Re: [gmx-users] salt concentration

[Alex]

I think that's high school stuff. :)

N -- number of ions.

V = a^3 -- volume (a is cube side length)

n -- concentration (1M = 6e+26 m-3, you have 0.002 M)

N = a^3*n > 1

a > (1/n)^(1/3).


On 11/14/2017 12:44 AM, Netaly Khazanov wrote:

It makes sense.
I am not sure that I follow how you calculated the critical box size
depending on the the concentration.

On Tue, Nov 14, 2017 at 9:12 AM, Alex  wrote:


It makes no difference whether you use -np/-nn or -conc. Your box is
simply too small to result in a nonzero ion count with something like 0.002
M. The check is rather simple: a cubic box has to be larger than
(1/n)^(1/3). For 0.002 M, that critical box size is 9.4 nm.

You can of course force any number of ions in there, but back-calculate
the corresponding concentration, given the box volume, and you'll see that
it's not what you want. This is exactly what GMX does when you call -conc.

Alex



On 11/13/2017 11:54 PM, Netaly Khazanov wrote:


Thanks for your prompt replay.
I thougnt it would be more elegant way to do it using the commands.
If not that is what I am going to do.
Best,
Netaly

On Mon, Nov 13, 2017 at 2:37 PM, Hermann, Johannes <
j.herm...@lrz.tu-muenchen.de> wrote:

Hi Netaly,

one way would be to calculate the number of Na, Cl, and Mg ions by hand,
i.e. with the box size and the respective concentrations, and add the
correct amount of ions in two steps, with the flags -np or -nn. E.g. in
the
first step you add Na and Cl and in the second you add Mg.

All the best

Johannes


On 13.11.2017 13:31, Netaly Khazanov wrote:

Dear Gromacs User,

Is it possible to simulate system with two salt concentrations , e.g.
NaCl
0.1 mol/L and MgCl2 0.002 mol/liter?

The commands that i am using you can see below:

grompp_d -f ions.mdp -c ligand_MG_box_water.gro -p topol.top -o ions.tpr
genion_d -s ions.tpr -o ligand_box_water_NaCL.gro -p topol.top -pname
NA -
nname CL -neutral -conc 0.1
grompp_d -f ions.mdp -c ligand_box_water_NACL.gro -p topol.top -o
ions.tpr
genion_d -s ions.tpr -o ligand_box_water_NaCL_MgCl2.gro -p topol.top
-pname
MG -pq 2 -nname CL -neutral -conc 0.002

The message that I got after the execution of the last command is :"No
ions
to add and no potential to calculate."

Is it right way to do it?
Thank you in advance.
Netaly



--

__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverf

ahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

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Re: [gmx-users] salt concentration

[Netaly Khazanov]

It makes sense.
I am not sure that I follow how you calculated the critical box size
depending on the the concentration.

On Tue, Nov 14, 2017 at 9:12 AM, Alex  wrote:

> It makes no difference whether you use -np/-nn or -conc. Your box is
> simply too small to result in a nonzero ion count with something like 0.002
> M. The check is rather simple: a cubic box has to be larger than
> (1/n)^(1/3). For 0.002 M, that critical box size is 9.4 nm.
>
> You can of course force any number of ions in there, but back-calculate
> the corresponding concentration, given the box volume, and you'll see that
> it's not what you want. This is exactly what GMX does when you call -conc.
>
> Alex
>
>
>
> On 11/13/2017 11:54 PM, Netaly Khazanov wrote:
>
>> Thanks for your prompt replay.
>> I thougnt it would be more elegant way to do it using the commands.
>> If not that is what I am going to do.
>> Best,
>> Netaly
>>
>> On Mon, Nov 13, 2017 at 2:37 PM, Hermann, Johannes <
>> j.herm...@lrz.tu-muenchen.de> wrote:
>>
>> Hi Netaly,
>>>
>>> one way would be to calculate the number of Na, Cl, and Mg ions by hand,
>>> i.e. with the box size and the respective concentrations, and add the
>>> correct amount of ions in two steps, with the flags -np or -nn. E.g. in
>>> the
>>> first step you add Na and Cl and in the second you add Mg.
>>>
>>> All the best
>>>
>>> Johannes
>>>
>>>
>>> On 13.11.2017 13:31, Netaly Khazanov wrote:
>>>
>>> Dear Gromacs User,

 Is it possible to simulate system with two salt concentrations , e.g.
 NaCl
 0.1 mol/L and MgCl2 0.002 mol/liter?

