date:20130612

Whether it would be that easy i will find it. I specified my own potential
(not LJ) - so how come I should choose option 1 or 2 in nbfunct? I changed
h(x) in my table 6th column.


On Wed, Jun 12, 2013 at 1:18 AM, Justin Lemkul  wrote:

>
>
> On 6/11/13 4:12 PM, Steven Neumann wrote:
>
>> Dear Gromacs Users,
>>
>> I got really confused: In manual [defualts ]:
>>
>> "nbfunc is the non-bonded function type. Use 1 (Lennard-Jones) or 2
>> (Buckingham)"
>>
>> I want to use mdrun -table table.xvg with my own potential, which one I
>> should choose?
>>
>> "gen-pairs - is for pair generation. The default is ‘no’, i.e. get 1-4
>> parameters from the pairtypes list. When parameters are not present in the
>> list, stop with a fatal error. Setting‘yes’ generates 1-4 parameters that
>> are not present in the pair list from normal Lennard-Jones parameters
>> using
>> fudgeLJ"
>>
>> I want to have all intramolecular atoms (within my chain) interacting (no
>> exclusions) with each other from [ atomtypes ] in ffnonbonded.itp
>> Does it mean "yes" with nrexcl =1 in my topology?
>>
>> And sth I also got confused:
>>
>> [ pairtypes ] are only 1-4 parameters or here I can specify parameters for
>> all atoms within my molecule? So [ atomtypes ] in ffnonbonded.itp also
>> correspond to intra molecular interactions?
>>
>>
> These topics are discussed frequently.  Please search the archive; surely
> you will find relevant topics.
>
> -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] Tutor directory in gromacs 4.6

2013-06-12 Thread colinbannister

Hope I'm not missing something obvious here - but I can't find the
'share/tutor' directory in my Gromacs 4.6 installation.  Should it be there
?

thanks,

Colin




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[gmx-users] dssp works fine, but do_dssp gives fatal error

Dear all,

I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
I am trying to use it for do_dssp command but get the following error each
time:

"Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 >
/dev/null 2> /dev/null
"

Is there any way to rectify it?

Thanks.
Nikunj
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Re: [gmx-users] Tutor directory in gromacs 4.6

2013-06-12 Thread Chandan Choudhury

There are no such directory.

Chandan


--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Wed, Jun 12, 2013 at 1:56 PM, colinbannister <
colin.bannis...@nottingham.ac.uk> wrote:

> Hope I'm not missing something obvious here - but I can't find the
> 'share/tutor' directory in my Gromacs 4.6 installation.  Should it be there
> ?
>
> thanks,
>
> Colin
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Tutor-directory-in-gromacs-4-6-tp5009078.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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Re: [gmx-users] dssp works fine, but do_dssp gives fatal error

Hi,

Search the mailing list. This problem and its solution has been repeatedly 
discussed.

Erik

On 12 Jun 2013, at 10:31, Nikunj Maheshwari  wrote:

> Dear all,
> 
> I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
> I am trying to use it for do_dssp command but get the following error each
> time:
> 
> "Fatal error:
> Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 >
> /dev/null 2> /dev/null
> "
> 
> Is there any way to rectify it?
> 
> Thanks.
> Nikunj
> -- 
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RE: [gmx-users] Tutor directory in gromacs 4.6

2013-06-12 Thread Colin Bannister

Chandan,

I was looking at :

http://manual.gromacs.org/online/getting_started.html#setup

Which mentions these files.  Is this wrong ?

thanks,

Colin

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Chandan Choudhury
Sent: 12 June 2013 09:32
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Tutor directory in gromacs 4.6

There are no such directory.

Chandan


--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Wed, Jun 12, 2013 at 1:56 PM, colinbannister < 
colin.bannis...@nottingham.ac.uk> wrote:

> Hope I'm not missing something obvious here - but I can't find the 
> 'share/tutor' directory in my Gromacs 4.6 installation.  Should it be 
> there ?
>
> thanks,
>
> Colin
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Tutor-directory-in-gromacs-4-6-tp500
> 9078.html Sent from the GROMACS Users Forum mailing list archive at 
> Nabble.com.
> --
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Re: [gmx-users] dssp works fine, but do_dssp gives fatal error

Yes I did searched. But for most people, there were issues regarding the
path or wrong DSSP.
DSSP runs for me, but do_dssp does not.


On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund  wrote:

> Hi,
>
> Search the mailing list. This problem and its solution has been repeatedly
> discussed.
>
> Erik
>
> On 12 Jun 2013, at 10:31, Nikunj Maheshwari 
> wrote:
>
> > Dear all,
> >
> > I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
> > I am trying to use it for do_dssp command but get the following error
> each
> > time:
> >
> > "Fatal error:
> > Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 >
> > /dev/null 2> /dev/null
> > "
> >
> > Is there any way to rectify it?
> >
> > Thanks.
> > Nikunj
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
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[gmx-users] Issues with energy when running in the microcanonical ensemble

2013-06-12 Thread C.M.Sampson

Dear all,

I'm using Gromacs 4.5.5 with the amber ff99SB forcefield to run NVE
simulations on ethane in 725 TIP3P water molecules.  I used antechamber
to parametrise my ethane.

I have 2 issues;

Firstly the energy conservation of my simulations seems to get worse as
I lower my timestep, here is an example .mdp file that I'm using:


integrator  = md-vv
gen_vel = no
nsteps  = 100
dt  = 0.001
nstlist = 10
rlist   = 1.3
coulombtype = pme
rcoulomb= 1.0
vdw-type= Shift
rvdw= 1.0
tcoupl  = no
pcoupl  = no
nstenergy   = 100

I found a link describing that it could be an issue with the precision
and that Gromacs can be installed with double precision:

http://www.gromacs.org/Documentation/Terminology/Conserving_Energy

but is this the only way to ensure energy conservation?

My second issue is with the calculation of the kinetic energy, I have
2183 atoms in my simulation box which means the kinetic energy should be
(roughly)

0.5 * 3*2183-3(degrees of freedom) * 0.001987204118(kB) * 300(T) *
4.184(conversion from kcal/mol to kJ/mol) = 8163.97

however, when I look in my simulation the kinetic energy Gromacs outputs
is 5498.20 

   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
   Bond  Angle Ryckaert-Bell.  LJ-14 Coulomb-14
5.95743e+001.96046e+014.71247e-015.73520e-013.92661e+00
LJ (SR)   Coulomb (SR)   Coul. recip.  PotentialKinetic En.
5.12842e+03   -3.20604e+04   -2.67111e+03   -2.95726e+045.49820e+03
Total EnergyTemperature Pressure (bar)
   -2.40744e+043.02575e+02   -1.82251e+03

By running in NVE I'm not using a thermostat and can't find any reason
in the manual to scale the kinetic energy.  Is there an a reason I'm
missing as to why my kinetic energy seems lower than it should be?

Best Wishes

Chris







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[gmx-users] Nonbonded parameters

Dear Gmx Users,

Please, correct me if I am wrong. In ffnonbonded.itp

[ atomtypes ] - these are nonbonded parameters between atoms of the same
type
[ nonbond_params ] these are nonbonded parameters between atoms of
different type
[ pairtypes ] - 1-4 interactions

If that is correct why amber force filed has only [atomtypes] column? How
nonbonded parameters are calculated between atoms of a different type?
The same with charmm - only [atomtypes ] and [pairtypes ] are provided.
Would you please explain?

Steven
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Re: [gmx-users] Re: distance_restraints




On 6/12/13 12:10 AM, maggin wrote:

Hi, Justin,

You are right, I should first fix the bad geometry.

I check 1dx0.pdb, and the problematic areas are:
atom1 atom2
   1  N1+  (GLY124   N) 4 H  (GLY124  HT3)
181  C  (PRO137  CD)182 H  (PRO137  HD1)
262  H  (PHE141  HD1)  263 C  (PHE141  CE2)
296 O1-(ASP144  OD2)  297 C  (ASP144  C)
685 O   (PRO165  O)  688 C  (VAL166 CA)

for these atoms bonds that rotated more than 30 degrees


1dx0.pdb is get from NMR.

So, for the initial structure , is there anyways to solve these LINCS
WARNING ?



What does visual inspection tell you about these areas: (1) from the NMR 
structure and (2) after steep minimization?


-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] Tutor directory in gromacs 4.6




On 6/12/13 4:52 AM, Colin Bannister wrote:

Chandan,

I was looking at :

http://manual.gromacs.org/online/getting_started.html#setup

Which mentions these files.  Is this wrong ?



Yes, it is.  Several pages in the online manual are outdated, and share/tutor 
was removed some time ago because it was agreed that these examples were less 
than useful.  Refer to http://www.gromacs.org/Documentation/Tutorials for far 
more detailed tutorials.


