ERROR: The cut-off length is longer than half the shortest box vector or
   longer than the smallest box diagonal element. Increase the box size or
   decrease rlist.


Removing all charge groups because cutoff-scheme=Verlet

---
Program: gmx grompp, version 2018
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1991)

Fatal error:
There was 1 error in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
mahmood@orca:~/gromacs-2018/bench/water-cut1.0_GMX50_bare/.65$ cat topol.top
#include "oplsaa.ff/forcefield.itp"
[ moleculetype ]
; molname    nrexcl
SOL        2

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
  1  opls_116   1    SOL OW  1  -0.8476
  2  opls_117   1    SOL    HW1  2   0.4238
  3  opls_117   1    SOL    HW2  3   0.4238

#ifndef FLEXIBLE
[ settles ]
; OW    funct    doh    dhh
1    1    0.1    0.16330

[ exclusions ]
1    2    3
2    1    3
3    1    2
#else
[ bonds ]
; i    j    funct    length    force.c.
1    2    1    0.1    345000    0.1 345000
1    3    1    0.1    345000    0.1 345000
 
[ angles ]

; i    j    k    funct    angle    force.c.
2    1    3    1    109.47    383    109.47    383
#endif

[ system ]
Water

[ molecules ]
SOL    216








I am not a researcher in this field. I just want to run
some test as a system admin.

The topol.top has 37 lines and the last line (after SOL)
is just an enter! What should I do?


The interaction cutoff length is a component of the physical model and 
therefore determines a minimum system size. You need to build a larger 
simulation system to satisfy this requirement.


-Justin

--
==

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

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

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

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Re: [gmx-users] Positive potential energy

[Mahsa]

Dear Mark,

Thank you for your reply. However, this is not clear for me yet since I
read this in the tutorial from Justin:

"There are two very important factors to evaluate and determine if EM was
successful. The first is the potential energy (printed at the end of the EM
process, even without -v). Epot should be negative. The second important
feature is the maximum force, Fmax, the target for which was set in
minim.mdp - "emtol = 1000.0" - indicating a target Fmax of no greater than
1000 kJ mol-1 nm-1."

So I don't know whether it is correct to continue a simulation which gives
positive potential energy after the energy minimisation or not?

And also as I mentioned in my first post (the two different mdp files), I
don't know if I should consider pbc or not, in my simulation.

Unfortunately, I didn't understand your answer to my previous questions. Do
you mean that the steep integrator is not good to do energy minimization
for this type of simulation?

Would you please help me to fix these problems?

Regards,
Mahsa

On Sat, Feb 24, 2018 at 8:54 AM, Mark Abraham 
wrote:

> Hi,
>
> Even if there are minima on the surface that have negative energy (which
> will depend how the model was developed, which you should look into)
> there's no reason to expect an arbitrary starting configuration will find
> one after a steepest descent search. A tangled pile of strings will stay
> tangled.
>
> Mark
>
> On Fri, Feb 23, 2018, 23:28 Mahsa E  wrote:
>
> > Hello,
> >
> > I want to simulate a box of polymer (32 chains) with salt. I started with
> > one chain of the polymer in the box. However, after the energy
> > minimisation, the energy is still positive. I found the discussion in the
> > link below very similar to the problem I have:
> >
> > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
> > /2017-February/111219.html
> >
> > and tried the tips from Justin in the link but I still get positive
> energy.
> >
> > This is my first MDP file:
> >
> > define   =
> > integrator   = steep
> > nsteps   = -1
> > nstcgsteep   = 10
> > constraints  = none
> > lincs_order  = 8
> > emtol= 20
> > emstep   = 0.01
> > comm-mode= Linear
> > nstcomm  = 1
> > nstcalcenergy= 1
> > ; Output frequency for energies to log file and energy file
> > nstlog   = 1
> > nstenergy= 1
> > ns_type  = grid
> > cutoff-scheme= verlet
> > coulombtype  = PME
> > nstlist  = 10
> > rlist= 1.0
> > rcoulomb = 1.0
> > rvdw = 1.0
> > Tcoupl   = no
> > Pcoupl   = no
> > gen_vel  = no
> > nstxout  = 1
> > pbc  = xyz
> >
> > and this is the second one which I tried to follow the tips from the link
> > mentioned  above:
> >
> > define   =
> > integrator   = steep
> > nsteps   = -1
> > nstcgsteep   = 10
> > constraints  = none
> > lincs_order  = 8
> > emtol= 20
> > emstep   = 0.01
> > comm-mode= Linear
> > nstcomm  = 1
> > nstcalcenergy= 1
> > ; Output frequency for energies to log file and energy file
> > nstlog   = 1
> > nstenergy= 1
> > ns_type  = grid
> > cutoff-scheme= group
> > coulombtype  = cut-off
> > nstlist  = 0
> > rlist= 0
> > rcoulomb = 0
> > rvdw = 0
> > Tcoupl   = no
> > Pcoupl   = no
> > gen_vel  = no
> > nstxout  = 1
> > pbc  = no
> >
> > My questions are:
> >
> > - I'm not sure if either of these MDP files are correct for the system
> I'm
> > trying to simulate?
> >
> > - Why energy is positive in this simulation? Is there something
> > fundamentally wrong in the simulation which I'm not aware of?
> >
> > Regards,
> > Mahsa
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> >
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> 