 The commands that i am using you can see below:

 grompp_d -f ions.mdp -c ligand_MG_box_water.gro -p topol.top -o ions.tpr
 genion_d -s ions.tpr -o ligand_box_water_NaCL.gro -p topol.top -pname
 NA -
 nname CL -neutral -conc 0.1
 grompp_d -f ions.mdp -c ligand_box_water_NACL.gro -p topol.top -o
 ions.tpr
 genion_d -s ions.tpr -o ligand_box_water_NaCL_MgCl2.gro -p topol.top
 -pname
 MG -pq 2 -nname CL -neutral -conc 0.002

 The message that I got after the execution of the last command is :"No
 ions
 to add and no potential to calculate."

 Is it right way to do it?
 Thank you in advance.
 Netaly



 --
>>> __
>>> *Technische Universität München*
>>> *Johannes Hermann, M.Sc.*
>>> Lehrstuhl für Bioverf
>>> 
>>> ahrenstechnik
>>> Boltzmannstr. 15
>>> D-85748 Garching
>>> Tel: +49 8928915730
>>> Fax: +49 8928915714
>>>
>>> Email: j.herm...@lrz.tum.de
>>> http://www.biovt.mw.tum.de/
>>>
>>> --
>>> 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.
>>>
>>
>>
>>
>>
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Re: [gmx-users] salt concentration

[Alex]

It makes no difference whether you use -np/-nn or -conc. Your box is 
simply too small to result in a nonzero ion count with something like 
0.002 M. The check is rather simple: a cubic box has to be larger than 
(1/n)^(1/3). For 0.002 M, that critical box size is 9.4 nm.


You can of course force any number of ions in there, but back-calculate 
the corresponding concentration, given the box volume, and you'll see 
that it's not what you want. This is exactly what GMX does when you call 
-conc.


Alex


On 11/13/2017 11:54 PM, Netaly Khazanov wrote:

Thanks for your prompt replay.
I thougnt it would be more elegant way to do it using the commands.
If not that is what I am going to do.
Best,
Netaly

On Mon, Nov 13, 2017 at 2:37 PM, Hermann, Johannes <
j.herm...@lrz.tu-muenchen.de> wrote:


Hi Netaly,

one way would be to calculate the number of Na, Cl, and Mg ions by hand,
i.e. with the box size and the respective concentrations, and add the
correct amount of ions in two steps, with the flags -np or -nn. E.g. in the
first step you add Na and Cl and in the second you add Mg.

All the best

Johannes


On 13.11.2017 13:31, Netaly Khazanov wrote:


Dear Gromacs User,

Is it possible to simulate system with two salt concentrations , e.g. NaCl
0.1 mol/L and MgCl2 0.002 mol/liter?

The commands that i am using you can see below:

grompp_d -f ions.mdp -c ligand_MG_box_water.gro -p topol.top -o ions.tpr
genion_d -s ions.tpr -o ligand_box_water_NaCL.gro -p topol.top -pname NA -
nname CL -neutral -conc 0.1
grompp_d -f ions.mdp -c ligand_box_water_NACL.gro -p topol.top -o ions.tpr
genion_d -s ions.tpr -o ligand_box_water_NaCL_MgCl2.gro -p topol.top
-pname
MG -pq 2 -nname CL -neutral -conc 0.002

The message that I got after the execution of the last command is :"No
ions
to add and no potential to calculate."

Is it right way to do it?
Thank you in advance.
Netaly




--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverf

ahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/

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Re: [gmx-users] salt concentration

[Netaly Khazanov]

Thanks for your prompt replay.
I thougnt it would be more elegant way to do it using the commands.
If not that is what I am going to do.
Best,
Netaly

On Mon, Nov 13, 2017 at 2:37 PM, Hermann, Johannes <
j.herm...@lrz.tu-muenchen.de> wrote:

> Hi Netaly,
>
> one way would be to calculate the number of Na, Cl, and Mg ions by hand,
> i.e. with the box size and the respective concentrations, and add the
> correct amount of ions in two steps, with the flags -np or -nn. E.g. in the
> first step you add Na and Cl and in the second you add Mg.
>
> All the best
>
> Johannes
>
>
> On 13.11.2017 13:31, Netaly Khazanov wrote:
>
>> Dear Gromacs User,
>>
>> Is it possible to simulate system with two salt concentrations , e.g. NaCl
>> 0.1 mol/L and MgCl2 0.002 mol/liter?
>>
>> The commands that i am using you can see below:
>>
>> grompp_d -f ions.mdp -c ligand_MG_box_water.gro -p topol.top -o ions.tpr
>> genion_d -s ions.tpr -o ligand_box_water_NaCL.gro -p topol.top -pname NA -
>> nname CL -neutral -conc 0.1
>> grompp_d -f ions.mdp -c ligand_box_water_NACL.gro -p topol.top -o ions.tpr
>> genion_d -s ions.tpr -o ligand_box_water_NaCL_MgCl2.gro -p topol.top
>> -pname
>> MG -pq 2 -nname CL -neutral -conc 0.002
>>
>> The message that I got after the execution of the last command is :"No
>> ions
>> to add and no potential to calculate."
>>
>> Is it right way to do it?
>> Thank you in advance.
>> Netaly
>>
>>
>>
> --
> __
> *Technische Universität München*
> *Johannes Hermann, M.Sc.*
> Lehrstuhl für Bioverf
> 
> ahrenstechnik
> Boltzmannstr. 15
> D-85748 Garching
> Tel: +49 8928915730
> Fax: +49 8928915714
>
> Email: j.herm...@lrz.tum.de
> http://www.biovt.mw.tum.de/
>
> --
> 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] mobile ligand with intermolecular interactions