-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] Nonbonded parameters




On 6/12/13 5:30 AM, Steven Neumann wrote:

Dear Gmx Users,

Please, correct me if I am wrong. In ffnonbonded.itp

[ atomtypes ] - these are nonbonded parameters between atoms of the same
type


No, these are the nonbonded parameters that are used when applying combination 
rules between any atoms.



[ nonbond_params ] these are nonbonded parameters between atoms of
different type


No, these override combination rules.


[ pairtypes ] - 1-4 interactions

If that is correct why amber force filed has only [atomtypes] column? How
nonbonded parameters are calculated between atoms of a different type?
The same with charmm - only [atomtypes ] and [pairtypes ] are provided.
Would you please explain?



Gromos force fields, for instance, have complex ways of generating nonbonded 
interactions that are not always the same for a given atomtype.  Other force 
fields just use straight combination rules and thus never need [nonbond_params].


-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] Nonbonded parameters

Thank you. That means that e.g. when two LJ atoms of a different type
approaching each other the non bonded LJ potential energy is a sum of two
potentials of those atoms?


On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul  wrote:

>
>
> On 6/12/13 5:30 AM, Steven Neumann wrote:
>
>> Dear Gmx Users,
>>
>> Please, correct me if I am wrong. In ffnonbonded.itp
>>
>> [ atomtypes ] - these are nonbonded parameters between atoms of the same
>> type
>>
>
> No, these are the nonbonded parameters that are used when applying
> combination rules between any atoms.
>
>
>  [ nonbond_params ] these are nonbonded parameters between atoms of
>> different type
>>
>
> No, these override combination rules.
>
>
>  [ pairtypes ] - 1-4 interactions
>>
>> If that is correct why amber force filed has only [atomtypes] column? How
>> nonbonded parameters are calculated between atoms of a different type?
>> The same with charmm - only [atomtypes ] and [pairtypes ] are provided.
>> Would you please explain?
>>
>>
> Gromos force fields, for instance, have complex ways of generating
> nonbonded interactions that are not always the same for a given atomtype.
>  Other force fields just use straight combination rules and thus never need
> [nonbond_params].
>
> -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] Nonbonded parameters




On 6/12/13 6:00 AM, Steven Neumann wrote:

Thank you. That means that e.g. when two LJ atoms of a different type
approaching each other the non bonded LJ potential energy is a sum of two
potentials of those atoms?



No, please refer to the Gromacs manual for discussion on "combination rules" and 
how they fit into the Lennard-Jones equation.


-Justin



On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul  wrote:




On 6/12/13 5:30 AM, Steven Neumann wrote:


Dear Gmx Users,

Please, correct me if I am wrong. In ffnonbonded.itp

[ atomtypes ] - these are nonbonded parameters between atoms of the same
type



No, these are the nonbonded parameters that are used when applying
combination rules between any atoms.


  [ nonbond_params ] these are nonbonded parameters between atoms of

different type



No, these override combination rules.


  [ pairtypes ] - 1-4 interactions


If that is correct why amber force filed has only [atomtypes] column? How
nonbonded parameters are calculated between atoms of a different type?
The same with charmm - only [atomtypes ] and [pairtypes ] are provided.
Would you please explain?



Gromos force fields, for instance, have complex ways of generating
nonbonded interactions that are not always the same for a given atomtype.
  Other force fields just use straight combination rules and thus never need
[nonbond_params].

-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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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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Fw: Aw: [gmx-users] Enthalpy Confusion

2013-06-12 Thread lloyd riggs

I appologise with the below, I got entropy and enthalpy confused for a mement. Funny.

Stephan

Gesendet: Dienstag, 11. Juni 2013 um 23:54 Uhr
Von: "lloyd riggs"
An: "Discussion list for GROMACS users"
Betreff: Aw: [gmx-users] Enthalpy Confusion

If you only want the total for the system or a delta for an entire run, indexed group there of, covarience (covar/aneig) does a good job. I found neither actually fit, but the covarience does, or if you do it by hand using only LJ parmeters for the indexed sets, however I was using proteins, so for the fluid system ?, but it took some publication look ups that were quite old. (well not that old 1980's)

Stephan

Gesendet: Dienstag, 11. Juni 2013 um 20:09 Uhr
Von: "Jeffery Perkins"
An: gmx-users@gromacs.org
Betreff: [gmx-users] Enthalpy Confusion

This may just be me not understanding what I'm looking at, but I'm trying to
get the Enthalpy of a simple test system of LJ fluid, running version 4.5.4
initially I've tried using the enthalpy option in g_energy but I noticed
that if i compare that value to H=U+pV using either the average or the
instantaneous values from g_energy switched over to SI so that there is no
issue there, the results are different (manual calculation is around 2x the
g_energy result).

So the question is, what am I overlooking in the analysis of the data i
have?

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Re: [gmx-users] Nonbonded parameters

On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul  wrote:

>
>
> On 6/12/13 6:00 AM, Steven Neumann wrote:
>
>> Thank you. That means that e.g. when two LJ atoms of a different type
>> approaching each other the non bonded LJ potential energy is a sum of two
>> potentials of those atoms?
>>
>>
> No, please refer to the Gromacs manual for discussion on "combination
> rules" and how they fit into the Lennard-Jones equation.
>
> -Justin
>

I read it.
I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that
means that when you provide in [atomtypes] in ffnonbonded your C and A
values each atom has a specific LJ potential shape. Right?
So two of them approaching each other in my system will have have the sum
of it.

Steven



>
>
>> On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 6/12/13 5:30 AM, Steven Neumann wrote:
>>>
>>>  Dear Gmx Users,

 Please, correct me if I am wrong. In ffnonbonded.itp

 [ atomtypes ] - these are nonbonded parameters between atoms of the same
 type


>>> No, these are the nonbonded parameters that are used when applying
>>> combination rules between any atoms.
>>>
>>>
>>>   [ nonbond_params ] these are nonbonded parameters between atoms of
>>>
 different type


>>> No, these override combination rules.
>>>
>>>
>>>   [ pairtypes ] - 1-4 interactions
>>>

 If that is correct why amber force filed has only [atomtypes] column?
 How
 nonbonded parameters are calculated between atoms of a different type?
 The same with charmm - only [atomtypes ] and [pairtypes ] are provided.
 Would you please explain?


  Gromos force fields, for instance, have complex ways of generating
>>> nonbonded interactions that are not always the same for a given atomtype.
>>>   Other force fields just use straight combination rules and thus never
>>> need
>>> [nonbond_params].
>>>
>>> -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
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
>>> ====
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
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>>> >
>>>
>>>
> --
> ==**==
>
> 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] dssp works fine, but do_dssp gives fatal error

Right. And what is its location?
On Jun 12, 2013 11:17 AM, "Nikunj Maheshwari" 
wrote:

> Yes I did searched. But for most people, there were issues regarding the
> path or wrong DSSP.
> DSSP runs for me, but do_dssp does not.
>
>
> On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund 
> wrote:
>
> > Hi,
> >
> > Search the mailing list. This problem and its solution has been
> repeatedly
> > discussed.
> >
> > Erik
> >
> > On 12 Jun 2013, at 10:31, Nikunj Maheshwari 
> > wrote:
> >
> > > Dear all,
> > >
> > > I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
> > > I am trying to use it for do_dssp command but get the following error
> > each
> > > time:
> > >
> > > "Fatal error:
> > > Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 >
> > > /dev/null 2> /dev/null
> > > "
> > >
> > > Is there any way to rectify it?
> > >
> > > Thanks.
> > > Nikunj
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] [ defaults ] and nonbonded

You've got a test case that shows your tables do what you think they do,
right? I would vary this setting and expect to see no effect.

