[gmx-users] Regarding error.

[Seera Suryanarayana]

Dear all,
While i am running gromacs software i am getting following
error.Let me know that error how to over come.


Fatal error:
Residue 'CSD' not found in residue topology database



Suryanarayana Seera,
PhD student,
Hyderabad,
India.
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Re: [gmx-users] Regarding errors.

[Mark Abraham]

On 18/05/2012 4:43 PM, Seera Suryanarayana wrote:


Dear all,
While i am running gromacs software i am getting following 
error.Let me know how to over come that error


Fatal error:
number of coordinates in coordinate file (208L_ion.gro, 62283)
 does not match topology (208L.top, 62293)


The number of coordinates must match. See discussion of the [molecules] 
section in chapter 5 of the manual. That's probably what you should fix, 
probably with the number of solvent and ion atoms changing. genion -p 
will do this for you if you tell it to do so.


Mark
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[gmx-users] Regarding errors.

[Seera Suryanarayana]

Dear all,
While i am running gromacs software i am getting following
error.Let me know how to over come that error

Fatal error:
number of coordinates in coordinate file (208L_ion.gro, 62283)
 does not match topology (208L.top, 62293)



Suryanarayana Seera,
PhD student,
Hyderabad,
India.
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Re: [gmx-users] grompp error - incorrect number of parameters

[Mark Abraham]

On 17/05/2012 11:47 PM, Lara Bunte wrote:

Hello


After


grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr


I got the error:

Incorrect number of parameters - found 2, expected 4 or 4 for U-B.


I thought that this could be an inconsistency be declaring the functions, but 
in my topology I have function 4 (for improper dihedrals):


Out of topol.top

[ dihedrals ]
;  aiajakal functc0c1c2 
   c3
 1 8 6 4 4180   100


And in my .rtp file in the CHARMM27 force field folder I have:

Out of .rtp file
; bonds  angles  dihedrals  impropers
  1   5  44


There's no aminoacids.rtp file for CHARMM27 that has ever looked like 
this. Any that did is not CHARMM27.


Mark




and in my ffbonded.itp file I have:
[ dihedraltypes ]
; i j   k   l   funcq0  cq
ON1 NN3A  CN1A   NN2U   4   180   100


So in alle three files, ffbonded.itp, topol.top and the .rtp parametrization 
file I have the function 4 for the improper dihedrals.


What is the problem?

Thanks for helping me
Greetings
Lara


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Re: [gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks.

[Mark Abraham]

On 17/05/2012 11:48 AM, kevin wrote:


Thanks.  I think I should have a look at some specific documents 
to understand the flow of control.
Namely, to understand what is purpose of the subroutines 
in src/mdlib/.  But I could not find such
information in the Gromacs user manual. Do anyone know such an 
document? Thanks.


Unfortunately the development of GROMACS is not fast enough to suit 
anybody's wishes, and too fast and complex to make it worth people's 
volunteer time to do much beyond what can be observed by inspecting the 
code. I suggest you step through a run of GROMACS with your favourite 
debugger on a similar calculation and observe the control flow.


There is some discussion of data structures on the GROMACS webpage which 
is more-or-less useful for the 4.0/4.5 series.


Mark



kevin.len
*From:* Mark Abraham 
*Date:* 2012-05-16 13:57
*To:* Discussion list for GROMACS users 
*Subject:* Re: [gmx-users] What is the subroutine for SHAKE or RATTLE? 
Thanks.

On 16/05/2012 12:28 PM, kevin wrote:

 Hi, everyone.
It is my first use of Gromacs  and I am 
looking for a numerical scheme for one specific constrained SDE, the 
constrain is a macroscopic one, i.e., overdamped Langevin(Brownian 
dynamics) equations with an equality constraint which is expressed in 
form of expectation(or moment of n-th order). This is unlike the 
common 'micro' constraint(simply function in terms of variable in 
SDE) . I can not find such a subrountine for solving constrained SDE 
in MD codes in Gromacs . I see there is an 
algorithm called "SHAKE" or "RATTLE "which and it seems they could 
implement Langevin(or Brownian) dynamics with constraints. If 
convenient, could anyone help to point out which subroutine is 
specific for implementing SHAKE/RATTLE? Thanks in advance.




Various files in src/mdlib/ deal with these kinds of algorithms.

Mark


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Re: [gmx-users] charm in gromacs

[Mark Abraham]

On 18/05/2012 2:52 AM, francesco oteri wrote:

Dear gromacs users,
I am trying to port a set of charm parameter in gromacs.

I am using the script convert_charmm_to_gromacs.pl 
 contained in the 
file charmm_to_gromacs.tgz (http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz).


Regarding dihedrals, the entry regarding the file says that pdb2gmx cannot

"generate multiple periodic dihedral functions such as CHARMM uses for 
some dihedrals -
these must be converted to Ryckaert-Bellemans functions, i.e. 
expressed as a cosine power expansion"


This assumption is no longer valid, is it?
As far as I know, infact, now gromacs support multiple periodic 
function (funtion 9), is it?




Correct, but with the inclusion of native CHARMM27 in GROMACS, I have 
had no reason to upgrade these conversion scripts to support function 
type 9.


Mark
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[gmx-users] Atom O5' not found in residue seq.nr. 1 while adding atom

[mahr]

 Dear Gromacs Users,

I m trying to simulate a DNA structure with amber03
force field. However, when I give first command of pdb2gmx.

Following error comes:

Fatal error: Atom O5' not found in residue seq.nr. 1 while adding atom.

As O5' is present in DA nucleic acid. So,I checked DNA.rtp file and
nomenclature of DA, DT and all other nucleic acid residues is same for both
.pdb and .rtp file.

Plz plz guide me how to solve this problem.

Following is my .rtp file for DA

[ DA ]

 [ atoms ]

 PP 1.16590 1

   O1PO2   -0.77610 2

   O2PO2   -0.77610 3

   O5'OS   -0.49540 4

   C5'CT   -0.00690 5

  H5'1H10.07540 6

  H5'2H10.07540 7

   C4'CT0.16290 8

   H4'H10.11760 9

   O4'OS   -0.3691010

   C1'CT0.0431011

   H1'H20.1838012

N9N*   -0.0268013

C8CK0.1607014

H8H50.1877015

N7NB   -0.6175016

C5CB0.0725017

C6CA0.6897018

N6N2   -0.9123019

   H61H 0.4167020

   H62H 0.4167021

N1NC   -0.7624022

C2CQ0.5716023

H2H50.0598024

N3NC   -0.7417025

C4CB0.3800026

   C3'CT0.0713027

   H3'H10.0985028

   C2'CT   -0.0854029

  H2'1HC0.0718030

  H2'2HC0.0718031

   O3'OS   -0.5232032

 [ bonds ]

 P   O1P

 P   O2P

 P   O5'

   O5'   C5'

   C5'  H5'1

   C5'  H5'2

   C5'   C4'

   C4'   H4'

   C4'   O4'

   C4'   C3'

   O4'   C1'

   C1'   H1'

   C1'N9

   C1'   C2'

N9C8

N9C4

C8H8

C8N7

N7C5

C5C6

C5C4

C6N6

C6N1

N6   H61

N6   H62

N1C2

C2H2

C2N3

N3C4

C3'   H3'

C3'   C2'

C3'   O3'

C2'  H2'1

C2'  H2'2

-O3' P

 [ impropers ]

C4C8N9   C1'

C6   H61N6   H62

N9N7C8H8

N1N3C2H2

C5N6C6N1

 

Following is DA part of my pdb file:

 

ATOM 28P   DA E   10-24.026  32.156 -43.818  1.00180.08
P

ATOM 29  O1P   DA E   10-23.715  31.139 -42.788  1.00173.83
O

ATOM 30  O2P   DA E   10-25.435  32.499 -44.114  1.00161.01
O

ATOM 31  O5'   DA E   10-23.255  33.516 -43.475  1.00127.88 O

ATOM 32  C5'   DA E   10-23.498  34.194 -42.247  1.00107.59
C

ATOM 33  C4'   DA E   10-23.169  33.299 -41.066  1.00102.86
C

ATOM 34  O4'   DA E   10-21.825  32.777 -41.221  1.00 93.42
O

ATOM 35  C3'   DA E   10-23.220  33.983 -39.705  1.00102.18
C

ATOM 36  O3'   DA E   10-23.829  33.119 -38.754  1.00 83.31
O

ATOM 37  C2'   DA E   10-21.755  34.244 -39.363  1.00102.50
C

ATOM 38  C1'   DA E   10-21.012  33.153 -40.128  1.00 81.75
C

ATOM 39  N9DA E   10-19.721  33.596 -40.647  1.00 82.20
N

ATOM 40  C8DA E   10-19.495  34.603 -41.544  1.00 94.12
C

ATOM 41  N7DA E   10-18.227  34.783 -41.832  1.00102.29
N

ATOM 42  C5DA E   10-17.576  33.827 -41.070  1.00 96.10
C

ATOM 43  C6DA E   10-16.215  33.496 -40.924  1.00 87.15
C

ATOM 44  N6DA E   10-15.230  34.125 -41.572  1.00 84.12
N

ATOM 45  N1DA E   10-15.903  32.488 -40.082  1.00 75.71
N

ATOM 46  C2DA E   10-16.891  31.860 -39.434  1.00 80.51
C

ATOM 47  N3DA E   10-18.203  32.081 -39.490  1.00 91.21
N

ATOM 48  C4DA E   10-18.482  33.087 -40.334  1.00 96.39
C

ATOM 49 H5'1   DA E   10-22.876  35.088 -42.203  1.00105.06
H

ATOM 50 H5'2   DA E   10-24.549  34.479 -42.198  1.00105.06
H

ATOM 51  H4'   DA E   10-23.867  32.462 -41.060  1.00105.06
H

ATOM 52  H3'   DA E   10-23.768  34.923 -39.772  1.00105.06
H

ATOM 53 H2'1   DA E   10-21.447  35.234 -39.699  1.00105.06
H

ATOM 54 H2'2   DA E   10-21.583  34.154 -38.290  1.00105.06
H

ATOM 55  H1'   DA E   10-20.863  32.292 -39.476  1.00105.06
H

ATOM 56  H8DA E   10-20.295  35.202 -41.980  1.00105.06
H

ATOM 57  H61   DA E   10-15.458  34.926 -42.244  1.00105.06
H

ATOM 58  H62   DA E   10-14.214  33.827 -41.419  1.00105.06
H

ATOM 59  H2DA E   10-16.579  31.056 -38.768  1.00105.06
H

 

I will be very thankful. 