[Justin Lemkul]

On 11/13/17 3:00 AM, Ahmet Yildirim wrote:

Sorry. The pymol and GROMACS give the same results for every three target
dihedrals. The updated results are here:
https://www.dropbox.com/s/7qgn7qa4rf2yc14/dih.pdf?dl=0

The results show that the average dihedrals are almost the same in both the
state A and state B for both [dihedrals] or [dihedral_restraints]. I think
this is normal?


Yes, because the purpose of selectively turning on the additional bond 
or restraint potential is to enforce the original geometry. Your results 
look fine to me, probably you just need a slightly larger force constant.


-Justin


On 13 November 2017 at 09:49, Ahmet Yildirim  wrote:


Hi,

Let me take that in reverse order:

Note that choosing appropriate atoms to apply restraints is not a trivial
matter, and results can vary depending on the choices made.


I know.

I doubt there's a bug. I tested this feature a lot myself and have used

it. How different are the dihedrals in the B-state vs. the A-state, and how
much do they differ from the target values?


The dihedrals are almost the same in both the state A and state B (except
for the first one) when the [dihedrals] or [dihedral_restraints] is used.
Please see the results https://www.dropbox.com/s/rdw6
lg0c4xviufk/dih.pdf?dl=0

I think there is bug?

On the other hand, the pymol and GROMACS calculate differently the first
target dihedral angle between 1587, 1581, 1579 and 14 atoms, respectively
-155 and 66. I don't know why? That is strange? Note that I used -155
degrees obtained from pymol as a target value of the first dihedral in the
simulation. The other two target dihedrals are the same for both pymol and
GROMACS.

Thanks.

On 13 November 2017 at 01:55, Justin Lemkul  wrote:



On 11/10/17 11:59 PM, Ahmet Yildirim wrote:


Hi,

Just tested it. The [ dihedral_restraints ] didn't help. The RMSD of the
ligand is the same when the [ dihedral_restraints ] or [ dihedrals ] is
used at end of the complex topology file. This is a bug?


I doubt there's a bug. I tested this feature a lot myself and have used
it. How different are the dihedrals in the B-state vs. the A-state, and how
much do they differ from the target values? Note that choosing appropriate
atoms to apply restraints is not a trivial matter, and results can vary
depending on the choices made.

-Justin

  From my first mail:

I think [ dihedral_restraints ] will be the same as [ dihedrals ] because

the eq. 4.84 in the manual will be equal to 4.61 if dphiA and dphiB are
taken as 0 (zero), right?


Checked also the position of the ligand during the simulation on the VMD.
It is very mobile in the decoupled state as I said in the previous mail.

*First test:*
[ intermolecular_interactions ]
[ bonds ]
; ai ajtype   bA  kA bB  kB
   13912615  6  0.654   0.00.654   4184.0

[ angles ]
; ai ajak typethA  fcAthB  fcB
   1393   1391   2615   1   88.8 0.088.8 41.84
   1391   2615   2614   1   32.9 0.032.9 41.84

[ dihedrals ]
; ai ajakaltype thA  fcA   thB  fcB
   1410  1393  1391  26152   -159.70.0-159.741.84
   1393  1391  2615  26142122.60.0 122.641.84
   1391  2615  2614  26102 12.80.0  12.841.84

*Second test:*

[ intermolecular_interactions ]
[ bonds ]
; ai ajtype   bA  kA bB  kB
   13912615  6  0.654   0.00.654   4184.0

[ angles ]
; ai ajak typethA  fcAthB  fcB
   1393   1391   2615   1   88.8 0.088.8 41.84
   1391   2615   2614   1   32.9 0.032.9 41.84