Mark
On Jun 12, 2013 10:03 AM, "Steven Neumann"  wrote:

> Whether it would be that easy i will find it. I specified my own potential
> (not LJ) - so how come I should choose option 1 or 2 in nbfunct? I changed
> h(x) in my table 6th column.
>
>
> On Wed, Jun 12, 2013 at 1:18 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 6/11/13 4:12 PM, Steven Neumann wrote:
> >
> >> Dear Gromacs Users,
> >>
> >> I got really confused: In manual [defualts ]:
> >>
> >> "nbfunc is the non-bonded function type. Use 1 (Lennard-Jones) or 2
> >> (Buckingham)"
> >>
> >> I want to use mdrun -table table.xvg with my own potential, which one I
> >> should choose?
> >>
> >> "gen-pairs - is for pair generation. The default is ‘no’, i.e. get 1-4
> >> parameters from the pairtypes list. When parameters are not present in
> the
> >> list, stop with a fatal error. Setting‘yes’ generates 1-4 parameters
> that
> >> are not present in the pair list from normal Lennard-Jones parameters
> >> using
> >> fudgeLJ"
> >>
> >> I want to have all intramolecular atoms (within my chain) interacting
> (no
> >> exclusions) with each other from [ atomtypes ] in ffnonbonded.itp
> >> Does it mean "yes" with nrexcl =1 in my topology?
> >>
> >> And sth I also got confused:
> >>
> >> [ pairtypes ] are only 1-4 parameters or here I can specify parameters
> for
> >> all atoms within my molecule? So [ atomtypes ] in ffnonbonded.itp also
> >> correspond to intra molecular interactions?
> >>
> >>
> > These topics are discussed frequently.  Please search the archive; surely
> > you will find relevant topics.
> >
> > -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<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >
> > ==**==
> > --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users>
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Re: [gmx-users] dssp works fine, but do_dssp gives fatal error

The location of dssp is /usr/local/bin/dssp


On Wed, Jun 12, 2013 at 3:43 PM, Mark Abraham wrote:

> Right. And what is its location?
> On Jun 12, 2013 11:17 AM, "Nikunj Maheshwari" 
> wrote:
>
> > Yes I did searched. But for most people, there were issues regarding the
> > path or wrong DSSP.
> > DSSP runs for me, but do_dssp does not.
> >
> >
> > On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund 
> > wrote:
> >
> > > Hi,
> > >
> > > Search the mailing list. This problem and its solution has been
> > repeatedly
> > > discussed.
> > >
> > > Erik
> > >
> > > On 12 Jun 2013, at 10:31, Nikunj Maheshwari 
> > > wrote:
> > >
> > > > Dear all,
> > > >
> > > > I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
> > > > I am trying to use it for do_dssp command but get the following error
> > > each
> > > > time:
> > > >
> > > > "Fatal error:
> > > > Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68
> >
> > > > /dev/null 2> /dev/null
> > > > "
> > > >
> > > > Is there any way to rectify it?
> > > >
> > > > Thanks.
> > > > Nikunj
> > > > --
> > > > gmx-users mailing listgmx-users@gromacs.org
> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > > * Please search the archive at
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> > >
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Re: [gmx-users] Nonbonded parameters

I got it. However,

I have 60  atoms in my chain all with given C6 and C12 with a combination
rule 1. When running grompp:

Generated 1830 of the 1830 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 1830 of the 1830 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_X'
Analysing residue names:
There are: 1Protein residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 118.00
This run will generate roughly 2 Mb of data

when changing nrexcl in my topology to 0:

Generated 1830 of the 1830 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 1830 of the 1830 1-4 parameter combinations
Excluding 0 bonded neighbours molecule type 'Protein_chain_X'
Analysing residue names:
There are: 1Protein residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 118.00
This run will generate roughly 2 Mb of data

So if I exclude 1-3 interactions I have the same number of nonbonded
parameters as well as 1-4 interactions. Can someone explain me this please?

On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann wrote:

>
>
>
> On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul  wrote:
>
>>
>>
>> On 6/12/13 6:00 AM, Steven Neumann wrote:
>>
>>> Thank you. That means that e.g. when two LJ atoms of a different type
>>> approaching each other the non bonded LJ potential energy is a sum of two
>>> potentials of those atoms?
>>>
>>>
>> No, please refer to the Gromacs manual for discussion on "combination
>> rules" and how they fit into the Lennard-Jones equation.
>>
>> -Justin
>>
>
> I read it.
> I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that
> means that when you provide in [atomtypes] in ffnonbonded your C and A
> values each atom has a specific LJ potential shape. Right?
> So two of them approaching each other in my system will have have the sum
> of it.
>
> Steven
>
>
>
>>
>>
>>> On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul  wrote:
>>>
>>>

 On 6/12/13 5:30 AM, Steven Neumann wrote:

  Dear Gmx Users,
>
> Please, correct me if I am wrong. In ffnonbonded.itp
>
> [ atomtypes ] - these are nonbonded parameters between atoms of the
> same
> type
>
>
 No, these are the nonbonded parameters that are used when applying
 combination rules between any atoms.

   [ nonbond_params ] these are nonbonded parameters between atoms of

> different type
>
>
 No, these override combination rules.

   [ pairtypes ] - 1-4 interactions

>
> If that is correct why amber force filed has only [atomtypes] column?
> How
> nonbonded parameters are calculated between atoms of a different type?
> The same with charmm - only [atomtypes ] and [pairtypes ] are provided.
> Would you please explain?
>
>
>  Gromos force fields, for instance, have complex ways of generating
 nonbonded interactions that are not always the same for a given
 atomtype.
   Other force fields just use straight combination rules and thus never
 need
 [nonbond_params].

 -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
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
 >

 ====

 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 http://lists.gromacs.org/mailman/listinfo/gmx-users>
 >
 * Please search the archive at http://www.gromacs.org/**
 Support/Mailing_Lists/Search>>> Mailing_Lists/Search>before
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 http://www.gromacs.org/Support/Mailing_Lists

 >

>> --
>> ==**==
>>
>> 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-user

Re: [gmx-users] dssp works fine, but do_dssp gives fatal error

Search again. The syntax for invoking dssp changed at some point and it took a 
while before do_dssp adapted to that. If your do_dssp is lacking the -ver 
option then I'm quite confident that it uses the old syntax, which doesn't work 
with the newer versions (v. 2.0+ I think) of dssp.

Erik
 
On 12 Jun 2013, at 11:17, Nikunj Maheshwari  wrote:

> Yes I did searched. But for most people, there were issues regarding the
> path or wrong DSSP.
> DSSP runs for me, but do_dssp does not.
> 
> 
> On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund  wrote:
> 
>> Hi,
>> 
>> Search the mailing list. This problem and its solution has been repeatedly
>> discussed.
>> 
>> Erik
>> 
>> On 12 Jun 2013, at 10:31, Nikunj Maheshwari 
>> wrote:
>> 
>>> Dear all,
>>> 
>>> I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
>>> I am trying to use it for do_dssp command but get the following error
>> each
>>> time:
>>> 
>>> "Fatal error:
>>> Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 >
>>> /dev/null 2> /dev/null
>>> "
>>> 
>>> Is there any way to rectify it?
>>> 
>>> Thanks.
>>> Nikunj
>>> --
>>> 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
>> 
>> --
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Re: [gmx-users] dssp works fine, but do_dssp gives fatal error

Yes I checked. do_dssp has no -ver option.
I also found out this link

https://gerrit.gromacs.org/#/c/687/

but dont know how to install/use it.

Or maybe I can install DsspOld and see?



On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund  wrote:

> Search again. The syntax for invoking dssp changed at some point and it
> took a while before do_dssp adapted to that. If your do_dssp is lacking the
> -ver option then I'm quite confident that it uses the old syntax, which
> doesn't work with the newer versions (v. 2.0+ I think) of dssp.
>
> Erik
>
> On 12 Jun 2013, at 11:17, Nikunj Maheshwari 
> wrote:
>
> > Yes I did searched. But for most people, there were issues regarding the
> > path or wrong DSSP.
> > DSSP runs for me, but do_dssp does not.
> >
> >
> > On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund 
> wrote:
> >
> >> Hi,
> >>
> >> Search the mailing list. This problem and its solution has been
> repeatedly
> >> discussed.
> >>
> >> Erik
> >>
> >> On 12 Jun 2013, at 10:31, Nikunj Maheshwari 
> >> wrote:
> >>
> >>> Dear all,
> >>>
> >>> I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
> >>> I am trying to use it for do_dssp command but get the following error
> >> each
> >>> time:
> >>>
> >>> "Fatal error:
> >>> Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 >
> >>> /dev/null 2> /dev/null
> >>> "
> >>>
> >>> Is there any way to rectify it?
> >>>
> >>> Thanks.
> >>> Nikunj
> >>> --
> >>> 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
> >>
> >> --
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> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] dssp works fine, but do_dssp gives fatal error

You have (at least) two easy options.

1) Install old_dssp that is available through the dssp web page.  
2) Install a newer version of gromacs than you have at the moment. What version 
do you currently use?