 

Best regards

mahreen

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Re: [gmx-users] Place water away from existing atoms

[Justin A. Lemkul]

On 5/17/12 4:45 PM, Steven Neumann wrote:



On Thu, May 17, 2012 at 5:48 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



On 5/17/12 11:50 AM, Steven Neumann wrote:

My tube is finite. I increased my box so the water could interact with
all water
molecules. The same problem: My minim.mdp

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator= steep; Algorithm (steep = steepest descent 
minimization)
emtol= 10.0  ;
emstep= 0.001
nsteps= 5; Maximum number of (minimization) steps to 
perform
nstxout = 1
; Parameters describing how to find the neighbors of each atom and how 
to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long
range forces
ns_type= grid; Method to determine neighbor list (simple, 
grid)
rlist= 1.4; Cut-off for making neighbor list (short
range forces)
coulombtype= PME; Treatment of long range electrostatic
interactions
rcoulomb= 1.4; Short-range electrostatic cut-off
rvdw= 1.4; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

Well... no clue...


Then the diagnostic tips I listed before still apply, as well as those
listed on the webpage linked from what I posted earlier.


-Justin


Thank you Jusin! By the way, how can I create infinite tube in gmx?



http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube

Also refer to the many posts in the mailing list archive on related topics.

-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Place water away from existing atoms

[Steven Neumann]

On Thu, May 17, 2012 at 5:48 PM, Justin A. Lemkul  wrote:

>
>
> On 5/17/12 11:50 AM, Steven Neumann wrote:
>
>> My tube is finite. I increased my box so the water could interact with
>> all water
>> molecules. The same problem: My minim.mdp
>>
>> ; minim.mdp - used as input into grompp to generate em.tpr
>> ; Parameters describing what to do, when to stop and what to save
>> integrator= steep; Algorithm (steep = steepest descent
>> minimization)
>> emtol= 10.0  ;
>> emstep= 0.001
>> nsteps= 5; Maximum number of (minimization) steps to
>> perform
>> nstxout = 1
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> nstlist= 1; Frequency to update the neighbor list and long
>> range forces
>> ns_type= grid; Method to determine neighbor list (simple,
>> grid)
>> rlist= 1.4; Cut-off for making neighbor list (short range
>> forces)
>> coulombtype= PME; Treatment of long range electrostatic
>> interactions
>> rcoulomb= 1.4; Short-range electrostatic cut-off
>> rvdw= 1.4; Short-range Van der Waals cut-off
>> pbc= xyz ; Periodic Boundary Conditions (yes/no)
>>
>> Well... no clue...
>>
>>
> Then the diagnostic tips I listed before still apply, as well as those
> listed on the webpage linked from what I posted earlier.
>
>
> -Justin
>

Thank you Jusin! By the way, how can I create infinite tube in gmx?

>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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[gmx-users] repulsive interaction i and i+2

[mohan maruthi sena]

Hi all,
  I have used a user define potential to describe attractive
potential beyond i and i+3 atoms(similar to lLJ). If i want to describe
repulsive interactions with in i and i+3 , how can i do it in gromacs? can
anyone suggest me a way,


Thanks and Regards,
Mohan
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Re: [gmx-users] Force Constants and Unit Systems

[Justin A. Lemkul]

On 5/17/12 3:32 PM, Lara Bunte wrote:

Hi

what I meant was, that if a force constant would have the unit kcal/mol, the 
corresponding potential will be a coulomb potential and I said that this makes 
no sense. Springs has a quadratic potential, not a Coulomb Potential, like V(r) 
= 1/r.
Please have a look on page 45, there you can see what is written in my 
supporting information (it's in English).



I just want to clarify something, though it isn't even really relevant, perhaps 
it will be instructional.  The 1/length issue does not mean the potential is 
calculated from 1/r.  In fact, neither is a Coulombic potential, though it is 
proportional to this factor.  The issue that was initially raised was to help 
you understand that force constants for bonds must have a length term in the 
denominator of the units, i.e. a 1/length (to some power) dependence.




http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&ved=0CG4QFjAJ&url=http%3A%2F%2Fedoc.ub.uni-muenchen.de%2F13660%2F1%2FRieff_Benjamin.pdf&ei=dVC1T_XJJIzO4QTojqXADg&usg=AFQjCNFOxi8Cf2eUshmA9rzPfLPra5u-gw&sig2=79QqmWk3b8LSFlVjey4FFg

Do you think it is a typo?



I would suspect so.  One cannot have a bond force constant that is not have a 
length term in the denominator.  Presumably the true units are kcal/(mol A^2), 
which can be easily converted to kJ/(mol nm^2) for use in Gromacs.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Force Constants and Unit Systems

[Lara Bunte]

Hi

what I meant was, that if a force constant would have the unit kcal/mol, the 
corresponding potential will be a coulomb potential and I said that this makes 
no sense. Springs has a quadratic potential, not a Coulomb Potential, like V(r) 
= 1/r.
Please have a look on page 45, there you can see what is written in my 
supporting information (it's in English). 


http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&ved=0CG4QFjAJ&url=http%3A%2F%2Fedoc.ub.uni-muenchen.de%2F13660%2F1%2FRieff_Benjamin.pdf&ei=dVC1T_XJJIzO4QTojqXADg&usg=AFQjCNFOxi8Cf2eUshmA9rzPfLPra5u-gw&sig2=79QqmWk3b8LSFlVjey4FFg

Do you think it is a typo?

Greetings
Lara







- Ursprüngliche Message -
Von: Justin A. Lemkul 
An: Lara Bunte ; Discussion list for GROMACS users 

CC: 
Gesendet: 20:37 Donnerstag, 17.Mai 2012
Betreff: Re: [gmx-users] Force Constants and Unit Systems



On 5/17/12 1:33 PM, Lara Bunte wrote:
> Hi
> 
>> Therefore either they have a potential of the form 1/[Length] or they
>> weren't using the term correctly.
> 
> But a 1/[lenght] potential, which is a coulomb potential makes no sense for
> springs, that have a quadratic potential, like V(x) = 1/2 * k * x^2 of a
> harmonic oscillator.
> 

Perhaps you should tell us the bonded term your force constant in question 
applies.  I don't see how this has anything to do with a Coulombic potential, 
as force constants are not involved.  The 1/length dependence (in terms of 
proportionality, not literally that your energy is calculated as 1/r) is in the 
units, e.g. kJ/(mol nm^2) - energy is dependent upon the length of the bond, in 
other words, the displacement from the equilibrium value.

If your term in question is an angle potential, then the force constant should 
indeed have units of energy, per the manual (Table 5.5).  If it is anything 
else, there is an error somewhere.

> So that means probably, that the writers of the paper did an error. Could
> such an error ruin my hole MD? My complete force field parametrization is out
> of this paper.
> 

It depends on what the error is, if it exists at all.  If it is a simple 
typographical mistake, then there's likely no harm.  If there is some larger 
calculation error, then the force constants may be flawed.  We have no way to 
know, as you've not said what your bonded term is or what the source of the 
parameters is.

The results you obtain in a simulation are only as good as the physical model 
itself and the assumptions it makes.  If you come to find out that there is 
some underlying mistake in the parameterization, I would have little or no 
faith in the results.  Whether you need to be concerned or not at this point is 
quit unclear.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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Re: [gmx-users] Force Constants and Unit Systems

[Justin A. Lemkul]

On 5/17/12 1:33 PM, Lara Bunte wrote:

Hi


Therefore either they have a potential of the form 1/[Length] or they
weren't using the term correctly.


But a 1/[lenght] potential, which is a coulomb potential makes no sense for
springs, that have a quadratic potential, like V(x) = 1/2 * k * x^2 of a
harmonic oscillator.



Perhaps you should tell us the bonded term your force constant in question 
applies.  I don't see how this has anything to do with a Coulombic potential, as 
force constants are not involved.  The 1/length dependence (in terms of 
proportionality, not literally that your energy is calculated as 1/r) is in the 
units, e.g. kJ/(mol nm^2) - energy is dependent upon the length of the bond, in 
other words, the displacement from the equilibrium value.


If your term in question is an angle potential, then the force constant should 
indeed have units of energy, per the manual (Table 5.5).  If it is anything 
else, there is an error somewhere.



So that means probably, that the writers of the paper did an error. Could
such an error ruin my hole MD? My complete force field parametrization is out
of this paper.



It depends on what the error is, if it exists at all.  If it is a simple 
typographical mistake, then there's likely no harm.  If there is some larger 
calculation error, then the force constants may be flawed.  We have no way to 
know, as you've not said what your bonded term is or what the source of the 
parameters is.


The results you obtain in a simulation are only as good as the physical model 
itself and the assumptions it makes.  If you come to find out that there is some 
underlying mistake in the parameterization, I would have little or no faith in 
the results.  Whether you need to be concerned or not at this point is quit unclear.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Force Constants and Unit Systems

[Lara Bunte]

Hi

>Therefore either they have a potential of the form 1/[Length] or they
>weren't using the term correctly.