[ dihedral_restraints ]
;   aiajakal  typephiA dphiA  fcAphiB  dphiB
fcB
   1410  1393  1391  2615 1-159.7   0.00.0-159.70.0
41.84
   1393  1391  2615  2614 1 122.6   0.00.0 122.60.0
41.84
   1393  1391  2615  2614 1  12.8   0.00.0 12.8 0.0
41.84

On 10 November 2017 at 22:36, Justin Lemkul  wrote:



On 11/10/17 2:21 PM, Ahmet Yildirim wrote:

Dear users,

I add the following [ intermolecular_interactions ] section into the
topology file of protein-ligand complex for free energy calculations.
Unfortunately this setting doesn't provide me what I want in the
decoupled
state. The ligand in the decoupled state is very mobile compared to the
coupled state. It means that the conformational sampling of the ligand
in
the decoupled state is quite different from the coupled state. That is
not
expected of course. Any suggestions as to why this might be?

Do you think that there is something wrong with the following settings,
e.g. [ dihedrals ] part?

Yes, because you're setting [dihedrals] as if they were restraints.

Dihedrals have a multiplicity, phase angle (not the angle you want it to
be, it's the shape and position of the 

Re: [gmx-users] GROMOS bond-stretching parameters

[Justin Lemkul]

On 11/13/17 5:24 AM, Faezeh Pousaneh wrote:

Hi,
Unfortunately I do not find in Gromos literature what is the third number
in front of
bond stretching parameters, e.g 1200 below:
:

; ICB(H)[N]CB[N] B0[N]
#define gb_50.1230  1.6600e+07
; C  - O1200

someone please tell me,


It's an integer code from the original GROMOS parameter files. Note that 
it is on a comment line and thus serves no function in GROMACS.


-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] Problem using gmx wham

[Justin Lemkul]

At least upgrade to the latest release in the series (5.1.4) or better 
yet, the actual latest version (2016.4) to see if this is a bug that's 
been fixed. I seem to recall this same behavior reported before and 
subsequently solved, but haven't dug it up.


-Justin

On 11/13/17 7:11 AM, Jefferies D.F. wrote:

Hey guys,

Sorry if it seems that I'm bumping this thread, but I was wondering if anyone 
had any other suggestions before I let this thread die.

Thanks.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Jefferies D.F. 
[dfj1...@soton.ac.uk]
Sent: Thursday, November 02, 2017 1:29 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem using gmx wham

Hi Justin,

Thanks for the response. The .dat files were created with the vi text editor, 
they contain lists of the .tpr and .xvg to be read, e.g.

umbrella0.tpr
umbrella1.tpr
umbrella2.tpr
..
umbrella52.tpr

I've tried to use dos2unix,  i.e.
~> dos2unix tpr-files.dat
and
~> dos2unix pullf-files.dat

but I still get the same error message i.e.

---
Program gmx wham, VERSION 5.1.2
Source code file: 
/Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 
1800

Fatal error:
Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

That being said, it seems you're correct in thinking something's weird with the 
input files. After I created new .dat files, I got this message:

---
Program gmx wham, VERSION 5.1.2
Source code file: 
/Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 
3610

Fatal error:
Found 53 file names in tpr-files.dat, but 54 in pullf-files.dat

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

gmx wham is registering 54 files, when only 53 were written.






From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul 
[jalem...@vt.edu]
Sent: Thursday, November 02, 2017 11:10 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem using gmx wham

On 11/1/17 4:26 PM, Jefferies D.F. wrote:

Hi,

I am attempting to use gmx wham to compute a potential of mean force. I have 
used the command line:

gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ

where tpr-files.dat and pullf-files.dat contain a list of the .tpr and 
pullf.xvg files from each umbrella sampling window, respectively.

It seems that gmx wham is having trouble reading the .tpr and .xvg files, as I 
get this error message:

---

Program gmx wham, VERSION 5.1.4

Source code file: 
/local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp,
 line: 1800


Fatal error:

Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.


The extra space after "tpr" in the printed error suggests something is
weird with the input .dat file. Did you create it with a proper plain
text editor? What about running dos2unix on it to make sure you've got
the right kind of line endings?

-Justin


For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

---


I have computed potential of mean force profiles before (using this Mac), but I 
haven't encountered this problem. Could someone help me with this problem?