Re: [gmx-users] Worse GROMACS performance with better specs?

[Harry Mark Greenblatt]

BS”D

 Someone has pointed out to me that the “Silver” line is not meant for HPC.  
For HPC, you need to go with the “Gold” series, even if you don’t want 4 
sockets.

The difference presumably lies is the fact that the Gold has 2 FMA units, and 
the Silver series has 1.

Harry


On 20 Feb 2018, at 6:42 PM, Szilárd Páll 
> wrote:

On Fri, Jan 12, 2018 at 2:35 AM, Jason Loo Siau Ee
> wrote:
Dear Carsten,

Look's like we're seeing the same thing here, but only when using gcc 4.5.3:

Original performance (gcc 5.3.1, AVX512, no hwloc support): 49 ns/day

With hwloc support:
gcc 4.5.3, AVX2_256 = 67 ns/day
gcc 4.5.3, AVX512 = can't compile
gcc 5.3.1, AVX2_256 = 36 ns/day
gcc 5.3.1, AVX512 = 60 ns/day

At the very least it's now comparable to my previous workstation. Will have to 
try with the gromacs 2018 next.

Have you tried? Any feedback?

I'd also recommend using gcc >=6.


Cheers for the info.

Jason

--

Message: 2
Date: Wed, 10 Jan 2018 08:39:22 +
From: "Kutzner, Carsten" >
To: "> GROMACS users" 
>
Subject: Re: [gmx-users] Worse GROMACS performance with better specs?
Message-ID: 
<816dea54-1e01-42ac-a78a-3680fdef0...@gwdg.de>
Content-Type: text/plain; charset="us-ascii"

Dear Jason,

1.)
we have observed a similar behavior comparing Intel Silver 4114 against 
E5-2630v4
processors in a server with one GTX 1080Ti. Both CPUs have 10 cores and run at
2.2 GHz. Using our standard benchmark systems (see 
https://arxiv.org/abs/1507.00898)
we were able to get 74.4 ns/day on the E5 but only 65.7 ns/day on the Silver 
machine
for the MEM (80k atoms), and 4.4 vs. 4.2 ns/day for the RIB (2M atoms) system.

Although the 4114 supports AVX512 SIMD instructions, compiling with AVX2_256
yielded higher performance (this is already included in the above numbers, so
all benchmarks were run with the exact same mdrun executable).

2.)
We recently bought a bunch of workstations with 2x Gold 6146 CPUs and 2x 
GTX1080Ti GPUs
and were very surprised to find that initial GROMACS 2016 performances differ a
lot between the identical machines (some were up to 40% slower).