But a 1/[lenght] potential, which is a coulomb potential makes no sense for 
springs, that have a quadratic potential, like V(x) = 1/2 * k * x^2 of a 
harmonic oscillator. 

So that means probably, that the writers of the paper did an error. Could such 
an error ruin my hole MD? My complete force field parametrization is out of 
this paper.

Thanks for helping me
Greetings
Lara








- Ursprüngliche Message -
Von: Richard Broadbent 
An: Lara Bunte ; Discussion list for GROMACS users 

CC: 
Gesendet: 19:18 Donnerstag, 17.Mai 2012
Betreff: Re: [gmx-users] Force Constants and Unit Systems

Hi Lara,

On Thu, 2012-05-17 at 17:58 +0100, Lara Bunte wrote: 
> Hi 
> 
> 
> >One cannot convert between these units, since kcal/mol is an energy term, and
> >kJ/(mol nm^2) is a force constant.
> 
> 
> This confuses me, because in the paper where that constants are from is 
> written, I quote:
Which paper? 
> 
> "Force constant k in kcal / mol calculated by DFT"

The unit of Force is  [Mass]*[Length] /[Time]^2 = [Energy]/[Length] in
any unit system.

Therefore either they have a potential of the form 1/[Length] or they
weren't using the term correctly.

A harmonic bond must have a force constant with units [ Energy ]/
[ Length ]^2 In gromacs this is therefore kJ/(mol nm^2)

The conversion from kcal/mol to kJ/mol is easily found by googling:
kcal/mol


Richard 
> 
> 
> In my parametrization I have this values. Could you please explain this?
> 
> Greetings and really thanks for your help
> 
> Lara
> 
> 
> 
> 
> 
> - Ursprüngliche Message -
> Von: Justin A. Lemkul 
> An: Lara Bunte ; Discussion list for GROMACS users 
> 
> CC: 
> Gesendet: 18:52 Donnerstag, 17.Mai 2012
> Betreff: Re: [gmx-users] Force Constants and Unit Systems
> 
> 
> 
> On 5/17/12 12:25 PM, Lara Bunte wrote:
> > Hello
> >
> > I never had contact with such units. Could you please help me and explain me
> > how to transform following units:
> >
> > 1.) kcal / mol -->  kJ / (mol * nm^2)
> >
> 
> One cannot convert between these units, since kcal/mol is an energy term, and
> kJ/(mol nm^2) is a force constant.
> 
> > 2.) kcal / (mol * rad^2) -->  kJ / (mol * rad^2)
> >
> 
> The transformation between kcal and kJ requires a simple multiplication.
> 
> > I have additionally some question to that:  Both should be units of a force
> > constant. From Hooke's law F = -kx follows for me, that the unit of a force
> > constant is Newton N over distance m, in S.I. units  kg/sec^2 (mass over 
> > time
> > square).
> >
> > What is the correspondence between above from Hooke's law and that units of
> > force constants in molecular dynamics simulations?
> 
> Force is also expressed as kJ/(mol nm) - see Chapter 2 of the Gromacs manual. 
> Thus, since x is in units of nm (distance), then k has units of kJ/(mol nm^2).
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
>
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Re: [gmx-users] Force Constants and Unit Systems

[Richard Broadbent]

Hi Lara,

On Thu, 2012-05-17 at 17:58 +0100, Lara Bunte wrote: 
> Hi 
> 
> 
> >One cannot convert between these units, since kcal/mol is an energy term, and
> >kJ/(mol nm^2) is a force constant.
> 
> 
> This confuses me, because in the paper where that constants are from is 
> written, I quote:
Which paper? 
> 
> "Force constant k in kcal / mol calculated by DFT"

The unit of Force is  [Mass]*[Length] /[Time]^2 = [Energy]/[Length] in
any unit system.

Therefore either they have a potential of the form 1/[Length] or they
weren't using the term correctly.

A harmonic bond must have a force constant with units [ Energy ]/
[ Length ]^2 In gromacs this is therefore kJ/(mol nm^2)

The conversion from kcal/mol to kJ/mol is easily found by googling:
kcal/mol


Richard 
> 
> 
> In my parametrization I have this values. Could you please explain this?
> 
> Greetings and really thanks for your help
> 
> Lara
> 
> 
> 
> 
> 
> - Ursprüngliche Message -
> Von: Justin A. Lemkul 
> An: Lara Bunte ; Discussion list for GROMACS users 
> 
> CC: 
> Gesendet: 18:52 Donnerstag, 17.Mai 2012
> Betreff: Re: [gmx-users] Force Constants and Unit Systems
> 
> 
> 
> On 5/17/12 12:25 PM, Lara Bunte wrote:
> > Hello
> >
> > I never had contact with such units. Could you please help me and explain me
> > how to transform following units:
> >
> > 1.) kcal / mol -->  kJ / (mol * nm^2)
> >
> 
> One cannot convert between these units, since kcal/mol is an energy term, and
> kJ/(mol nm^2) is a force constant.
> 
> > 2.) kcal / (mol * rad^2) -->  kJ / (mol * rad^2)
> >
> 
> The transformation between kcal and kJ requires a simple multiplication.
> 
> > I have additionally some question to that:  Both should be units of a force
> > constant. From Hooke's law F = -kx follows for me, that the unit of a force
> > constant is Newton N over distance m, in S.I. units  kg/sec^2 (mass over 
> > time
> > square).
> >
> > What is the correspondence between above from Hooke's law and that units of
> > force constants in molecular dynamics simulations?
> 
> Force is also expressed as kJ/(mol nm) - see Chapter 2 of the Gromacs manual. 
> Thus, since x is in units of nm (distance), then k has units of kJ/(mol nm^2).
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> 


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Re: [gmx-users] Force Constants and Unit Systems

[Justin A. Lemkul]

On 5/17/12 12:58 PM, Lara Bunte wrote:

Hi



One cannot convert between these units, since kcal/mol is an energy term, and
kJ/(mol nm^2) is a force constant.



This confuses me, because in the paper where that constants are from is 
written, I quote:

"Force constant k in kcal / mol calculated by DFT"


In my parametrization I have this values. Could you please explain this?



If this is a force constant for an angle, then it needs to simply be converted 
to kJ/mol.  See Table 5.5 of the manual for all force constant requirements. 
Your original question is not solvable; one cannot convert kcal/mol to kJ/(mol 
nm^2) as you cannot create a distance term out of nothing.


-Justin


Greetings and really thanks for your help

Lara





- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Lara Bunte; Discussion list for GROMACS 
users
CC:
Gesendet: 18:52 Donnerstag, 17.Mai 2012
Betreff: Re: [gmx-users] Force Constants and Unit Systems



On 5/17/12 12:25 PM, Lara Bunte wrote:

Hello

I never had contact with such units. Could you please help me and explain me
how to transform following units:

1.) kcal / mol -->   kJ / (mol * nm^2)



One cannot convert between these units, since kcal/mol is an energy term, and
kJ/(mol nm^2) is a force constant.


2.) kcal / (mol * rad^2) -->   kJ / (mol * rad^2)



The transformation between kcal and kJ requires a simple multiplication.


I have additionally some question to that:  Both should be units of a force
constant. From Hooke's law F = -kx follows for me, that the unit of a force
constant is Newton N over distance m, in S.I. units  kg/sec^2 (mass over time
square).

What is the correspondence between above from Hooke's law and that units of
force constants in molecular dynamics simulations?


Force is also expressed as kJ/(mol nm) - see Chapter 2 of the Gromacs manual.
Thus, since x is in units of nm (distance), then k has units of kJ/(mol nm^2).

-Justin



--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] Force Constants and Unit Systems

[Lara Bunte]

Hi 


>One cannot convert between these units, since kcal/mol is an energy term, and
>kJ/(mol nm^2) is a force constant.


This confuses me, because in the paper where that constants are from is 
written, I quote:

"Force constant k in kcal / mol calculated by DFT"


In my parametrization I have this values. Could you please explain this?

Greetings and really thanks for your help

Lara





- Ursprüngliche Message -
Von: Justin A. Lemkul 
An: Lara Bunte ; Discussion list for GROMACS users 

CC: 
Gesendet: 18:52 Donnerstag, 17.Mai 2012
Betreff: Re: [gmx-users] Force Constants and Unit Systems



On 5/17/12 12:25 PM, Lara Bunte wrote:
> Hello
>
> I never had contact with such units. Could you please help me and explain me
> how to transform following units:
>
> 1.) kcal / mol -->  kJ / (mol * nm^2)
>

One cannot convert between these units, since kcal/mol is an energy term, and
kJ/(mol nm^2) is a force constant.

> 2.) kcal / (mol * rad^2) -->  kJ / (mol * rad^2)
>

The transformation between kcal and kJ requires a simple multiplication.

> I have additionally some question to that:  Both should be units of a force
> constant. From Hooke's law F = -kx follows for me, that the unit of a force
> constant is Newton N over distance m, in S.I. units  kg/sec^2 (mass over time
> square).
>
> What is the correspondence between above from Hooke's law and that units of
> force constants in molecular dynamics simulations?

Force is also expressed as kJ/(mol nm) - see Chapter 2 of the Gromacs manual. 
Thus, since x is in units of nm (distance), then k has units of kJ/(mol nm^2).

-Justin

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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Re: [gmx-users] Force Constants and Unit Systems

[Justin A. Lemkul]

On 5/17/12 12:25 PM, Lara Bunte wrote:

Hello

I never had contact with such units. Could you please help me and explain me
how to transform following units:

1.) kcal / mol -->  kJ / (mol * nm^2)



One cannot convert between these units, since kcal/mol is an energy term, and
kJ/(mol nm^2) is a force constant.


2.) kcal / (mol * rad^2) -->  kJ / (mol * rad^2)



The transformation between kcal and kJ requires a simple multiplication.