--
==

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

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

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[gmx-users] Protein almost detaching from the micellar core

[soumadwip ghosh]

Hi all,

I am simulating a membrane protein embedded in a detegent micelle
(didodecyl maltoside DDM micelle). I am using total 167 number of DDM
monomers and 17 cholesterol hemisuccinate (CHS) molecules for mimicking
experimental conditions under which it has been attempted to be
crystallized. Thus the protein I have is not a crystal structure its a
homology model based on a close analog. The experimental aggregation number
of DDM forming a micelle is ~145 and I am taking 167 for building my
initial micelle followed by replacing some of them randomly with CHS
molecules. I did 50 ns of NPT equilibration using gradual release of
position restraints on all the components of the system. My production run
is 300 ns long. I am using gromos54a7 force field and the united-atom
formalism. I am observing that the protein is detached from the micellar
core and comes near the periphery of the preformed micelle after 300 ns.
The protein is exposed to solvent. Now I dont have any doubt about my
equilibration but am I getting something weird? I dont know if my initial
DDM model was erroneous. Have someone else come across such thing? The
model has been used frequently in our research group(
pubs.acs.org/doi/abs/10.1021/jacs.6b08742) and for crystal structures have
been shown located near the core of the micelle. The other part of the
story is the protein I am studying is experimentally known
to be prone to aggregation. So I dont know whether I should be happy or sad
about the results. One possible thing may be an inadequate number of DDM
monomers to begin with but then how for a well-
resolved crystal structure the protein-detergent complex (PDC) with the
identical initial DDM construct is very stable? Is the protein going
outside since due to its inherent tendency to aggregate or this is
an artifact of my simulation which was wrong to begin with. In that case, I
have to alter to monomers to construct the pre-formed micelle.

I looked up literature and could not see anything similar. It seems like
the PDC is quite stable over time as suggested by some of references from
Prof Mark Sansom's eminent research group.

I will be obliged if someone guides me a little bit in this regard. Any
literature or material which include such observation will be really
helpful in understanding whats going on.

Thanks in advance
Soumadwip Ghosh
Post Doctoral Research Associate
Prof. Vaidehi Nagarajan's Research Group
City of Hope Cancer Research Center
Duarte, CA
United States
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Re: [gmx-users] Compilation error - Gromacs 2016.4

[Hoa Trinh]

Dear Mark,
Your guess is great :) Thanks for advising me to use version control.
Best regards,

*Lan Hoa*

2017-11-13 18:18 GMT-06:00 Mark Abraham :

> Hi,
>
> That should never happen - which compiler was it? and are you sure this is
> unmodified 2016.4?
>
> Mark
>
> On Mon, Nov 13, 2017 at 3:17 PM Hoa Trinh  wrote:
>
> > Dear GMX users,
> > I encountered the following error when compiling Gromacs 2016.4:
> >
> >  error: expected primary-expression before ‘>’ token
> > k_S   = load(coeff);
> > 
> >
> > Does anyone face the same situation? What is the solution?
> > Thanks in advance.
> > Best regards,
> >
> > *Lan Hoa*
> > --
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Re: [gmx-users] Compilation error - Gromacs 2016.4

[Mark Abraham]

Hi,

That should never happen - which compiler was it? and are you sure this is
unmodified 2016.4?

Mark

On Mon, Nov 13, 2017 at 3:17 PM Hoa Trinh  wrote:

> Dear GMX users,
> I encountered the following error when compiling Gromacs 2016.4:
>
>  error: expected primary-expression before ‘>’ token
> k_S   = load(coeff);
> 
>
> Does anyone face the same situation? What is the solution?
> Thanks in advance.
> Best regards,
>
> *Lan Hoa*
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[gmx-users] Compilation error - Gromacs 2016.4

[Hoa Trinh]

Dear GMX users,
I encountered the following error when compiling Gromacs 2016.4:

 error: expected primary-expression before ‘>’ token
k_S   = load(coeff);


Does anyone face the same situation? What is the solution?
Thanks in advance.
Best regards,

*Lan Hoa*
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Re: [gmx-users] Ewald summation in 2 dimensions with correction

[Dan Gil]

Hi,

I am using gmx potential to measure the electric field. I've reported the
values from field.xvg in my previous email. The field at the edges of the
ionic liquid near the walls will oscillate because of the electric double
layer but it is the bulk field I am concerned with.

I read the supporting information - I thought that the Ewald summation
correction for 2 dimensions was supposed to cancel out interactions between
periodic images in the z direction?

Were you using the regular 3-D Ewald summation in this work? I might try
carrying out the calculations that way.