Erik

On 12 Jun 2013, at 12:56, Nikunj Maheshwari  wrote:

> Yes I checked. do_dssp has no -ver option.
> I also found out this link
> 
> https://gerrit.gromacs.org/#/c/687/
> 
> but dont know how to install/use it.
> 
> Or maybe I can install DsspOld and see?
> 
> 
> 
> On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund  wrote:
> 
>> Search again. The syntax for invoking dssp changed at some point and it
>> took a while before do_dssp adapted to that. If your do_dssp is lacking the
>> -ver option then I'm quite confident that it uses the old syntax, which
>> doesn't work with the newer versions (v. 2.0+ I think) of dssp.
>> 
>> Erik
>> 
>> On 12 Jun 2013, at 11:17, Nikunj Maheshwari 
>> wrote:
>> 
>>> Yes I did searched. But for most people, there were issues regarding the
>>> path or wrong DSSP.
>>> DSSP runs for me, but do_dssp does not.
>>> 
>>> 
>>> On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund 
>> wrote:
>>> 
 Hi,
 
 Search the mailing list. This problem and its solution has been
>> repeatedly
 discussed.
 
 Erik
 
 On 12 Jun 2013, at 10:31, Nikunj Maheshwari 
 wrote:
 
> Dear all,
> 
> I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
> I am trying to use it for do_dssp command but get the following error
 each
> time:
> 
> "Fatal error:
> Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 >
> /dev/null 2> /dev/null
> "
> 
> Is there any way to rectify it?
> 
> Thanks.
> Nikunj
> --
> 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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>>> --
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>> 
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Re: [gmx-users] dssp works fine, but do_dssp gives fatal error

My current Gromacs version is 4.5.5
I think using the first option will be easy and quick.


On Wed, Jun 12, 2013 at 4:41 PM, Erik Marklund  wrote:

> You have (at least) two easy options.
>
> 1) Install old_dssp that is available through the dssp web page.
> 2) Install a newer version of gromacs than you have at the moment. What
> version do you currently use?
>
> Erik
>
> On 12 Jun 2013, at 12:56, Nikunj Maheshwari 
> wrote:
>
> > Yes I checked. do_dssp has no -ver option.
> > I also found out this link
> >
> > https://gerrit.gromacs.org/#/c/687/
> >
> > but dont know how to install/use it.
> >
> > Or maybe I can install DsspOld and see?
> >
> >
> >
> > On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund 
> wrote:
> >
> >> Search again. The syntax for invoking dssp changed at some point and it
> >> took a while before do_dssp adapted to that. If your do_dssp is lacking
> the
> >> -ver option then I'm quite confident that it uses the old syntax, which
> >> doesn't work with the newer versions (v. 2.0+ I think) of dssp.
> >>
> >> Erik
> >>
> >> On 12 Jun 2013, at 11:17, Nikunj Maheshwari 
> >> wrote:
> >>
> >>> Yes I did searched. But for most people, there were issues regarding
> the
> >>> path or wrong DSSP.
> >>> DSSP runs for me, but do_dssp does not.
> >>>
> >>>
> >>> On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund 
> >> wrote:
> >>>
>  Hi,
> 
>  Search the mailing list. This problem and its solution has been
> >> repeatedly
>  discussed.
> 
>  Erik
> 
>  On 12 Jun 2013, at 10:31, Nikunj Maheshwari  >
>  wrote:
> 
> > Dear all,
> >
> > I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
> > I am trying to use it for do_dssp command but get the following error
>  each
> > time:
> >
> > "Fatal error:
> > Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68
> >
> > /dev/null 2> /dev/null
> > "
> >
> > Is there any way to rectify it?
> >
> > Thanks.
> > Nikunj
> > --
> > 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
> 
>  --
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> 
> >>> --
> >>> gmx-users mailing listgmx-users@gromacs.org
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >>
> >> --
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> >>
> > --
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[gmx-users] Umbrella Sampling Force component output

2013-06-12 Thread Kenny Bravo Rodriguez


Dear Gromacs Users,

I runned and Umbrella Sampling simulation but I made a mistake in the 
value of the pull_dim option, so gromacs printed the z component of the 
force instead of the x component that i need (with the option -pf of 
mdrun). I have all files from the simulation.
Is there a way to get the x component of the force without running the 
simulation again?


Thanks in advanced,
Kenny
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Re: [gmx-users] Nonbonded parameters

An why do I have 1830 non bonded? 60*60/2 = 1800. There are 57 of 1-4
combinations so it should be lower than 1800...
And why 1830 1-4 interactions as I have only 57... Please, help/

Steven


On Wed, Jun 12, 2013 at 11:40 AM, Steven Neumann wrote:

> I got it. However,
>
> I have 60  atoms in my chain all with given C6 and C12 with a combination
> rule 1. When running grompp:
>
> Generated 1830 of the 1830 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 1830 of the 1830 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_X'
> Analysing residue names:
> There are: 1Protein residues
> Analysing Protein...
> Number of degrees of freedom in T-Coupling group rest is 118.00
> This run will generate roughly 2 Mb of data
>
> when changing nrexcl in my topology to 0:
>
>
> Generated 1830 of the 1830 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 1830 of the 1830 1-4 parameter combinations
> Excluding 0 bonded neighbours molecule type 'Protein_chain_X'
> Analysing residue names:
> There are: 1Protein residues
> Analysing Protein...
> Number of degrees of freedom in T-Coupling group rest is 118.00
> This run will generate roughly 2 Mb of data
>
> So if I exclude 1-3 interactions I have the same number of nonbonded
> parameters as well as 1-4 interactions. Can someone explain me this please?
>
>
>
> On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann wrote:
>
>>
>>
>>
>> On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul  wrote:
>>
>>>
>>>
>>> On 6/12/13 6:00 AM, Steven Neumann wrote:
>>>
 Thank you. That means that e.g. when two LJ atoms of a different type
 approaching each other the non bonded LJ potential energy is a sum of
 two
 potentials of those atoms?


>>> No, please refer to the Gromacs manual for discussion on "combination
>>> rules" and how they fit into the Lennard-Jones equation.
>>>
>>> -Justin
>>>
>>
>> I read it.
>> I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that
>> means that when you provide in [atomtypes] in ffnonbonded your C and A
>> values each atom has a specific LJ potential shape. Right?
>> So two of them approaching each other in my system will have have the sum
>> of it.
>>
>> Steven
>>
>>
>>
>>>
>>>
 On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul 
 wrote:


>
> On 6/12/13 5:30 AM, Steven Neumann wrote:
>
>  Dear Gmx Users,
>>
>> Please, correct me if I am wrong. In ffnonbonded.itp
>>
>> [ atomtypes ] - these are nonbonded parameters between atoms of the
>> same
>> type
>>
>>
> No, these are the nonbonded parameters that are used when applying
> combination rules between any atoms.
>
>
>   [ nonbond_params ] these are nonbonded parameters between atoms of
>
>> different type
>>
>>
> No, these override combination rules.
>
>
>   [ pairtypes ] - 1-4 interactions
>
>>
>> If that is correct why amber force filed has only [atomtypes] column?
>> How
>> nonbonded parameters are calculated between atoms of a different type?
>> The same with charmm - only [atomtypes ] and [pairtypes ] are
>> provided.
>> Would you please explain?
>>
>>
>>  Gromos force fields, for instance, have complex ways of generating
> nonbonded interactions that are not always the same for a given
> atomtype.
>   Other force fields just use straight combination rules and thus
> never need
> [nonbond_params].
>
> -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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >
>
> ====
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> >
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search 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
> 
> >
>
>
>>> --
>>> ==**==

Re: [gmx-users] Nonbonded parameters

grompp is just enumerating the possible combinations of parameters given
your inputs. Whether any of those will be used in the simulation will
depend on whether atoms of given types are close enough and not excluded.

Mark


On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann wrote:

> I got it. However,
>
> I have 60  atoms in my chain all with given C6 and C12 with a combination
> rule 1. When running grompp:
>
> Generated 1830 of the 1830 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 1830 of the 1830 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_X'
> Analysing residue names:
> There are: 1Protein residues
> Analysing Protein...
> Number of degrees of freedom in T-Coupling group rest is 118.00
> This run will generate roughly 2 Mb of data
>
> when changing nrexcl in my topology to 0:
>
>
> Generated 1830 of the 1830 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 1830 of the 1830 1-4 parameter combinations
> Excluding 0 bonded neighbours molecule type 'Protein_chain_X'
> Analysing residue names:
> There are: 1Protein residues
> Analysing Protein...
> Number of degrees of freedom in T-Coupling group rest is 118.00
> This run will generate roughly 2 Mb of data
>
> So if I exclude 1-3 interactions I have the same number of nonbonded
> parameters as well as 1-4 interactions. Can someone explain me this please?
>
>
>
> On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann  >wrote:
>
> >
> >
> >
> > On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 6/12/13 6:00 AM, Steven Neumann wrote:
> >>
> >>> Thank you. That means that e.g. when two LJ atoms of a different type
> >>> approaching each other the non bonded LJ potential energy is a sum of
> two
> >>> potentials of those atoms?
> >>>
> >>>
> >> No, please refer to the Gromacs manual for discussion on "combination
> >> rules" and how they fit into the Lennard-Jones equation.
> >>
> >> -Justin
> >>
> >
> > I read it.
> > I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that
> > means that when you provide in [atomtypes] in ffnonbonded your C and A
> > values each atom has a specific LJ potential shape. Right?
> > So two of them approaching each other in my system will have have the sum
> > of it.
> >
> > Steven
> >
> >
> >
> >>
> >>
> >>> On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul 
> wrote:
> >>>
> >>>
> 
>  On 6/12/13 5:30 AM, Steven Neumann wrote:
> 
>   Dear Gmx Users,
> >
> > Please, correct me if I am wrong. In ffnonbonded.itp
> >
> > [ atomtypes ] - these are nonbonded parameters between atoms of the
> > same
> > type
> >
> >
>  No, these are the nonbonded parameters that are used when applying
>  combination rules between any atoms.
> 
> 
>    [ nonbond_params ] these are nonbonded parameters between atoms of
> 
> > different type
> >
> >
>  No, these override combination rules.
> 
> 
>    [ pairtypes ] - 1-4 interactions
> 
> >
> > If that is correct why amber force filed has only [atomtypes] column?
> > How
> > nonbonded parameters are calculated between atoms of a different
> type?
> > The same with charmm - only [atomtypes ] and [pairtypes ] are
> provided.
> > Would you please explain?
> >
> >
> >  Gromos force fields, for instance, have complex ways of generating
>  nonbonded interactions that are not always the same for a given
>  atomtype.
>    Other force fields just use straight combination rules and thus
> never
>  need
>  [nonbond_params].
> 
>  -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<
> http://vt.edu/Pages/Personal/justin>
>   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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Re: [gmx-users] Nonbonded parameters

On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham wrote:

> grompp is just enumerating the possible combinations of parameters given
> your inputs. Whether any of those will be used in the simulation will
> depend on whether atoms of given types are close enough and not excluded.
>
> Mark


I understand...but why for 60 mer polypeptide there are 1830 nonbonded
interactions ?

>
>
> On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann  >wrote:
>
> > I got it. However,
> >
> > I have 60  atoms in my chain all with given C6 and C12 with a combination
> > rule 1. When running grompp:
> >
> > Generated 1830 of the 1830 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 1
> > Generated 1830 of the 1830 1-4 parameter combinations
> > Excluding 3 bonded neighbours molecule type 'Protein_chain_X'
> > Analysing residue names:
> > There are: 1Protein residues
> > Analysing Protein...
> > Number of degrees of freedom in T-Coupling group rest is 118.00
> > This run will generate roughly 2 Mb of data
> >
> > when changing nrexcl in my topology to 0:
> >
> >
> > Generated 1830 of the 1830 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 1
> > Generated 1830 of the 1830 1-4 parameter combinations
> > Excluding 0 bonded neighbours molecule type 'Protein_chain_X'
> > Analysing residue names:
> > There are: 1Protein residues
> > Analysing Protein...
> > Number of degrees of freedom in T-Coupling group rest is 118.00
> > This run will generate roughly 2 Mb of data
> >
> > So if I exclude 1-3 interactions I have the same number of nonbonded
> > parameters as well as 1-4 interactions. Can someone explain me this
> please?
> >
> >
> >
> > On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann  > >wrote:
> >
> > >
> > >
> > >
> > > On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul 
> wrote:
> > >
> > >>
> > >>
> > >> On 6/12/13 6:00 AM, Steven Neumann wrote:
> > >>
> > >>> Thank you. That means that e.g. when two LJ atoms of a different type
> > >>> approaching each other the non bonded LJ potential energy is a sum of
> > two
> > >>> potentials of those atoms?
> > >>>
> > >>>
> > >> No, please refer to the Gromacs manual for discussion on "combination
> > >> rules" and how they fit into the Lennard-Jones equation.
> > >>
> > >> -Justin
> > >>
> > >
> > > I read it.
> > > I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So
> that
> > > means that when you provide in [atomtypes] in ffnonbonded your C and A
> > > values each atom has a specific LJ potential shape. Right?
> > > So two of them approaching each other in my system will have have the
> sum
> > > of it.
> > >
> > > Steven
> > >
> > >
> > >
> > >>
> > >>
> > >>> On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul 
> > wrote:
> > >>>
> > >>>
> > 
> >  On 6/12/13 5:30 AM, Steven Neumann wrote:
> > 
> >   Dear Gmx Users,
> > >
> > > Please, correct me if I am wrong. In ffnonbonded.itp
> > >
> > > [ atomtypes ] - these are nonbonded parameters between atoms of the
> > > same
> > > type
> > >
> > >
> >  No, these are the nonbonded parameters that are used when applying
> >  combination rules between any atoms.
> > 
> > 
> >    [ nonbond_params ] these are nonbonded parameters between atoms of
> > 
> > > different type
> > >
> > >
> >  No, these override combination rules.
> > 
> > 
> >    [ pairtypes ] - 1-4 interactions
> > 
> > >
> > > If that is correct why amber force filed has only [atomtypes]
> column?
> > > How
> > > nonbonded parameters are calculated between atoms of a different
> > type?
> > > The same with charmm - only [atomtypes ] and [pairtypes ] are
> > provided.
> > > Would you please explain?
> > >
> > >
> > >  Gromos force fields, for instance, have complex ways of generating
> >  nonbonded interactions that are not always the same for a given
> >  atomtype.
> >    Other force fields just use straight combination rules and thus
> > never
> >  need
> >  [nonbond_params].
> > 
> >  -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<
> > http://vt.edu/Pages/Personal/justin>
> >   > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >  >
> > 
> >  ====
> > 
> >  --
> >  gmx-users mailing listgmx-users@gromacs.org
> >  http://lists.gromacs.org/mailman/listinfo/gmx-users<
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users>
> >   > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> >  >
> >  * Please search the archive at http

Re: [gmx-users] Umbrella Sampling Force component output

Hi,

No, I'm afraid not. pull-dim not only determines what components are to be 
printed, it also determines in what dimensions the force is to be applied 
during the simulation.

Erik

On 12 Jun 2013, at 13:32, Kenny Bravo Rodriguez  
wrote:

> Dear Gromacs Users,
> 
> I runned and Umbrella Sampling simulation but I made a mistake in the value 
> of the pull_dim option, so gromacs printed the z component of the force 
> instead of the x component that i need (with the option -pf of mdrun). I have 
> all files from the simulation.
> Is there a way to get the x component of the force without running the 
> simulation again?
> 
> Thanks in advanced,
> Kenny
> -- 
> 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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Re: [gmx-users] Nonbonded parameters

"Parameters for possible interactions" is not the same as "interactions."
The latter depend on the configuration and cut-offs... grompp is not doing
a neighbor search!

Mark


On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann wrote:

> On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham  >wrote:
>
> > grompp is just enumerating the possible combinations of parameters given
> > your inputs. Whether any of those will be used in the simulation will
> > depend on whether atoms of given types are close enough and not excluded.
> >
> > Mark
>
>
> I understand...but why for 60 mer polypeptide there are 1830 nonbonded
> interactions ?
>
> >
> >
> > On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann  > >wrote:
> >
> > > I got it. However,
> > >
> > > I have 60  atoms in my chain all with given C6 and C12 with a
> combination
> > > rule 1. When running grompp:
> > >
> > > Generated 1830 of the 1830 non-bonded parameter combinations
> > > Generating 1-4 interactions: fudge = 1
> > > Generated 1830 of the 1830 1-4 parameter combinations
> > > Excluding 3 bonded neighbours molecule type 'Protein_chain_X'
> > > Analysing residue names:
> > > There are: 1Protein residues
> > > Analysing Protein...
> > > Number of degrees of freedom in T-Coupling group rest is 118.00
> > > This run will generate roughly 2 Mb of data
> > >
> > > when changing nrexcl in my topology to 0:
> > >
> > >
> > > Generated 1830 of the 1830 non-bonded parameter combinations
> > > Generating 1-4 interactions: fudge = 1
> > > Generated 1830 of the 1830 1-4 parameter combinations
> > > Excluding 0 bonded neighbours molecule type 'Protein_chain_X'
> > > Analysing residue names:
> > > There are: 1Protein residues
> > > Analysing Protein...
> > > Number of degrees of freedom in T-Coupling group rest is 118.00
> > > This run will generate roughly 2 Mb of data
> > >
> > > So if I exclude 1-3 interactions I have the same number of nonbonded
> > > parameters as well as 1-4 interactions. Can someone explain me this
> > please?
> > >
> > >
> > >
> > > On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann <
> s.neuman...@gmail.com
> > > >wrote:
> > >
> > > >
> > > >
> > > >
> > > > On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul 
> > wrote:
> > > >
> > > >>
> > > >>
> > > >> On 6/12/13 6:00 AM, Steven Neumann wrote:
> > > >>
> > > >>> Thank you. That means that e.g. when two LJ atoms of a different
> type
> > > >>> approaching each other the non bonded LJ potential energy is a sum
> of
> > > two
> > > >>> potentials of those atoms?
> > > >>>
> > > >>>
> > > >> No, please refer to the Gromacs manual for discussion on
> "combination
> > > >> rules" and how they fit into the Lennard-Jones equation.
> > > >>
> > > >> -Justin
> > > >>
> > > >
> > > > I read it.
> > > > I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So
> > that
> > > > means that when you provide in [atomtypes] in ffnonbonded your C and
> A
> > > > values each atom has a specific LJ potential shape. Right?
> > > > So two of them approaching each other in my system will have have the
> > sum
> > > > of it.
> > > >
> > > > Steven
> > > >
> > > >
> > > >
> > > >>
> > > >>
> > > >>> On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul 
> > > wrote:
> > > >>>
> > > >>>
> > > 
> > >  On 6/12/13 5:30 AM, Steven Neumann wrote:
> > > 
> > >   Dear Gmx Users,
> > > >
> > > > Please, correct me if I am wrong. In ffnonbonded.itp
> > > >
> > > > [ atomtypes ] - these are nonbonded parameters between atoms of
> the
> > > > same
> > > > type
> > > >
> > > >
> > >  No, these are the nonbonded parameters that are used when applying
> > >  combination rules between any atoms.
> > > 
> > > 
> > >    [ nonbond_params ] these are nonbonded parameters between atoms
> of
> > > 
> > > > different type
> > > >
> > > >
> > >  No, these override combination rules.
> > > 
> > > 
> > >    [ pairtypes ] - 1-4 interactions
> > > 
> > > >
> > > > If that is correct why amber force filed has only [atomtypes]
> > column?
> > > > How
> > > > nonbonded parameters are calculated between atoms of a different
> > > type?
> > > > The same with charmm - only [atomtypes ] and [pairtypes ] are
> > > provided.
> > > > Would you please explain?
> > > >
> > > >
> > > >  Gromos force fields, for instance, have complex ways of
> generating
> > >  nonbonded interactions that are not always the same for a given
> > >  atomtype.
> > >    Other force fields just use straight combination rules and thus
> > > never
> > >  need
> > >  [nonbond_params].
> > > 
> > >  -Justin
> > > 
> > >  --
> > >  ====
> > > 
> > > 
> > >  Justin A. Lemkul, Ph.D.
> > >  Research Scientist
> > >  Department of Biochemistry
> > >  Virginia Tech
> > >  Blacksburg, VA
> > >  jalemkul[at]vt.edu | (540) 231-9080
>

Re: [gmx-users] Nonbonded parameters

"All possible interactions = 60*60/2 = 1800. Where grompp takes another 30
from?


On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham wrote:

> "Parameters for possible interactions" is not the same as "interactions."
> The latter depend on the configuration and cut-offs... grompp is not doing
> a neighbor search!
>
> Mark
>
>
> On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann  >wrote:
>
> > On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham  > >wrote:
> >
> > > grompp is just enumerating the possible combinations of parameters
> given
> > > your inputs. Whether any of those will be used in the simulation will
> > > depend on whether atoms of given types are close enough and not
> excluded.
> > >
> > > Mark
> >
> >
> > I understand...but why for 60 mer polypeptide there are 1830 nonbonded
> > interactions ?
> >
> > >
> > >
> > > On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann <
> s.neuman...@gmail.com
> > > >wrote:
> > >
> > > > I got it. However,
> > > >
> > > > I have 60  atoms in my chain all with given C6 and C12 with a
> > combination
> > > > rule 1. When running grompp:
> > > >
> > > > Generated 1830 of the 1830 non-bonded parameter combinations
> > > > Generating 1-4 interactions: fudge = 1
> > > > Generated 1830 of the 1830 1-4 parameter combinations
> > > > Excluding 3 bonded neighbours molecule type 'Protein_chain_X'
> > > > Analysing residue names:
> > > > There are: 1Protein residues
> > > > Analysing Protein...
> > > > Number of degrees of freedom in T-Coupling group rest is 118.00
> > > > This run will generate roughly 2 Mb of data
> > > >
> > > > when changing nrexcl in my topology to 0:
> > > >
> > > >
> > > > Generated 1830 of the 1830 non-bonded parameter combinations
> > > > Generating 1-4 interactions: fudge = 1
> > > > Generated 1830 of the 1830 1-4 parameter combinations
> > > > Excluding 0 bonded neighbours molecule type 'Protein_chain_X'
> > > > Analysing residue names:
> > > > There are: 1Protein residues
> > > > Analysing Protein...
> > > > Number of degrees of freedom in T-Coupling group rest is 118.00
> > > > This run will generate roughly 2 Mb of data
> > > >
> > > > So if I exclude 1-3 interactions I have the same number of nonbonded
> > > > parameters as well as 1-4 interactions. Can someone explain me this
> > > please?
> > > >
> > > >
> > > >
> > > > On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann <
> > s.neuman...@gmail.com
> > > > >wrote:
> > > >
> > > > >
> > > > >
> > > > >
> > > > > On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul 
> > > wrote:
> > > > >
> > > > >>
> > > > >>
> > > > >> On 6/12/13 6:00 AM, Steven Neumann wrote:
> > > > >>
> > > > >>> Thank you. That means that e.g. when two LJ atoms of a different
> > type
> > > > >>> approaching each other the non bonded LJ potential energy is a
> sum
> > of
> > > > two
> > > > >>> potentials of those atoms?
> > > > >>>
> > > > >>>
> > > > >> No, please refer to the Gromacs manual for discussion on
> > "combination
> > > > >> rules" and how they fit into the Lennard-Jones equation.
> > > > >>
> > > > >> -Justin
> > > > >>
> > > > >
> > > > > I read it.
> > > > > I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 -
> So
> > > that
> > > > > means that when you provide in [atomtypes] in ffnonbonded your C
> and
> > A
> > > > > values each atom has a specific LJ potential shape. Right?
> > > > > So two of them approaching each other in my system will have have
> the
> > > sum
> > > > > of it.
> > > > >
> > > > > Steven
> > > > >
> > > > >
> > > > >
> > > > >>
> > > > >>
> > > > >>> On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul  >
> > > > wrote:
> > > > >>>
> > > > >>>
> > > > 
> > > >  On 6/12/13 5:30 AM, Steven Neumann wrote:
> > > > 
> > > >   Dear Gmx Users,
> > > > >
> > > > > Please, correct me if I am wrong. In ffnonbonded.itp
> > > > >
> > > > > [ atomtypes ] - these are nonbonded parameters between atoms of
> > the
> > > > > same
> > > > > type
> > > > >
> > > > >
> > > >  No, these are the nonbonded parameters that are used when
> applying
> > > >  combination rules between any atoms.
> > > > 
> > > > 
> > > >    [ nonbond_params ] these are nonbonded parameters between
> atoms
> > of
> > > > 
> > > > > different type
> > > > >
> > > > >
> > > >  No, these override combination rules.
> > > > 
> > > > 
> > > >    [ pairtypes ] - 1-4 interactions
> > > > 
> > > > >
> > > > > If that is correct why amber force filed has only [atomtypes]
> > > column?
> > > > > How
> > > > > nonbonded parameters are calculated between atoms of a
> different
> > > > type?
> > > > > The same with charmm - only [atomtypes ] and [pairtypes ] are
> > > > provided.
> > > > > Would you please explain?
> > > > >
> > > > >
> > > > >  Gromos force fields, for instance, have complex ways of
> > generating
> > > >  nonbonded interactions that are not always the same for a given
>

Re: [gmx-users] Nonbonded parameters

and 1830 1-4 interactions... there are "57 all possible 1-4 interactions"


On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann wrote:

> "All possible interactions = 60*60/2 = 1800. Where grompp takes another 30
> from?
>
>
> On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham 
> wrote:
>
>> "Parameters for possible interactions" is not the same as "interactions."
>> The latter depend on the configuration and cut-offs... grompp is not doing
>> a neighbor search!
>>
>> Mark
>>
>>
>> On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann > >wrote:
>>
>> > On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham <
>> mark.j.abra...@gmail.com
>> > >wrote:
>> >
>> > > grompp is just enumerating the possible combinations of parameters
>> given
>> > > your inputs. Whether any of those will be used in the simulation will
>> > > depend on whether atoms of given types are close enough and not
>> excluded.
>> > >
>> > > Mark
>> >
>> >
>> > I understand...but why for 60 mer polypeptide there are 1830 nonbonded
>> > interactions ?
>> >
>> > >
>> > >
>> > > On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann <
>> s.neuman...@gmail.com
>> > > >wrote:
>> > >
>> > > > I got it. However,
>> > > >
>> > > > I have 60  atoms in my chain all with given C6 and C12 with a
>> > combination
>> > > > rule 1. When running grompp:
>> > > >
>> > > > Generated 1830 of the 1830 non-bonded parameter combinations
>> > > > Generating 1-4 interactions: fudge = 1
>> > > > Generated 1830 of the 1830 1-4 parameter combinations
>> > > > Excluding 3 bonded neighbours molecule type 'Protein_chain_X'
>> > > > Analysing residue names:
>> > > > There are: 1Protein residues
>> > > > Analysing Protein...
>> > > > Number of degrees of freedom in T-Coupling group rest is 118.00
>> > > > This run will generate roughly 2 Mb of data
>> > > >
>> > > > when changing nrexcl in my topology to 0:
>> > > >
>> > > >
>> > > > Generated 1830 of the 1830 non-bonded parameter combinations
>> > > > Generating 1-4 interactions: fudge = 1
>> > > > Generated 1830 of the 1830 1-4 parameter combinations
>> > > > Excluding 0 bonded neighbours molecule type 'Protein_chain_X'
>> > > > Analysing residue names:
>> > > > There are: 1Protein residues
>> > > > Analysing Protein...
>> > > > Number of degrees of freedom in T-Coupling group rest is 118.00
>> > > > This run will generate roughly 2 Mb of data
>> > > >
>> > > > So if I exclude 1-3 interactions I have the same number of nonbonded
>> > > > parameters as well as 1-4 interactions. Can someone explain me this
>> > > please?
>> > > >
>> > > >
>> > > >
>> > > > On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann <
>> > s.neuman...@gmail.com
>> > > > >wrote:
>> > > >
>> > > > >
>> > > > >
>> > > > >
>> > > > > On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul 
>> > > wrote:
>> > > > >
>> > > > >>
>> > > > >>
>> > > > >> On 6/12/13 6:00 AM, Steven Neumann wrote:
>> > > > >>
>> > > > >>> Thank you. That means that e.g. when two LJ atoms of a different
>> > type
>> > > > >>> approaching each other the non bonded LJ potential energy is a
>> sum
>> > of
>> > > > two
>> > > > >>> potentials of those atoms?
>> > > > >>>
>> > > > >>>
>> > > > >> No, please refer to the Gromacs manual for discussion on
>> > "combination
>> > > > >> rules" and how they fit into the Lennard-Jones equation.
>> > > > >>
>> > > > >> -Justin
>> > > > >>
>> > > > >
>> > > > > I read it.
>> > > > > I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 -
>> So
>> > > that
>> > > > > means that when you provide in [atomtypes] in ffnonbonded your C
>> and
>> > A
>> > > > > values each atom has a specific LJ potential shape. Right?
>> > > > > So two of them approaching each other in my system will have have
>> the
>> > > sum
>> > > > > of it.
>> > > > >
>> > > > > Steven
>> > > > >
>> > > > >
>> > > > >
>> > > > >>
>> > > > >>
>> > > > >>> On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul <
>> jalem...@vt.edu>
>> > > > wrote:
>> > > > >>>
>> > > > >>>
>> > > > 
>> > > >  On 6/12/13 5:30 AM, Steven Neumann wrote:
>> > > > 
>> > > >   Dear Gmx Users,
>> > > > >
>> > > > > Please, correct me if I am wrong. In ffnonbonded.itp
>> > > > >
>> > > > > [ atomtypes ] - these are nonbonded parameters between atoms
>> of
>> > the
>> > > > > same
>> > > > > type
>> > > > >
>> > > > >
>> > > >  No, these are the nonbonded parameters that are used when
>> applying
>> > > >  combination rules between any atoms.
>> > > > 
>> > > > 
>> > > >    [ nonbond_params ] these are nonbonded parameters between
>> atoms
>> > of
>> > > > 
>> > > > > different type
>> > > > >
>> > > > >
>> > > >  No, these override combination rules.
>> > > > 
>> > > > 
>> > > >    [ pairtypes ] - 1-4 interactions
>> > > > 
>> > > > >
>> > > > > If that is correct why amber force filed has only [atomtypes]
>> > > column?
>> > > > > How
>> > > > > nonbonded parameters are calculated between atoms of a
>

Re: [gmx-users] Umbrella Sampling Force component output

2013-06-12 Thread Kenny Bravo Rodriguez


Thanks Erik

On 06/12/2013 01:50 PM, Erik Marklund wrote:

Hi,

No, I'm afraid not. pull-dim not only determines what components are to be 
printed, it also determines in what dimensions the force is to be applied 
during the simulation.

Erik

On 12 Jun 2013, at 13:32, Kenny Bravo Rodriguez  
wrote:


Dear Gromacs Users,

I runned and Umbrella Sampling simulation but I made a mistake in the value of 
the pull_dim option, so gromacs printed the z component of the force instead of 
the x component that i need (with the option -pf of mdrun). I have all files 
from the simulation.
Is there a way to get the x component of the force without running the 
simulation again?

Thanks in advanced,
Kenny
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
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Re: [gmx-users] Nonbonded parameters

How many atom *types* are there?


On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann wrote:

> and 1830 1-4 interactions... there are "57 all possible 1-4 interactions"
>
>
> On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann  >wrote:
>
> > "All possible interactions = 60*60/2 = 1800. Where grompp takes another
> 30
> > from?
> >
> >
> > On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham  >wrote:
> >
> >> "Parameters for possible interactions" is not the same as
> "interactions."
> >> The latter depend on the configuration and cut-offs... grompp is not
> doing
> >> a neighbor search!
> >>
> >> Mark
> >>
> >>
> >> On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann  >> >wrote:
> >>
> >> > On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham <
> >> mark.j.abra...@gmail.com
> >> > >wrote:
> >> >
> >> > > grompp is just enumerating the possible combinations of parameters
> >> given
> >> > > your inputs. Whether any of those will be used in the simulation
> will
> >> > > depend on whether atoms of given types are close enough and not
> >> excluded.
> >> > >
> >> > > Mark
> >> >
> >> >
> >> > I understand...but why for 60 mer polypeptide there are 1830 nonbonded
> >> > interactions ?
> >> >
> >> > >
> >> > >
> >> > > On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann <
> >> s.neuman...@gmail.com
> >> > > >wrote:
> >> > >
> >> > > > I got it. However,
> >> > > >
> >> > > > I have 60  atoms in my chain all with given C6 and C12 with a
> >> > combination
> >> > > > rule 1. When running grompp:
> >> > > >
> >> > > > Generated 1830 of the 1830 non-bonded parameter combinations
> >> > > > Generating 1-4 interactions: fudge = 1
> >> > > > Generated 1830 of the 1830 1-4 parameter combinations
> >> > > > Excluding 3 bonded neighbours molecule type 'Protein_chain_X'
> >> > > > Analysing residue names:
> >> > > > There are: 1Protein residues
> >> > > > Analysing Protein...
> >> > > > Number of degrees of freedom in T-Coupling group rest is 118.00
> >> > > > This run will generate roughly 2 Mb of data
> >> > > >
> >> > > > when changing nrexcl in my topology to 0:
> >> > > >
> >> > > >
> >> > > > Generated 1830 of the 1830 non-bonded parameter combinations
> >> > > > Generating 1-4 interactions: fudge = 1
> >> > > > Generated 1830 of the 1830 1-4 parameter combinations
> >> > > > Excluding 0 bonded neighbours molecule type 'Protein_chain_X'
> >> > > > Analysing residue names:
> >> > > > There are: 1Protein residues
> >> > > > Analysing Protein...
> >> > > > Number of degrees of freedom in T-Coupling group rest is 118.00
> >> > > > This run will generate roughly 2 Mb of data
> >> > > >
> >> > > > So if I exclude 1-3 interactions I have the same number of
> nonbonded
> >> > > > parameters as well as 1-4 interactions. Can someone explain me
> this
> >> > > please?
> >> > > >
> >> > > >
> >> > > >
> >> > > > On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann <
> >> > s.neuman...@gmail.com
> >> > > > >wrote:
> >> > > >
> >> > > > >
> >> > > > >
> >> > > > >
> >> > > > > On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul <
> jalem...@vt.edu>
> >> > > wrote:
> >> > > > >
> >> > > > >>
> >> > > > >>
> >> > > > >> On 6/12/13 6:00 AM, Steven Neumann wrote:
> >> > > > >>
> >> > > > >>> Thank you. That means that e.g. when two LJ atoms of a
> different
> >> > type
> >> > > > >>> approaching each other the non bonded LJ potential energy is a
> >> sum
> >> > of
> >> > > > two
> >> > > > >>> potentials of those atoms?
> >> > > > >>>
> >> > > > >>>
> >> > > > >> No, please refer to the Gromacs manual for discussion on
> >> > "combination
> >> > > > >> rules" and how they fit into the Lennard-Jones equation.
> >> > > > >>
> >> > > > >> -Justin
> >> > > > >>
> >> > > > >
> >> > > > > I read it.
> >> > > > > I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12
> -
> >> So
> >> > > that
> >> > > > > means that when you provide in [atomtypes] in ffnonbonded your C
> >> and
> >> > A
> >> > > > > values each atom has a specific LJ potential shape. Right?
> >> > > > > So two of them approaching each other in my system will have
> have
> >> the
> >> > > sum
> >> > > > > of it.
> >> > > > >
> >> > > > > Steven
> >> > > > >
> >> > > > >
> >> > > > >
> >> > > > >>
> >> > > > >>
> >> > > > >>> On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul <
> >> jalem...@vt.edu>
> >> > > > wrote:
> >> > > > >>>
> >> > > > >>>
> >> > > > 
> >> > > >  On 6/12/13 5:30 AM, Steven Neumann wrote:
> >> > > > 
> >> > > >   Dear Gmx Users,
> >> > > > >
> >> > > > > Please, correct me if I am wrong. In ffnonbonded.itp
> >> > > > >
> >> > > > > [ atomtypes ] - these are nonbonded parameters between atoms
> >> of
> >> > the
> >> > > > > same
> >> > > > > type
> >> > > > >
> >> > > > >
> >> > > >  No, these are the nonbonded parameters that are used when
> >> applying
> >> > > >  combination rules between any atoms.
> >> > > > 
> >> > > > 
> >> > > >    [ nonbond_params ] these are nonbonded parameters between