I have additionally some question to that:  Both should be units of a force
constant. From Hooke's law F = -kx follows for me, that the unit of a force
constant is Newton N over distance m, in S.I. units  kg/sec^2 (mass over time
square).

What is the correspondence between above from Hooke's law and that units of
force constants in molecular dynamics simulations?


Force is also expressed as kJ/(mol nm) - see Chapter 2 of the Gromacs manual. 
Thus, since x is in units of nm (distance), then k has units of kJ/(mol nm^2).


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] charm in gromacs

[francesco oteri]

Dear gromacs users,
I am trying to port a set of charm parameter in gromacs.

I am using the script convert_charmm_to_gromacs.pl contained in the
file charmm_to_gromacs.tgz (
http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz).

Regarding dihedrals, the entry regarding the file says that pdb2gmx cannot

"generate multiple periodic dihedral functions such as CHARMM uses for some
dihedrals -
these must be converted to Ryckaert-Bellemans functions, i.e. expressed as
a cosine power expansion"

This assumption is no longer valid, is it?
As far as I know, infact, now gromacs support multiple periodic function
(funtion 9), is it?


Francesco
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Re: [gmx-users] Place water away from existing atoms

[Justin A. Lemkul]

On 5/17/12 11:50 AM, Steven Neumann wrote:

My tube is finite. I increased my box so the water could interact with all water
molecules. The same problem: My minim.mdp

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator= steep; Algorithm (steep = steepest descent minimization)
emtol= 10.0  ;
emstep= 0.001
nsteps= 5; Maximum number of (minimization) steps to perform
nstxout = 1
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long range 
forces
ns_type= grid; Method to determine neighbor list (simple, grid)
rlist= 1.4; Cut-off for making neighbor list (short range 
forces)
coulombtype= PME; Treatment of long range electrostatic interactions
rcoulomb= 1.4; Short-range electrostatic cut-off
rvdw= 1.4; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

Well... no clue...



Then the diagnostic tips I listed before still apply, as well as those listed on 
the webpage linked from what I posted earlier.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Force Constants and Unit Systems

[Lara Bunte]

Hello

I never had contact with such units. Could you please help me and explain me 
how to transform following units:
 
1.)
kcal / mol --> kJ / (mol * nm^2)

2.)
kcal / (mol * rad^2) --> kJ / (mol * rad^2)

I have additionally some question to that:  Both should be units of a force 
constant. From Hooke's law F = -kx follows for me, that the unit of a force 
constant is Newton N over distance m, in S.I. units  kg/sec^2 (mass over time 
square).

What is the correspondence between above from Hooke's law and that units of 
force constants in molecular dynamics simulations? 

Thanks for helping me
Greetings
Lara
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Re: [gmx-users] Two [ dihedrals ] sections in topology

[francesco oteri]

Hi

2012/5/17 Lara Bunte 

> Hi
>
> Just for correct understanding: In this "empty" [ dihedrals ] bock are 11
> lines without equilibrium angle and force constant, that looks like:
>
>
> [ dihedrals ]
> ;  aiajakal functc0c1
> c2c3c4c5
> 2 119 8 2
> 6 8 910 2
>
>
> Did this mean, that this are really physical dihedrals, that were given by
> pdb2gmx and the only reason that they are "empty" is, that they are not
> parametrized?
> Is this correct?
>
>
No, it means that defaukt values (i.e. listed in [ dihedraltypes ] section
)  will be applied


> Greetings
> Lara
>
>
>
>
>
>
>
> - Ursprüngliche Message -
> Von: Justin A. Lemkul 
> An: Lara Bunte ; Discussion list for GROMACS users <
> gmx-users@gromacs.org>
> CC:
> Gesendet: 17:02 Donnerstag, 17.Mai 2012
> Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology
>
>
>
> On 5/17/12 10:48 AM, Lara Bunte wrote:
> > Hi
> >
> > grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
> >
> > gives me errors like
> >
> > ERROR 1 [file topol.top, line 233]:
> >No default Improper Dih. types
> >
> > and so on. This line 233 is the starting of my empty [ dihedrals ]
> block. I erase it by hand out of my topology, so that only the correct [
> dihedrals ] out of the .rtp and ffbonded.itp file are in the topology.
> After this grompp works without error and even without any warning.
> >
> >
> > So the question how to force pdb2gmx to use only my [ dihedrals ] block
> is important for me, because I don't like to erase it always by hand out of
> the topol.top file.
> >
>
> This goes back to something that has been stated several times now, and
> was discussed the other day.  If pdb2gmx finds 4 atoms connected via bonds,
> it assigns a dihedral to it.  That's just physically real.  If your force
> field then doesn't have parameters for that particular interaction, you get
> the error shown above.  That doesn't mean you should go deleting things
> until grompp "works" because what will result will likely be senseless.
>
> If your "empty" (which is not really empty, as we've been saying)
> dihedrals are causing the problems, then you need to add parameters for
> them in ffbonded.itp or in the topology itself, not hack the topology apart.
>
> -Justin
>
> -- 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Cordiali saluti, Dr.Oteri Francesco
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Re: [gmx-users] Place water away from existing atoms

[Steven Neumann]

My tube is finite. I increased my box so the water could interact with all
water molecules. The same problem: My minim.mdp

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator= steep; Algorithm (steep = steepest descent minimization)
emtol= 10.0  ;
emstep= 0.001
nsteps= 5; Maximum number of (minimization) steps to perform
nstxout = 1
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long
range forces
ns_type= grid; Method to determine neighbor list (simple, grid)
rlist= 1.4; Cut-off for making neighbor list (short range
forces)
coulombtype= PME; Treatment of long range electrostatic
interactions
rcoulomb= 1.4; Short-range electrostatic cut-off
rvdw= 1.4; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

Well... no clue...



On Thu, May 17, 2012 at 4:16 PM, Steven Neumann wrote:

> Thank you. Is it possible that this is caused by the trapped molecules
> inside my tube? My tube ends are on the box edges so water cannot migrate
> outside the tube where are the other water molecules.
>
> Steven
>
>
> On Thu, May 17, 2012 at 3:59 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> On 5/17/12 10:38 AM, Steven Neumann wrote:
>>
>>> Well, I am still getting the same error when I try to do minimization:
>>> "water
>>> molecule on atom X cannot be settled" - these water molecules are not
>>> close to
>>> the Tube surface. If I will remove them the same error will occur but on
>>> the
>>> other atoms. If I specified only vdwradii for my Tube atoms why in the
>>> bulk of
>>> water there are some overlaps? Can you please help?
>>>
>>>
>> The problem is not necessarily with the water molecule, but is more often
>> indicative of some other instability in the system, such that forces are
>> transmitted to that poor unsuspecting water molecule and it blows up.
>>
>> http://www.gromacs.org/**Documentation/Errors#LINCS.**
>> 2fSETTLE.2fSHAKE_warnings
>>
>> It's hard to diagnose, so make sure you're EM step is very small and you
>> save configurations frequently in order to diagnose what's happening.  It
>> could be a problem with the .mdp file, topology, or perhaps some weird
>> water overlap, but if that's the case, then genbox didn't do it, something
>> else caused it.
>>
>> -Justin
>>
>>
>> --
>> ==**==
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>>
>> ==**==
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Searchbefore
>>  posting!
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>
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Re: [gmx-users] Place water away from existing atoms

[Justin A. Lemkul]

On 5/17/12 11:16 AM, Steven Neumann wrote:

Thank you. Is it possible that this is caused by the trapped molecules inside my
tube? My tube ends are on the box edges so water cannot migrate outside the tube
where are the other water molecules.



I take it that your tube is finite, not infinite?  I guess I'm confused at this 
point - there are water molecules inside the tube?  I thought the whole point 
was to not have water inside.


In any case, if your tube is finite with the ends at the box edges, you likely 
have clashes between tube atoms that cause the water to start kicking around. 
If you have a small number of molecules within the tube, then yes, they can 
become unstable in isolation.  This commonly occurs with voids in simulation boxes.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Two [ dihedrals ] sections in topology

[Lara Bunte]

Hi

Just for correct understanding: In this "empty" [ dihedrals ] bock are 11 lines 
without equilibrium angle and force constant, that looks like:


[ dihedrals ]
;  ai    aj    ak    al funct    c0    c1    
c2    c3    c4    c5
    2 1    19 8 2
    6 8 9    10 2


Did this mean, that this are really physical dihedrals, that were given by 
pdb2gmx and the only reason that they are "empty" is, that they are not 
parametrized? 
Is this correct?

Greetings
Lara







- Ursprüngliche Message -
Von: Justin A. Lemkul 
An: Lara Bunte ; Discussion list for GROMACS users 

CC: 
Gesendet: 17:02 Donnerstag, 17.Mai 2012
Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology



On 5/17/12 10:48 AM, Lara Bunte wrote:
> Hi
> 
> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
> 
> gives me errors like
> 
> ERROR 1 [file topol.top, line 233]:
>    No default Improper Dih. types
> 
> and so on. This line 233 is the starting of my empty [ dihedrals ] block. I 
> erase it by hand out of my topology, so that only the correct [ dihedrals ] 
> out of the .rtp and ffbonded.itp file are in the topology. After this grompp 
> works without error and even without any warning.
> 
> 
> So the question how to force pdb2gmx to use only my [ dihedrals ] block is 
> important for me, because I don't like to erase it always by hand out of the 
> topol.top file.
> 

This goes back to something that has been stated several times now, and was 
discussed the other day.  If pdb2gmx finds 4 atoms connected via bonds, it 
assigns a dihedral to it.  That's just physically real.  If your force field 
then doesn't have parameters for that particular interaction, you get the error 
shown above.  That doesn't mean you should go deleting things until grompp 
"works" because what will result will likely be senseless.