Dan

On Mon, Nov 13, 2017 at 2:23 AM, David van der Spoel 
wrote:

> On 11/11/17 16:44, Dan Gil wrote:
>
>> Hi,
>>
>> Just wanted to see if anyone had any thoughts...
>>
>> For more information, if I use:
>> wall-ewald-zfac = 3
>> E-z= 1 5 0
>> The electric field from ionic liquid has a magnitude of 7.5 V/nm in the
>> opposite direction to the applied electric field. This makes no sense to
>> me
>> at all.
>>
>> With
>> wall-ewald-zfac = 5
>> E-z= 1 5 0
>> The ionic liquid E is -6.2
>>
> How do you measure the electric field? Using gmx potential?
> What numbers does the (optional?) file field.xvg contain?
>
> There can of course be a difference between applied field and effective
> field, in particular with PBC. I sugges you read the supporting information
> for our paper: Carl Caleman and David van der Spoel: Picosecond Melting of
> Ice by an Infrared Laser Pulse - A Simulation Study Angew. Chem. Intl. Ed.
> 47 pp. 1417-1420 (2008)
>
>>
>> With
>> wall-ewald-zfac = 10
>> E-z= 1 5 0
>> The electric field is still slightly above the expected 5 V/nm.
>>
>> The dimensions of the box is about 5x5x20 nm3.
>>
>> Reading various sources say that the wall factor should not matter as long
>> as it is sufficiently large (x3) but in my case it seems to matter a lot.
>> Should I report this as a bug or do you think I can investigate this
>> further?
>>
>> Best Regards,
>>
>> Dan
>>
>> > source=link_campaign=sig-email_content=webmail>
>> Virus-free.
>> www.avg.com
>> > source=link_campaign=sig-email_content=webmail>
>> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>>
>>
>> On Wed, Nov 8, 2017 at 11:37 AM, Dan Gil  wrote:
>>
>> Hello,
>>>
>>> I am studying room-temperature ionic liquids in slab geometry and I am
>>> experiencing that I cannot get rid of the interactions between periodic
>>> images in the z-direction. Is there something wrong with what I am doing
>>> or
>>> is this inevitable?
>>>
>>> The reason I think this is because when I change "wall-ewald-zfac" the
>>> results change also.
>>>
>>> Gromacs 5.1
>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>>> ;Integration Method and Parameters
>>> integrator   = md
>>> nsteps   = 400
>>> dt= 0.002
>>> nstenergy= 100
>>> nstcalcenergy= 100
>>> nstlog   = 5000
>>>
>>> ;Output Control
>>> nstxout = 100
>>> nstvout = 1000
>>>
>>> ;Cutoff Schemes
>>> cutoff-scheme= verlet
>>> rlist= 1.0
>>> vdw-type = cut-off
>>> rvdw = 1.0
>>> DispCorr = EnerPres
>>>
>>> ;Coulomb interactions
>>> coulombtype  = pme
>>> rcoulomb = 1.0
>>> fourierspacing   = 0.4
>>>
>>> ;Constraints
>>> constraints  = all-bonds
>>>
>>> ;Temperature coupling
>>> gen-vel  = yes
>>> tcoupl   = v-rescale
>>> tc-grps  = System
>>> tau-t= 0
>>> ref-t= 300
>>>
>>> ;Walls
>>> pbc  = xy
>>> nwall= 2
>>> wall-type= 10-4
>>> ewald-geometry   = 3dc
>>> wall-atomtype= cp cm
>>> wall-density = 5 5
>>> wall-ewald-zfac  = 10
>>>
>>> ;Electric Field
>>> ;Cosine with freq=0, Field V/nm, Phase=n/a
>>> E-z  = 1 0 0
>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>>>
>>> Best Regards,
>>>
>>> Dan
>>>
>>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
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Re: [gmx-users] salt concentration

[Hermann, Johannes]

Hi Netaly,

one way would be to calculate the number of Na, Cl, and Mg ions by hand, 
i.e. with the box size and the respective concentrations, and add the 
correct amount of ions in two steps, with the flags -np or -nn. E.g. in 
the first step you add Na and Cl and in the second you add Mg.


All the best

Johannes


On 13.11.2017 13:31, Netaly Khazanov wrote:

Dear Gromacs User,

Is it possible to simulate system with two salt concentrations , e.g. NaCl
0.1 mol/L and MgCl2 0.002 mol/liter?

The commands that i am using you can see below:

grompp_d -f ions.mdp -c ligand_MG_box_water.gro -p topol.top -o ions.tpr
genion_d -s ions.tpr -o ligand_box_water_NaCL.gro -p topol.top -pname NA -
nname CL -neutral -conc 0.1
grompp_d -f ions.mdp -c ligand_box_water_NACL.gro -p topol.top -o ions.tpr
genion_d -s ions.tpr -o ligand_box_water_NaCL_MgCl2.gro -p topol.top -pname
MG -pq 2 -nname CL -neutral -conc 0.002

The message that I got after the execution of the last command is :"No ions
to add and no potential to calculate."

Is it right way to do it?
Thank you in advance.
Netaly




--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/

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[gmx-users] salt concentration

[Netaly Khazanov]

Dear Gromacs User,

Is it possible to simulate system with two salt concentrations , e.g. NaCl
0.1 mol/L and MgCl2 0.002 mol/liter?