This was the reported difference in the md.log files:
- mdrun logs show Hardware Topology: Basic versus Hardware Topology: Only 
logical processor count


For some reason, the logical processor count was reported in a mixed-up way
for the slower machines so that mdrun is unable to correctly determine the
hardware topology. We solved this CPU problem by installing GROMACS with hwloc
support. Then performances were equal over all 6146 nodes.

Best,
 Carsten


On 10. Jan 2018, at 07:45, Jason Loo Siau Ee 
> wrote:

Dear gmx users,



I recently purchased a second GPU workstation and tried compiling GROMACS on 
it, but despite the better (and more expensive) specs the performance is 
significantly worse on my test system. To test things I standardized the 
version (2016.4). Some details below:



Workstation 1:

2 x Intel Xeon E5-2680v4 (14 cores), 2 x GTX 1080

gmx mdrun -ntmpi 8 -ntomp 7 -gpu_id 

Performance: 61ns/day



Workstation 2:

2 x Intel Xeon Gold 6126 (12 cores), 2 x GTX 1080Ti

gmx mdrun -ntmpi 8 -ntomp 6 -gpu_id 

Performance: 49ns/day



I'm guessing it's an issue during compilation but I can't figure it out. I 
wouldn't claim to have any knowledge about how GROMACS interacts with the 
hardware, so some observations as below (not sure idea which is actually 
relevant):



- Compilation command for both: cmake .. -DGMX_BUILD_OWN_FFTW=ON  
-DREGRESSIONTEST_DOWNLOAD=ON  -DGMX_GPU=ON  -DCMAKE_INSTALL_PREFIX=/opt/gromacs



- When compiling on Workstation 2 I originally got a CMake error "Cannot find 
AVX512F compiler flag". Updated my gcc version to 5.3.1 to solve this.



- Some regression tests fail for Workstation 2 during compilation: 4 
-FTUnitTest (SEGFAULT), 16 - CorrelationTest



- mdrun logs show Hardware Topology: Basic versus Hardware Topology: Only 
logical processor count



- Running CPU-only (export CUDA_VISIBLE_DEVICES="") I get 21ns/day versus 23 
ns/day , so the CPUs in Workstation 2 are definitely faster.



- Upgraded both to 2018.rc1 (used cmake3) I get a regression test fail for 
Workstation 1 (9 - GPUUtilUnitTest) and Workstation 2 (8 - FFTUnitTests, 9 - 
GPUUtilsUnitTest, 26 - CorrelationTest). Performance is 66.5ns/day versus 
51.95ns/day. The GPU load actually looks similar to previous versions (~70% for 
Workstation 1 and 50-60% for Workstation 2). I actually got the best 
performance with Workstation 1 running 2016.1 (69ns/day).



Any help on how I can optimize performance on Workstation 2 would 

Re: [gmx-users] energy minimization

[farial tavakoli]

Dear Justin
In according to obtaining positive binding free energy using g_mmpbsa for my 
complex which has 2 phosphotyrosine residues and is simulated by charmm36 force 
field , I sent an email to g_mmpbsa mailing list and informed them to help me 
for solving my problem, but they replied me : " we have not tested the g_mmpbsa 
with charmm36 so we can't say about the validity. Other members of g_mmpbsa 
tool, also previously reported about the positive binding energy when using 
charmm36 force field." I sent another email to them :would you please advice me 
how could I calculate the  free binding energy of my complex (receptor and 
ligand that has 2 phosphotyrosine residues ) which has been simulated by 
charmm36 all atom force field? but I have not any response yet.
 so I decided to use a modified amber99s force field to use in gromacs to 
simulate my complex. and then use g_mmpbsa to calculate the binding energy. I 
searched the net and found this one to modify the amber99s ff : 
http://www.pharmacy.manchester.ac.uk/bryce/amberbut it is not for gromacs. 
Would you please advice me how can I get a modified amber force field to 
simulate my complex using gromacs?or help me how  can I calcualte the binding 
energy of my complex which is simulated by charmm36 in gromacs?
with best regardsFarial
 

On Tuesday, February 20, 2018, 10:24:49 PM GMT+3:30, Justin Lemkul 
 wrote:  
 
 

On 2/20/18 12:52 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  Dear Justin
> Thank you for the reply
> You meant , to tweak the emtol doesn't have noticable affects on the 
> conformational enssemble generated by MD?
>  

Precisely what I said, yes.