If your "empty" (which is not really empty, as we've been saying) dihedrals are 
causing the problems, then you need to add parameters for them in ffbonded.itp 
or in the topology itself, not hack the topology apart.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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Re: [gmx-users] Place water away from existing atoms

[Steven Neumann]

Thank you. Is it possible that this is caused by the trapped molecules
inside my tube? My tube ends are on the box edges so water cannot migrate
outside the tube where are the other water molecules.

Steven

On Thu, May 17, 2012 at 3:59 PM, Justin A. Lemkul  wrote:

>
>
> On 5/17/12 10:38 AM, Steven Neumann wrote:
>
>> Well, I am still getting the same error when I try to do minimization:
>> "water
>> molecule on atom X cannot be settled" - these water molecules are not
>> close to
>> the Tube surface. If I will remove them the same error will occur but on
>> the
>> other atoms. If I specified only vdwradii for my Tube atoms why in the
>> bulk of
>> water there are some overlaps? Can you please help?
>>
>>
> The problem is not necessarily with the water molecule, but is more often
> indicative of some other instability in the system, such that forces are
> transmitted to that poor unsuspecting water molecule and it blows up.
>
> http://www.gromacs.org/**Documentation/Errors#LINCS.**
> 2fSETTLE.2fSHAKE_warnings
>
> It's hard to diagnose, so make sure you're EM step is very small and you
> save configurations frequently in order to diagnose what's happening.  It
> could be a problem with the .mdp file, topology, or perhaps some weird
> water overlap, but if that's the case, then genbox didn't do it, something
> else caused it.
>
> -Justin
>
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
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> Can't post? Read 
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[gmx-users] Re: mixing Urey-Bradley and armonic in the same rtp file

[francesco oteri]

Dear gromacs users,
I think I solved the problem.
I converted armonic angle potentials in the  Urey-Bradley potentials using
0 as constant for the
1-3 bond potential.

Is it right in your opinion?

Francesco

2012/5/16 francesco oteri 

> Dear gromacs users,
>
> I am trying to port in gromacs the CHARMM36 all-atom carbohydrate force
> field.
>
> I downloaded the charmm files toppar_carb_apr12.tgz  from
> http://mackerell.umaryland.edu/CHARMM_ff_params.html
> and I converted  bonded and nonbonded parameters in gromacs format through
> the script convert_charmm_to_gromacs.pl.
>
> I have successfully generated the .top, using pdb2gmx, as well.
>
> But  when I run grompp, it complains with errors like:
>
> *No default Angle types *
> *
> *
> and
>
> *No default Improper Dih. types*
>
>
> Look at the attacched file for the complete output from grompp.
>
>
> Now I inspected the missed interaction and, at least for the angle part, I
> figured out the problem.
> In the original charm parametrization there are angles parametrized as
> armonic and other angles
> parametrized as Urey-Bradley.  Moreover, as far as I know, in the rtp file
> only one form can be used
> because of the [ bondedtypes ]  clause.
>
> So my question is: Is there any way to mix, in the same residue (and
> hopefully in the same .rtp file),
> angles parametrized in the armonic form and Urey-Bradley parametrized
> angles?
>
> Is a correct solution parametrizing everything as armonic angles and mimic
> the bond potential between
> atom 1 and 3 present Urey-Bradley as a bond with same strenght and force
> value?
>
>
> Francesco
>



-- 
Cordiali saluti, Dr.Oteri Francesco
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Re: [gmx-users] Two [ dihedrals ] sections in topology

[Justin A. Lemkul]

On 5/17/12 10:48 AM, Lara Bunte wrote:

Hi

grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr

gives me errors like

ERROR 1 [file topol.top, line 233]:
   No default Improper Dih. types

and so on. This line 233 is the starting of my empty [ dihedrals ] block. I 
erase it by hand out of my topology, so that only the correct [ dihedrals ] out 
of the .rtp and ffbonded.itp file are in the topology. After this grompp works 
without error and even without any warning.


So the question how to force pdb2gmx to use only my [ dihedrals ] block is 
important for me, because I don't like to erase it always by hand out of the 
topol.top file.



This goes back to something that has been stated several times now, and was 
discussed the other day.  If pdb2gmx finds 4 atoms connected via bonds, it 
assigns a dihedral to it.  That's just physically real.  If your force field 
then doesn't have parameters for that particular interaction, you get the error 
shown above.  That doesn't mean you should go deleting things until grompp 
"works" because what will result will likely be senseless.


If your "empty" (which is not really empty, as we've been saying) dihedrals are 
causing the problems, then you need to add parameters for them in ffbonded.itp 
or in the topology itself, not hack the topology apart.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Place water away from existing atoms

[Justin A. Lemkul]

On 5/17/12 10:38 AM, Steven Neumann wrote:

Well, I am still getting the same error when I try to do minimization: "water
molecule on atom X cannot be settled" - these water molecules are not close to
the Tube surface. If I will remove them the same error will occur but on the
other atoms. If I specified only vdwradii for my Tube atoms why in the bulk of
water there are some overlaps? Can you please help?



The problem is not necessarily with the water molecule, but is more often 
indicative of some other instability in the system, such that forces are 
transmitted to that poor unsuspecting water molecule and it blows up.


http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

It's hard to diagnose, so make sure you're EM step is very small and you save 
configurations frequently in order to diagnose what's happening.  It could be a 
problem with the .mdp file, topology, or perhaps some weird water overlap, but 
if that's the case, then genbox didn't do it, something else caused it.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Two [ dihedrals ] sections in topology

[Lara Bunte]

Hi

grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr

gives me errors like

ERROR 1 [file topol.top, line 233]:
  No default Improper Dih. types

and so on. This line 233 is the starting of my empty [ dihedrals ] block. I 
erase it by hand out of my topology, so that only the correct [ dihedrals ] out 
of the .rtp and ffbonded.itp file are in the topology. After this grompp works 
without error and even without any warning. 


So the question how to force pdb2gmx to use only my [ dihedrals ] block is 
important for me, because I don't like to erase it always by hand out of the 
topol.top file.

Greetings
Lara






- Ursprüngliche Message -
Von: Mark Abraham 
An: Discussion list for GROMACS users 
CC: 
Gesendet: 2:35 Mittwoch, 16.Mai 2012
Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology

On 16/05/2012 4:53 AM, Lara Bunte wrote:
> Hi
>
>> Is there some reason to believe you should not have dihedrals?  That doesn't
>> make much physical sense.
> I want and have dihedrals in my topology. I don't want an additional empty 
> dihedrals block in the topology. In my force field I gave impropers.

An empty block of dihedrals doesn't hurt, but you don't have one of 
these. A block of dihedrals lacking parameters gets those parameters 
looked up from ffbonded.itp. You likely can't have only improper 
dihedrals and expect any resemblance to the behaviour of the CHARMM27 
forcefield.

It sounds to me like you're trying to do something that might not be 
worth attempting, but this thread hasn't revealed your objective. 
There's no point moving deckchairs on the Titanic if there's icebergs 
all around.

Mark

>
> Greetings
>
>
>
>
>
>
>
> - Ursprüngliche Message -
> Von: Justin A. Lemkul
> An: Lara Bunte; Discussion list for GROMACS 
> users
> CC:
> Gesendet: 17:02 Dienstag, 15.Mai 2012
> Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology
>
>
>
> On 5/15/12 10:43 AM, Lara Bunte wrote:
>> Hi
>>
>> You wrote:
>>
>>> Two blocks of dihedrals are normal output for pdb2gmx - one for proper
>>> and one for improper dihedrals.
>>
>> Is there a way to force pdb2gmx that there is only my block with improper 
>> dihedrals in the topology?
>>
> Normally pdb2gmx will generate proper dihedrals based on bonded connectivity.
> Is there some reason to believe you should not have dihedrals?  That doesn't
> make much physical sense.
>
>> Could that be a problem in further calculations, i.e. energy minimization if 
>> there is this empty [ dihedrals ] block in the topology?
>>
> What you've been defining as "empty" is not necessarily so.  The fact that
> parameters are not explicitly printed is not inherently indicative of a 
> problem,
> since the parameters are looked up from ffbonded.itp and not necessarily
> recapitulated in the topology.  If you get fatal errors about missing
> parameters, that's a separate issue.
>
 [ bondedtypes ]
 ; bonds  angles  dihedrals  impropers
           1       1          5          5
>>> Those are angle, dihedral and improper function types that are abnormal
>>> for CHARMM27. Using these in your .rtp means that you are no longer
>>> using CHARMM27. It might be reasonable for you to do this, but you need
>>> to be absolutely sure why. Importing a topology from another force field
>>> is not an acceptable reason.
>> What would be the correct numbers in the [ bondedtypes ] for using CHARMM27 
>> force field?
>>
> Look in charmm27.ff/aminoacids.rtp.
>
> -Justin
>

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Re: [gmx-users] Place water away from existing atoms

[Steven Neumann]

Well, I am still getting the same error when I try to do minimization:
"water molecule on atom X cannot be settled" - these water molecules are
not close to the Tube surface. If I will remove them the same error will
occur but on the other atoms. If I specified only vdwradii for my Tube
atoms why in the bulk of water there are some overlaps? Can you please help?