The commands that i am using you can see below:

grompp_d -f ions.mdp -c ligand_MG_box_water.gro -p topol.top -o ions.tpr
genion_d -s ions.tpr -o ligand_box_water_NaCL.gro -p topol.top -pname NA -
nname CL -neutral -conc 0.1
grompp_d -f ions.mdp -c ligand_box_water_NACL.gro -p topol.top -o ions.tpr
genion_d -s ions.tpr -o ligand_box_water_NaCL_MgCl2.gro -p topol.top -pname
MG -pq 2 -nname CL -neutral -conc 0.002

The message that I got after the execution of the last command is :"No ions
to add and no potential to calculate."

Is it right way to do it?
Thank you in advance.
Netaly


-- 
Netaly
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Re: [gmx-users] Problem using gmx wham

[Jefferies D . F .]

Hey guys,

Sorry if it seems that I'm bumping this thread, but I was wondering if anyone 
had any other suggestions before I let this thread die. 

Thanks.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Jefferies D.F. 
[dfj1...@soton.ac.uk]
Sent: Thursday, November 02, 2017 1:29 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem using gmx wham

Hi Justin,

Thanks for the response. The .dat files were created with the vi text editor, 
they contain lists of the .tpr and .xvg to be read, e.g.

umbrella0.tpr
umbrella1.tpr
umbrella2.tpr
..
umbrella52.tpr

I've tried to use dos2unix,  i.e.
~> dos2unix tpr-files.dat
and
~> dos2unix pullf-files.dat

but I still get the same error message i.e.

---
Program gmx wham, VERSION 5.1.2
Source code file: 
/Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 
1800

Fatal error:
Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

That being said, it seems you're correct in thinking something's weird with the 
input files. After I created new .dat files, I got this message:

---
Program gmx wham, VERSION 5.1.2
Source code file: 
/Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 
3610

Fatal error:
Found 53 file names in tpr-files.dat, but 54 in pullf-files.dat

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

gmx wham is registering 54 files, when only 53 were written.






From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul 
[jalem...@vt.edu]
Sent: Thursday, November 02, 2017 11:10 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem using gmx wham

On 11/1/17 4:26 PM, Jefferies D.F. wrote:
> Hi,
>
> I am attempting to use gmx wham to compute a potential of mean force. I have 
> used the command line:
>
> gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ
>
> where tpr-files.dat and pullf-files.dat contain a list of the .tpr and 
> pullf.xvg files from each umbrella sampling window, respectively.
>
> It seems that gmx wham is having trouble reading the .tpr and .xvg files, as 
> I get this error message:
>
> ---
>
> Program gmx wham, VERSION 5.1.4
>
> Source code file: 
> /local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp,
>  line: 1800
>
>
> Fatal error:
>
> Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.
>

The extra space after "tpr" in the printed error suggests something is
weird with the input .dat file. Did you create it with a proper plain
text editor? What about running dos2unix on it to make sure you've got
the right kind of line endings?

-Justin

> For more information and tips for troubleshooting, please check the GROMACS
>
> website at http://www.gromacs.org/Documentation/Errors
>
> ---
>
>
> I have computed potential of mean force profiles before (using this Mac), but 
> I haven't encountered this problem. Could someone help me with this problem?
>
>

--
==

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] GROMOS bond-stretching parameters

[Faezeh Pousaneh]

Hi,
Unfortunately I do not find in Gromos literature what is the third number
in front of
bond stretching parameters, e.g 1200 below:
:

; ICB(H)[N]CB[N] B0[N]
#define gb_50.1230  1.6600e+07
; C  - O1200

someone please tell me,
Best regards
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[gmx-users] Pİezoelectricity analyse

[ali akgün]

Hi,

İ am newbie in Gromacs i processed pvdf(polymer) simulation in Gromacs for
analyze piezoelectricity effect of pvdf in the different pressure and
temperature.(using gmx dipole) Can i process different methods for analyze
piezoelectric effect of pvdf. İ only know analyze dipole moments of system.
Do you know another methods in gromacs ?


Thank you.
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Re: [gmx-users] mobile ligand with intermolecular interactions

[Ahmet Yildirim]

Sorry. The pymol and GROMACS give the same results for every three target
dihedrals. The updated results are here:
https://www.dropbox.com/s/7qgn7qa4rf2yc14/dih.pdf?dl=0

The results show that the average dihedrals are almost the same in both the
state A and state B for both [dihedrals] or [dihedral_restraints]. I think
this is normal?