-Justin

>
> Sent from Yahoo Mail for iPhone
>
>
> On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul  wrote:
>
>
>
> On 2/20/18 4:52 AM, farial tavakoli wrote:
>> Dear GMX users
>> I used CHARMM36 all atom force field to generate .top and .gro files for my 
>> complex composed of a receptor protein and a ligand with 2 phosphotyrosine 
>> residues, then ran a md simulation on it and then used g_mmpbsa to calculate 
>> the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, 
>> respectively. While, I calculated binding energy before for many other 
>> complexes without any phosphate groups using OPLS all atom force field and 
>> pdie = 2 and obtained minus energy. But this time , I dont know why I got 
>> positive binding energy? Is it because of charmm36 all atom force field , 
>> the phosphate groups or it is needed to be energy minimized under more 
>> restriction situations?
>> I am checking different factors to understand its reason, so I wanted to 
>> know , would it be ok if I energy minimize the complex with more restriction 
>> situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 
>> ? I think the positive binding energy might be because of the complex didnt 
>> minimized well. however I checked the em.log file and saw it was minimized 
>> well:
>>
>> Steepest Descents converged to Fmax < 1000 in 241 steps
>> Potential Energy  = -6.5047744e+05
>> Maximum force =  9.8285083e+02 on atom 3335
>> Norm of force =  3.6905827e+01
>> Is there anyone can advice me in energy minimization with emtol 800?
> The purpose of energy minimization is to establish a reasonable starting
> point for your simulation. Tweaks to emtol will have little to no
> noticeable bearing on the conformational ensemble generated by MD.
>
> -Justin
>

-- 
==

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

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

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

==

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[gmx-users] Inconsistent Shifts

[Iman Ahmadabadi]

Dear Dallas,

I have tried the 2016.5 version of gromacs that it has the same warning
about the inconsistent shifts. I don't know why it should arises as a
warning and what is the problem. Is there another way to fix this warning?

Sincerely
Iman

On Wed, Feb 21, 2018 at 11:26 AM, Iman Ahmadabadi <
imanahmadabad...@gmail.com> wrote:

> Dear Dallas,
>
> Yes, the system has periodic molecules (periodic-molecules = yes) and the
> version of gromacs is 5.1.2. So, I should use for calculating the
> properties of the system by gromacs 2016 and newer ones?
>
> Respectfully,
> Iman
>
> On Tue, Feb 20, 2018 at 2:57 PM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com> wrote:
>
>> Dear Gromacs users,
>>
>> In using some commands in gromacs, the sentence "There were 240
>> inconsistent shifts. Check your topology" come up on the screen and I don't
>> know what is wrong in my topology file, however it calculates correctly the
>> features of the system but I would like to know the reason of this warning.
>>
>> Respectfully,
>> Iman
>>
>
>
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[gmx-users] walls with slab of water

[Adriano Santana Sanchez]

Hi,

I am trying to run a SLAB of water with a solute and I want to put a wall
on the z axis edge.

My problem is how to define *wall_atomtype *in the topology file or in the
.itp

I am using oplsaa.ff force field with SPC/E water.

This is a section of the .mpd:

Neighborsearching and short-range nonbonded interactions
cutoff-scheme= verlet
nstlist  = 1
ns_type  = grid
pbc  = xy
nwall= 2
*wall_atomtype= W1 W2*
wall_type= 10-4
wall_r_linpot= -1
wall_density = 5 5
wall_ewald_zfac  = 3
ewald_geometry   = 3dc
rlist= 1.2
---
ERROR 1 [file topol.top, line 45]:
  Specified wall atom type W1 is not defined
ERROR 2 [file topol.top, line 45]:
  Specified wall atom type W2 is not defined

 Thanks,
Adriano

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