Steven

On Thu, May 17, 2012 at 2:44 PM, Steven Neumann wrote:

>
>
> On Thu, May 17, 2012 at 2:30 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> On 5/17/12 9:24 AM, Steven Neumann wrote:
>>
>>>
>>>
>>> On Thu, May 17, 2012 at 2:06 PM, Justin A. Lemkul >> > wrote:
>>>
>>>
>>>
>>>On 5/17/12 9:00 AM, Steven Neumann wrote:
>>>
>>>
>>>
>>>On Thu, May 17, 2012 at 11:52 AM, Javier Cerezo >> >>
>>>
>>>
>>>wrote:
>>>
>>>genbox calculates overlaps based on vdW radii as included in
>>>vdwradii.dat in
>>>the topology folder. Increase the vdW radii of carbons to
>>> avoid water to
>>>closer that you want. Other possibilities are patiently
>>> removing
>>>undesired
>>>waters by hand after solvation or using a "ad-hoc" script.
>>>
>>>Javier
>>>
>>>
>>>Thank you Javier. Can you please explain what is ad-hoc script
>>> and where
>>>I can
>>>find it?
>>>
>>>
>>>The term "ad hoc" simply means something designed for a specific
>>> task, i.e.
>>>a script you would write yourself.
>>>
>>>The logic behind such a script is discussed in the following wiki
>>> page,
>>>though it is designed for membrane solvation and you would have to
>>> amend it
>>>considerably to suit your purpose.
>>>
>>>http://www.gromacs.org/__**Documentation/How-tos/__**
>>> Membrane_Simulations
>>>
>>>>> Membrane_Simulations
>>> >
>>>
>>>-Justin
>>>
>>>
>>>
>>> Thank you. Ok, I added the residues and atoms to vdwradii.dat with
>>> higher vdw
>>> radius as I created my own atoms belonging to the tube. Without
>>> vdwradii.dat
>>> containing atoms of my tube 10 000 water molecules were added (denity
>>> app 1000
>>> g/L). Using the vdwradii.dat app 6000 water molecules were added
>>> decreasing
>>> density of water obviosuly.
>>> My question: Are distances between water molecules will be affected or
>>> just
>>> between my Tube atoms (specified in vdwradii.dat) and water molecules as
>>> the
>>> number of water molecules decreased rapidly?
>>>
>>>
>> Changes to vdwradii.dat make the atoms seem larger, so that genbox
>> detects a clash when it tries to add a water molecule near the "larger"
>> atoms.  The end result is a void around the "larger" atoms such that your
>> density decreases. This strategy simply makes it less likely that there
>> will be a water molecule near a tube atom.  It may become impractical to
>> continually increase the radius/radii of your tube atom type(s) in such a
>> way that it will completely eliminate the addition of water inside, in
>> which case scripting or manual deletion is necessary.
>>
>> -Justin
>
>
> Thank you Justin. In my case each atoms is a representation of a residue.
> I do not want to have any water inside of my tube as well. Now as less
> atoms are inside I can easier remove them manually.
>
> Steven
>
>
>>
>>
>> --
>> ==**==
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>>
>> ==**==
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Searchbefore
>>  posting!
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>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists
>>
>
>
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Re: [gmx-users] grompp error - incorrect number of parameters

[Justin A. Lemkul]

On 5/17/12 9:47 AM, Lara Bunte wrote:

Hello


After


grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr


I got the error:

Incorrect number of parameters - found 2, expected 4 or 4 for U-B.


I thought that this could be an inconsistency be declaring the functions, but 
in my topology I have function 4 (for improper dihedrals):


Out of topol.top

[ dihedrals ]
;  aiajakal functc0c1c2 
   c3
 1 8 6 4 4180   100


And in my .rtp file in the CHARMM27 force field folder I have:

Out of .rtp file
; bonds  angles  dihedrals  impropers
  1   5  44


and in my ffbonded.itp file I have:
[ dihedraltypes ]
; i j   k   l   funcq0  cq
ON1 NN3A  CN1A   NN2U   4   180   100


So in alle three files, ffbonded.itp, topol.top and the .rtp parametrization 
file I have the function 4 for the improper dihedrals.


What is the problem?



The U-B function type is the Urey-Bradley angle potential.  It is unrelated to 
dihedrals.  See the [angletypes] directive of ffbonded.itp and the manual for 
the proper format of U-B parameters.


-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] grompp error - incorrect number of parameters

[Lara Bunte]

Hello 


After 


grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr


I got the error:

Incorrect number of parameters - found 2, expected 4 or 4 for U-B.


I thought that this could be an inconsistency be declaring the functions, but 
in my topology I have function 4 (for improper dihedrals):


Out of topol.top

[ dihedrals ]
;  ai    aj    ak    al funct    c0    c1    
c2    c3
    1 8 6 4 4    180   100


And in my .rtp file in the CHARMM27 force field folder I have:

Out of .rtp file
; bonds  angles  dihedrals  impropers
 1   5  4    4


and in my ffbonded.itp file I have:
[ dihedraltypes ]
; i j   k   l   func    q0  cq
ON1 NN3A  CN1A   NN2U   4   180   100


So in alle three files, ffbonded.itp, topol.top and the .rtp parametrization 
file I have the function 4 for the improper dihedrals. 


What is the problem?

Thanks for helping me
Greetings
Lara
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Re: [gmx-users] Place water away from existing atoms

[Steven Neumann]

On Thu, May 17, 2012 at 2:30 PM, Justin A. Lemkul  wrote:

>
>
> On 5/17/12 9:24 AM, Steven Neumann wrote:
>
>>
>>
>> On Thu, May 17, 2012 at 2:06 PM, Justin A. Lemkul > > wrote:
>>
>>
>>
>>On 5/17/12 9:00 AM, Steven Neumann wrote:
>>
>>
>>
>>On Thu, May 17, 2012 at 11:52 AM, Javier Cerezo > >>
>>
>>
>>wrote:
>>
>>genbox calculates overlaps based on vdW radii as included in
>>vdwradii.dat in
>>the topology folder. Increase the vdW radii of carbons to
>> avoid water to
>>closer that you want. Other possibilities are patiently
>> removing
>>undesired
>>waters by hand after solvation or using a "ad-hoc" script.
>>
>>Javier
>>
>>
>>Thank you Javier. Can you please explain what is ad-hoc script and
>> where
>>I can
>>find it?
>>
>>
>>The term "ad hoc" simply means something designed for a specific task,
>> i.e.
>>a script you would write yourself.
>>
>>The logic behind such a script is discussed in the following wiki page,
>>though it is designed for membrane solvation and you would have to
>> amend it
>>considerably to suit your purpose.
>>
>>http://www.gromacs.org/__**Documentation/How-tos/__**
>> Membrane_Simulations
>>
>>
>> 
>> >
>>
>>-Justin
>>
>>
>>
>> Thank you. Ok, I added the residues and atoms to vdwradii.dat with higher
>> vdw
>> radius as I created my own atoms belonging to the tube. Without
>> vdwradii.dat
>> containing atoms of my tube 10 000 water molecules were added (denity app
>> 1000
>> g/L). Using the vdwradii.dat app 6000 water molecules were added
>> decreasing
>> density of water obviosuly.
>> My question: Are distances between water molecules will be affected or
>> just
>> between my Tube atoms (specified in vdwradii.dat) and water molecules as
>> the
>> number of water molecules decreased rapidly?
>>
>>
> Changes to vdwradii.dat make the atoms seem larger, so that genbox detects
> a clash when it tries to add a water molecule near the "larger" atoms.  The
> end result is a void around the "larger" atoms such that your density
> decreases. This strategy simply makes it less likely that there will be a
> water molecule near a tube atom.  It may become impractical to continually
> increase the radius/radii of your tube atom type(s) in such a way that it
> will completely eliminate the addition of water inside, in which case
> scripting or manual deletion is necessary.
>
> -Justin


Thank you Justin. In my case each atoms is a representation of a residue. I
do not want to have any water inside of my tube as well. Now as less atoms
are inside I can easier remove them manually.

Steven


>
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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Re: [gmx-users] Place water away from existing atoms

[Justin A. Lemkul]

On 5/17/12 9:24 AM, Steven Neumann wrote:



On Thu, May 17, 2012 at 2:06 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



On 5/17/12 9:00 AM, Steven Neumann wrote:



On Thu, May 17, 2012 at 11:52 AM, Javier Cerezo mailto:j...@um.es> >>

wrote:

genbox calculates overlaps based on vdW radii as included in
vdwradii.dat in
the topology folder. Increase the vdW radii of carbons to avoid 
water to
closer that you want. Other possibilities are patiently removing
undesired
waters by hand after solvation or using a "ad-hoc" script.

Javier


Thank you Javier. Can you please explain what is ad-hoc script and where
I can
find it?


The term "ad hoc" simply means something designed for a specific task, i.e.
a script you would write yourself.

The logic behind such a script is discussed in the following wiki page,
though it is designed for membrane solvation and you would have to amend it
considerably to suit your purpose.

http://www.gromacs.org/__Documentation/How-tos/__Membrane_Simulations


-Justin



Thank you. Ok, I added the residues and atoms to vdwradii.dat with higher vdw
radius as I created my own atoms belonging to the tube. Without vdwradii.dat
containing atoms of my tube 10 000 water molecules were added (denity app 1000
g/L). Using the vdwradii.dat app 6000 water molecules were added decreasing
density of water obviosuly.
My question: Are distances between water molecules will be affected or just
between my Tube atoms (specified in vdwradii.dat) and water molecules as the
number of water molecules decreased rapidly?