On 13 November 2017 at 09:49, Ahmet Yildirim  wrote:

> Hi,
>
> Let me take that in reverse order:
>>
>> Note that choosing appropriate atoms to apply restraints is not a trivial
>> matter, and results can vary depending on the choices made.
>>
> I know.
>
> I doubt there's a bug. I tested this feature a lot myself and have used
>> it. How different are the dihedrals in the B-state vs. the A-state, and how
>> much do they differ from the target values?
>>
>
> The dihedrals are almost the same in both the state A and state B (except
> for the first one) when the [dihedrals] or [dihedral_restraints] is used.
> Please see the results https://www.dropbox.com/s/rdw6
> lg0c4xviufk/dih.pdf?dl=0
>
> I think there is bug?
>
> On the other hand, the pymol and GROMACS calculate differently the first
> target dihedral angle between 1587, 1581, 1579 and 14 atoms, respectively
> -155 and 66. I don't know why? That is strange? Note that I used -155
> degrees obtained from pymol as a target value of the first dihedral in the
> simulation. The other two target dihedrals are the same for both pymol and
> GROMACS.
>
> Thanks.
>
> On 13 November 2017 at 01:55, Justin Lemkul  wrote:
>
>>
>>
>> On 11/10/17 11:59 PM, Ahmet Yildirim wrote:
>>
>>> Hi,
>>>
>>> Just tested it. The [ dihedral_restraints ] didn't help. The RMSD of the
>>> ligand is the same when the [ dihedral_restraints ] or [ dihedrals ] is
>>> used at end of the complex topology file. This is a bug?
>>>
>>
>> I doubt there's a bug. I tested this feature a lot myself and have used
>> it. How different are the dihedrals in the B-state vs. the A-state, and how
>> much do they differ from the target values? Note that choosing appropriate
>> atoms to apply restraints is not a trivial matter, and results can vary
>> depending on the choices made.
>>
>> -Justin
>>
>>  From my first mail:
>>>
>>> I think [ dihedral_restraints ] will be the same as [ dihedrals ] because
 the eq. 4.84 in the manual will be equal to 4.61 if dphiA and dphiB are
 taken as 0 (zero), right?

>>>
>>> Checked also the position of the ligand during the simulation on the VMD.
>>> It is very mobile in the decoupled state as I said in the previous mail.
>>>
>>> *First test:*
>>> [ intermolecular_interactions ]
>>> [ bonds ]
>>> ; ai ajtype   bA  kA bB  kB
>>>   13912615  6  0.654   0.00.654   4184.0
>>>
>>> [ angles ]
>>> ; ai ajak typethA  fcAthB  fcB
>>>   1393   1391   2615   1   88.8 0.088.8 41.84
>>>   1391   2615   2614   1   32.9 0.032.9 41.84
>>>
>>> [ dihedrals ]
>>> ; ai ajakaltype thA  fcA   thB  fcB
>>>   1410  1393  1391  26152   -159.70.0-159.741.84
>>>   1393  1391  2615  26142122.60.0 122.641.84
>>>   1391  2615  2614  26102 12.80.0  12.841.84
>>>
>>> *Second test:*
>>>
>>> [ intermolecular_interactions ]
>>> [ bonds ]
>>> ; ai ajtype   bA  kA bB  kB
>>>   13912615  6  0.654   0.00.654   4184.0
>>>
>>> [ angles ]
>>> ; ai ajak typethA  fcAthB  fcB
>>>   1393   1391   2615   1   88.8 0.088.8 41.84
>>>   1391   2615   2614   1   32.9 0.032.9 41.84
>>>
>>> [ dihedral_restraints ]
>>> ;   aiajakal  typephiA dphiA  fcAphiB  dphiB
>>> fcB
>>>   1410  1393  1391  2615 1-159.7   0.00.0-159.70.0
>>> 41.84
>>>   1393  1391  2615  2614 1 122.6   0.00.0 122.60.0
>>> 41.84
>>>   1393  1391  2615  2614 1  12.8   0.00.0 12.8 0.0
>>> 41.84
>>>
>>> On 10 November 2017 at 22:36, Justin Lemkul  wrote:
>>>
>>>
 On 11/10/17 2:21 PM, Ahmet Yildirim wrote:

 Dear users,
>
> I add the following [ intermolecular_interactions ] section into the
> topology file of protein-ligand complex for free energy calculations.
> Unfortunately this setting doesn't provide me what I want in the
> decoupled
> state. The ligand in the decoupled state is very mobile compared to the
> coupled state. It means that the conformational sampling of the ligand
> in
> the decoupled state is quite different from the coupled state. That is
> not
> expected of course. Any suggestions as to why this might be?
>
> Do you think that there is something wrong with the following settings,
> e.g. [ dihedrals ] part?
>
> Yes, because you're setting [dihedrals] as if they were