Changes to vdwradii.dat make the atoms seem larger, so that genbox detects a 
clash when it tries to add a water molecule near the "larger" atoms.  The end 
result is a void around the "larger" atoms such that your density decreases. 
This strategy simply makes it less likely that there will be a water molecule 
near a tube atom.  It may become impractical to continually increase the 
radius/radii of your tube atom type(s) in such a way that it will completely 
eliminate the addition of water inside, in which case scripting or manual 
deletion is necessary.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Place water away from existing atoms

[Steven Neumann]

On Thu, May 17, 2012 at 2:06 PM, Justin A. Lemkul  wrote:

>
>
> On 5/17/12 9:00 AM, Steven Neumann wrote:
>
>>
>>
>> On Thu, May 17, 2012 at 11:52 AM, Javier Cerezo > j...@um.es>>
>>
>> wrote:
>>
>>genbox calculates overlaps based on vdW radii as included in
>> vdwradii.dat in
>>the topology folder. Increase the vdW radii of carbons to avoid water
>> to
>>closer that you want. Other possibilities are patiently removing
>> undesired
>>waters by hand after solvation or using a "ad-hoc" script.
>>
>>Javier
>>
>>
>> Thank you Javier. Can you please explain what is ad-hoc script and where
>> I can
>> find it?
>>
>>
> The term "ad hoc" simply means something designed for a specific task,
> i.e. a script you would write yourself.
>
> The logic behind such a script is discussed in the following wiki page,
> though it is designed for membrane solvation and you would have to amend it
> considerably to suit your purpose.
>
> http://www.gromacs.org/**Documentation/How-tos/**Membrane_Simulations
>
> -Justin
>


Thank you. Ok, I added the residues and atoms to vdwradii.dat with higher
vdw radius as I created my own atoms belonging to the tube. Without
vdwradii.dat containing atoms of my tube 10 000 water molecules were added
(denity app 1000 g/L). Using the vdwradii.dat app 6000 water molecules were
added decreasing density of water obviosuly.
My question: Are distances between water molecules will be affected or just
between my Tube atoms (specified in vdwradii.dat) and water molecules as
the number of water molecules decreased rapidly?

Steven


> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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> Support/Mailing_Lists/Searchbefore
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Re: [gmx-users] Place water away from existing atoms

[Justin A. Lemkul]

On 5/17/12 9:00 AM, Steven Neumann wrote:



On Thu, May 17, 2012 at 11:52 AM, Javier Cerezo mailto:j...@um.es>>
wrote:

genbox calculates overlaps based on vdW radii as included in vdwradii.dat in
the topology folder. Increase the vdW radii of carbons to avoid water to
closer that you want. Other possibilities are patiently removing undesired
waters by hand after solvation or using a "ad-hoc" script.

Javier


Thank you Javier. Can you please explain what is ad-hoc script and where I can
find it?



The term "ad hoc" simply means something designed for a specific task, i.e. a 
script you would write yourself.


The logic behind such a script is discussed in the following wiki page, though 
it is designed for membrane solvation and you would have to amend it 
considerably to suit your purpose.


http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Place water away from existing atoms

[Steven Neumann]

On Thu, May 17, 2012 at 11:52 AM, Javier Cerezo  wrote:

>  genbox calculates overlaps based on vdW radii as included in vdwradii.dat
> in the topology folder. Increase the vdW radii of carbons to avoid water to
> closer that you want. Other possibilities are patiently removing undesired
> waters by hand after solvation or using a "ad-hoc" script.
>
> Javier
>

Thank you Javier. Can you please explain what is ad-hoc script and where I
can find it?

Steven



>
> El 17/05/12 12:25, Steven Neumann escribió:
>
> Dear Gmx users,
>
> My system consists of a tube which is representated by atoms which are not
> connected via bonds.
> genbox somehow place water molecules overlapping my tube atoms resulting
> in bad contacts.
>
> Is there anyway to add water e.g. 4A away from existing index file of my
> tube?
>
> Please, help.
>
> Steven
>
>
>
> --
> Javier CEREZO BASTIDA
> PhD Student
> Physical Chemistry
> Universidad de Murcia
> Murcia (Spain)
> Tel: (+34)868887434
>
> --
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[gmx-users] Re: Pressure at constant volume

[Dr. Vitaly V. Chaban]

> Hello everyone,
>
> I am trying to estimate the thermodynamic expression, dP/dw at
> constant V and T, for my polymer-solvent system. Where P is the
Hello J. -

> pressure, w is the mass fraction, V volume and T temperature. I guess
> this task can not be done by MD, as for constant Volume, pressure is
> meaningless. Since what g_energy reports is not the actual pressure
> which corresponds to that fixed Volume. Am I correct?


I do not think you are correct here. My belief is that your pressure
is just very uncertain for a [relatively] small simulated system.


> (I mean building different binary systems with different mass
> fractions of w, and measuring average P (dP/dw) while keeping T and V
> constant does not produce meaningful results by MD)

I think you have just to increase sampling to get trustworthy
pressures for a range of your systems.

Vitaly Chaban

Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA
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Re: [gmx-users] Weird result of Umbrella Sampling

[Justin A. Lemkul]

On 5/17/12 7:45 AM, Du Jiangfeng (BIOCH) wrote:

Dear Justin and gmx friends,

Sorry to bother you again, but I am really not sure what went wrong with the
umbrella sampling simulation, which I followed Justin's tutorial. The energy
curve increased from zero to the maximum but suddenly went down (no plateau).
I think the reason probably is my small simulation box, and the periodic
boundary, by which the periodic element made an attraction force to the
pulled part, which made the energy curve went down. But I am not sure. What
are your ideas? Thank you very much, please don't ignore my request again.



You didn't get ignored.  You got two replies, one of which was mine:

http://lists.gromacs.org/pipermail/gmx-users/2012-May/071463.html

I posed several questions there that need to be answered before anyone can help 
you beyond guessing.


-Justin

--


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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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[gmx-users] Weird result of Umbrella Sampling

[Du Jiangfeng (BIOCH)]

Dear Justin and gmx friends,

Sorry to bother you again, but I am really not sure what went wrong with the 
umbrella sampling simulation, which I followed Justin's tutorial. The energy 
curve increased from zero to the maximum but suddenly went down (no plateau). I 
think the reason probably is my small simulation box, and the periodic 
boundary, by which the periodic element made an attraction force to the pulled 
part, which made the energy curve went down. But I am not sure. What are your 
ideas? Thank you very much, please don't ignore my request again.

Jiangfeng. 


Jiangfeng Du, PhD Student
Cardiovascular Research Institute Maastricht
Department of Biochemistry
P.O. Box 616
Mobile: +31-681741859
FAX: +31-43-3884159
6200 MD Maastricht
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Re: [gmx-users] Pressure at constant volume

[Juliette N.]

On 17 May 2012 05:10, Erik Marklund  wrote:
>
> 17 maj 2012 kl. 05.00 skrev Juliette N.:
>
> Hello everyone,
>
> I am trying to estimate the thermodynamic expression, dP/dw at
> constant V and T, for my polymer-solvent system. Where P is the
> pressure, w is the mass fraction, V volume and T temperature. I guess
> this task can not be done by MD, as for constant Volume, pressure is
> meaningless. Since what g_energy reports is not the actual pressure
> which corresponds to that fixed Volume. Am I correct?
>
>
> Hi, I lost you there. Why is pressure meaningless at constant volume?

Thanks. Because in NVT pressure is not controlled by thermostat. I
have seen this issue discussed many times on the list archive that in
NVT pressure values has no significance. I have seen this myself in
simulations too, when I fix the pressure by NPT, get the density
corresponding to that P. But when creating a box size of that density
and running NVT, the pressure that NVT produces is far away from what
it should be (Sometimes large negative values).

>
> Best,
>
> Erik
>
>
> (I mean building different binary systems with different mass
> fractions of w, and measuring average P (dP/dw) while keeping T and V
> constant does not produce meaningful results by MD)
>
> Please comment if this makes sense in MD or not.
>
> Thanks,
> J.
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>
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> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
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> er...@xray.bmc.uu.se
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>
>
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-- 
Thanks,
J. N.
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Re: [gmx-users] Regarding Gas Phase Torsional Energetics

[Javier Cerezo]

Yes, you can use dihedral restraints.

I performed some dihedral scans and what I did was to add an extra 
optimization step, after the one with restraints, with the atoms of the 
dihedral frozen (note that l-bfgs may not work in optimizations, I 
noticed that). This was to remove any side effect of restraint potential 
on the overall optimization. Actually, I iterated several 
restraint/frozen cycles.


Javier

El 17/05/12 13:14, Ravi Kumar Venkatraman escribió:

Dear All,
 How to get torsional energetics in gas phase? We can 
restraint the dihedral at different angle and calculate the energy at 
each angle or any other way is available.


Thank you in advance

*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.

+91-9686933963.*





--
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PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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Re: [gmx-users] distance restraints

[Justin A. Lemkul]

On 5/17/12 2:51 AM, Banafsheh Mehrazma wrote:

Dear all
I 'd like to do NOE distance restraints;  according to the chapter 4 of the 
manual;
I should specify a section for [ distance_restraints] :

[ distance_restraints ]
; ai  aj  type  index  type’  low  up1  up2  fac
10   161010.00.30.41.0
10   281110.00.30.41.0
10   461110.00.30.41.0
16   221210.00.30.42.5
16   341310.00.50.61.0
.
althought I've studied the manual, it is still unclear to me, that how is the
index column defined? what are the numbers (0,1,2,3) implying? what about the
low, up1,up2, fac columns?



All of this information is in the manual, section 4.3.4, under the heading 
"Using distance restraints."


With respect to indices:

"The type column should always be 1. As explained in sec. 4.3.4, multiple 
distances can contribute to a single NOE signal. In the topology this can be set 
using the index column. In our example, the restraints 10-28 and 10-46 both have 
index 1, therefore they are treated simultaneously."


With respect to low, up1, and up2:

"The columns low, up1, and up2 hold the values of r0, r1, and r2 from eqn. 
4.77."

For fac:

"In some cases it can be useful to have different force constants for some 
restraints; this is controlled by the column fac. The force constant in the 
parameter file is multiplied by the value in the column fac for each restraint."


-Justin

--


Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Regarding topology error.

[Justin A. Lemkul]

On 5/17/12 7:05 AM, Seera Suryanarayana wrote:

DEar all,
 While i am running gromacs software i am getting following
error.Let me know that error how to over come.

Fatal error:
Topology include file "ion.itp" not found



The name of the file is "ions.itp" not "ion.itp."

-Justin

--


Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Regarding topology error.

[Seera Suryanarayana]

DEar all,
While i am running gromacs software i am getting following
error.Let me know that error how to over come.

Fatal error:
Topology include file "ion.itp" not found

Suryanarayana Seera,
PhD student,
Hyderabad,
India.
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Re: [gmx-users] Place water away from existing atoms

[Javier Cerezo]

genbox calculates overlaps based on vdW radii as included in 
vdwradii.dat in the topology folder. Increase the vdW radii of carbons 
to avoid water to closer that you want. Other possibilities are 
patiently removing undesired waters by hand after solvation or using a 
"ad-hoc" script.


Javier

El 17/05/12 12:25, Steven Neumann escribió:

Dear Gmx users,

My system consists of a tube which is representated by atoms which are 
not connected via bonds.
genbox somehow place water molecules overlapping my tube atoms 
resulting in bad contacts.


Is there anyway to add water e.g. 4A away from existing index file of 
my tube?


Please, help.

Steven




--
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PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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Re: [gmx-users] parameterization of new metal ion

[Justin A. Lemkul]

On 5/17/12 5:12 AM, priya thiyagarajan wrote:

hello sir,

thanks for your kind reply..

while setting new parameters for metal ion NI2+

i edited my ions.itp by including the following lines..

[ moleculetype ]
; molname   nrexcl
NI  1

[ atoms ]
; idat type res nr  residu name at name  cg nr  charge   mass
1   NI2+1   NI  NI   1  257.9339


also edited .rtp file by including the following lines

[ NI ]
  [ atoms ]
NI  NI2+ 2.0 0
  [ bonds ]
  [ angles ]
;  aiajak   gromos type
  [ impropers ]
;  aiajakal   gromos type
  [ dihedrals ]
;  aiajakal   gromos type

but still i am getting the error


Fatal error:
Atomtype NI2+ not found


can you tell me how to solve this error..



Parameters for all atom types must be listed in ffnonbonded.itp, and 
atomtypes.atp if you're having pdb2gmx build the topology (which is also where 
the .rtp entry comes into play).


-Justin

--


Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Place water away from existing atoms

[Steven Neumann]

Dear Gmx users,

My system consists of a tube which is representated by atoms which are not
connected via bonds.
genbox somehow place water molecules overlapping my tube atoms resulting in
bad contacts.

Is there anyway to add water e.g. 4A away from existing index file of my
tube?

Please, help.

Steven
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[gmx-users] Software inconsistency error with GROMACS4.5.5

[Anirban]

Hi ALL,

I am running a protein+lipid+water+ions simulation using GROAMCS4.5.5
(compiled with intel compilers on RedHat OS). The EM, NVT and few thousand
steps of NPT ran fine beforw throwing up the following error:

---
Not all bonded interactions have been properly assigned to the domain
decomposition cells

A list of missing interactions:
Bond of  36787 missing  2
 U-B of  70200 missing  3
 Proper Dih. of 124764 missing  6
   LJ-14 of  98070 missing 12
  exclusions of 277654 missing  9

---
Program mdrun_mpi, VERSION 4.5.5
Source code file: domdec_top.c, line: 173

Software inconsistency error:
Some interactions seem to be assigned multiple times
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Why is this error coming? Is it a bug?
Any suggestion is welcome.

Thanks and regards,

Anirban
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Re: [gmx-users] Fwd: How to overcome syntax errors

[Erik Marklund]

17 maj 2012 kl. 09.01 skrev Seera Suryanarayana:

> 
> 
> -- Forwarded message --
> From: Seera Suryanarayana 
> Date: Thu, May 17, 2012 at 12:07 PM
> Subject: How to overcome syntax errors
> To: jalem...@vt.edu
> 
> 
> Dear Justin,
>  While i am running gromacs software i am getting the 
> following syntax errors.
> 
> 
> Fatal error:
> Syntax error - File 1AX8.top, line 7934
> Last line read:
> '## #include"ions.itp"'
> 
> 
> I am unable to create" _b4em.gro files".Please let me know at what 
> position i have to add ## #include"ions.itp" and Add NA ions or CL ions

So if you want to include ions.itp, then you should first of all have a space 
between the "include" and the filename. Secondly, you should not have three 
hashes, just one, without trailing spaces.

Erik

> 
> Is there any explanation why is this happening? I would aooreciate any help.I 
> am new in using MD and gromacs in particular. 
> 
> Suryanarayana Seera,
> PhD student,
> Hyderabad,
> India.
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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[gmx-users] parameterization of new metal ion

[priya thiyagarajan]

hello sir,

thanks for your kind reply..

while setting new parameters for metal ion NI2+

i edited my ions.itp by including the following lines..

[ moleculetype ]
; molname   nrexcl
NI  1

[ atoms ]
; idat type res nr  residu name at name  cg nr  charge   mass
1   NI2+1   NI  NI   1  257.9339


also edited .rtp file by including the following lines

[ NI ]
 [ atoms ]
   NI  NI2+ 2.0 0
 [ bonds ]
 [ angles ]
;  aiajak   gromos type
 [ impropers ]
;  aiajakal   gromos type
 [ dihedrals ]
;  aiajakal   gromos type

but still i am getting the error


Fatal error:
Atomtype NI2+ not found


can you tell me how to solve this error..

thanking you,
-- 
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Re: [gmx-users] How to over come syntax errors

[Erik Marklund]

17 maj 2012 kl. 08.40 skrev Seera Suryanarayana:

> Dear all Gromacs users,
> 
> While i am running gromacs software i am getting the following syntax errors.
> 
> 
> Fatal error:
> Syntax error - File 1AX8.top, line 7934
> Last line read:
> '## #include"ions.itp"'

Aren't semicolons used to make comments in top-files? I assume you intended to 
comment out the include statement.

Erik

> 
> 
> I am unable to create _b4em.gro files
> 
> Is there any explanation why is this happening? I would aooreciate any help.I 
> am new in using MD and gromacs in particular.
> 
> Suryanarayana Seera,
> PhD student,
> Hyderabad,
> India.
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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Re: [gmx-users] Pressure at constant volume

[Erik Marklund]

17 maj 2012 kl. 05.00 skrev Juliette N.:

> Hello everyone,
> 
> I am trying to estimate the thermodynamic expression, dP/dw at
> constant V and T, for my polymer-solvent system. Where P is the
> pressure, w is the mass fraction, V volume and T temperature. I guess
> this task can not be done by MD, as for constant Volume, pressure is
> meaningless. Since what g_energy reports is not the actual pressure
> which corresponds to that fixed Volume. Am I correct?

Hi, I lost you there. Why is pressure meaningless at constant volume?

Best,

Erik

> 
> (I mean building different binary systems with different mass
> fractions of w, and measuring average P (dP/dw) while keeping T and V
> constant does not produce meaningful results by MD)
> 
> Please comment if this makes sense in MD or not.
> 
> Thanks,
> J.
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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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Re: [gmx-users] What is the autocorrelation time

[Erik Marklund]

16 maj 2012 kl. 23.39 skrev Christopher Neale:

> Thank you Stephane.
> 
> Unfortunately, neither of those links contains the information that I am 
> seeking. Those links contain some example plots of autocorrelation functions 
> including a discussion of time-spans over which the example time-series is 
> autocorrelated and when it is not, but neither link defines the (exponential 
> or integral) autocorrelation time except to show a plot and indicate when it 
> is non-zero and when it fluctuates about zero. 
> 
> For example, I already know that the autocorrelation time describes the 
> exponential decay of the correlation and that two values drawn from the same 
> simulation are statistically independent if they are separated by a 
> sufficient number of (accurate) autocorrelation times, but this information 
> is not exactly a definition of the autocorrelation time.
> 
> I am hoping to find a definition of the autocorrelation time in terms of the 
> probability of drawing uncorrelated samples, although any complete definition 
> will do.

Aren't you looking for an interpretation rather than a definition? And will 
this not depend on the nature of the data?

Best,

Erik

> 
> If anybody else has the time, I would appreciate it.
> 
> Thank you,
> Chris.
> 
> -- original message --
> 
> Probably these links give you simple and clear response for your question 
> http://idlastro.gsfc.nasa.gov/idl_html_help/Time-Series_Analysis.html and 
> http://www.statsoft.com/textbook/time-series-analysis/ HTH Stephane
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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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[gmx-users] Water molecule cannot be settled

[Steven Neumann]

Dear Gmx Users,

My system consists of a tube which is representated by atoms which are not
connected via bonds. The terminals of the tube are on the edge of the box.
I try to run minimization and get an error of many "water molecule cannot
be settled". I observed EM with nstxout = 1 and using VMD I observed that
mentioned water atoms collide with NA ions. These water molecules are not
trapped inside of my tube but outside. Why gromacs put water molecules like
this and by replacement of ions these collisions appear? Do you have any
solution for this?

Another thing: How can I select all the atoms inside my tube? I know
g_select but no clue how to define criteria.

Thank you,

Steven
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[gmx-users] Fwd: How to overcome syntax errors

[Seera Suryanarayana]

-- Forwarded message --
From: Seera Suryanarayana 
Date: Thu, May 17, 2012 at 12:07 PM
Subject: How to overcome syntax errors
To: jalem...@vt.edu


Dear Justin,
 While i am running gromacs software i am getting the
following syntax errors.


Fatal error:
Syntax error - File 1AX8.top, line 7934
Last line read:
'## #include"ions.itp"'


I am unable to create" _b4em.gro files".Please let me know at what
position i have to add ## #include"ions.itp" and Add NA ions or CL ions

Is there any explanation why is this happening? I would aooreciate any
help.I am new in using MD and gromacs in particular.

Suryanarayana Seera,
PhD student,
Hyderabad,
India.
-- 
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