Re: [gmx-users] Nonbonded parameters

60 types of atoms and 60 atoms in total belonging to one residue


On Wed, Jun 12, 2013 at 12:59 PM, Mark Abraham wrote:

> How many atom *types* are there?
>
>
> On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann  >wrote:
>
> > and 1830 1-4 interactions... there are "57 all possible 1-4 interactions"
> >
> >
> > On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann  > >wrote:
> >
> > > "All possible interactions = 60*60/2 = 1800. Where grompp takes another
> > 30
> > > from?
> > >
> > >
> > > On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham <
> mark.j.abra...@gmail.com
> > >wrote:
> > >
> > >> "Parameters for possible interactions" is not the same as
> > "interactions."
> > >> The latter depend on the configuration and cut-offs... grompp is not
> > doing
> > >> a neighbor search!
> > >>
> > >> Mark
> > >>
> > >>
> > >> On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann <
> s.neuman...@gmail.com
> > >> >wrote:
> > >>
> > >> > On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham <
> > >> mark.j.abra...@gmail.com
> > >> > >wrote:
> > >> >
> > >> > > grompp is just enumerating the possible combinations of parameters
> > >> given
> > >> > > your inputs. Whether any of those will be used in the simulation
> > will
> > >> > > depend on whether atoms of given types are close enough and not
> > >> excluded.
> > >> > >
> > >> > > Mark
> > >> >
> > >> >
> > >> > I understand...but why for 60 mer polypeptide there are 1830
> nonbonded
> > >> > interactions ?
> > >> >
> > >> > >
> > >> > >
> > >> > > On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann <
> > >> s.neuman...@gmail.com
> > >> > > >wrote:
> > >> > >
> > >> > > > I got it. However,
> > >> > > >
> > >> > > > I have 60  atoms in my chain all with given C6 and C12 with a
> > >> > combination
> > >> > > > rule 1. When running grompp:
> > >> > > >
> > >> > > > Generated 1830 of the 1830 non-bonded parameter combinations
> > >> > > > Generating 1-4 interactions: fudge = 1
> > >> > > > Generated 1830 of the 1830 1-4 parameter combinations
> > >> > > > Excluding 3 bonded neighbours molecule type 'Protein_chain_X'
> > >> > > > Analysing residue names:
> > >> > > > There are: 1Protein residues
> > >> > > > Analysing Protein...
> > >> > > > Number of degrees of freedom in T-Coupling group rest is 118.00
> > >> > > > This run will generate roughly 2 Mb of data
> > >> > > >
> > >> > > > when changing nrexcl in my topology to 0:
> > >> > > >
> > >> > > >
> > >> > > > Generated 1830 of the 1830 non-bonded parameter combinations
> > >> > > > Generating 1-4 interactions: fudge = 1
> > >> > > > Generated 1830 of the 1830 1-4 parameter combinations
> > >> > > > Excluding 0 bonded neighbours molecule type 'Protein_chain_X'
> > >> > > > Analysing residue names:
> > >> > > > There are: 1Protein residues
> > >> > > > Analysing Protein...
> > >> > > > Number of degrees of freedom in T-Coupling group rest is 118.00
> > >> > > > This run will generate roughly 2 Mb of data
> > >> > > >
> > >> > > > So if I exclude 1-3 interactions I have the same number of
> > nonbonded
> > >> > > > parameters as well as 1-4 interactions. Can someone explain me
> > this
> > >> > > please?
> > >> > > >
> > >> > > >
> > >> > > >
> > >> > > > On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann <
> > >> > s.neuman...@gmail.com
> > >> > > > >wrote:
> > >> > > >
> > >> > > > >
> > >> > > > >
> > >> > > > >
> > >> > > > > On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul <
> > jalem...@vt.edu>
> > >> > > wrote:
> > >> > > > >
> > >> > > > >>
> > >> > > > >>
> > >> > > > >> On 6/12/13 6:00 AM, Steven Neumann wrote:
> > >> > > > >>
> > >> > > > >>> Thank you. That means that e.g. when two LJ atoms of a
> > different
> > >> > type
> > >> > > > >>> approaching each other the non bonded LJ potential energy
> is a
> > >> sum
> > >> > of
> > >> > > > two
> > >> > > > >>> potentials of those atoms?
> > >> > > > >>>
> > >> > > > >>>
> > >> > > > >> No, please refer to the Gromacs manual for discussion on
> > >> > "combination
> > >> > > > >> rules" and how they fit into the Lennard-Jones equation.
> > >> > > > >>
> > >> > > > >> -Justin
> > >> > > > >>
> > >> > > > >
> > >> > > > > I read it.
> > >> > > > > I used combination rule 1 in which C=4epsSig^6 and
> A=4epsSig^12
> > -
> > >> So
> > >> > > that
> > >> > > > > means that when you provide in [atomtypes] in ffnonbonded
> your C
> > >> and
> > >> > A
> > >> > > > > values each atom has a specific LJ potential shape. Right?
> > >> > > > > So two of them approaching each other in my system will have
> > have
> > >> the
> > >> > > sum
> > >> > > > > of it.
> > >> > > > >
> > >> > > > > Steven
> > >> > > > >
> > >> > > > >
> > >> > > > >
> > >> > > > >>
> > >> > > > >>
> > >> > > > >>> On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul <
> > >> jalem...@vt.edu>
> > >> > > > wrote:
> > >> > > > >>>
> > >> > > > >>>
> > >> > > > 
> > >> > > >  On 6/12/13 5:30 AM, Steven Neumann wrote:
> > >> > > > 
> > >> > > >   Dear Gmx Users,
> > >> > > > >
> > >> > > >

Re: [gmx-users] Nonbonded parameters



On 6/12/13 8:01 AM, Steven Neumann wrote:

60 types of atoms and 60 atoms in total belonging to one residue


The number of possible combinations is (N(N+1))/2, thus you get 1830 from 60 
atom types.


-Justin




On Wed, Jun 12, 2013 at 12:59 PM, Mark Abraham wrote:


How many atom *types* are there?


On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann 
wrote:



and 1830 1-4 interactions... there are "57 all possible 1-4 interactions"


On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann 
wrote:



"All possible interactions = 60*60/2 = 1800. Where grompp takes another

30

from?


On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham <

mark.j.abra...@gmail.com

wrote:


"Parameters for possible interactions" is not the same as

"interactions."

The latter depend on the configuration and cut-offs... grompp is not

doing

a neighbor search!

Mark


On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann <

s.neuman...@gmail.com

wrote:



On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham <

mark.j.abra...@gmail.com

wrote:



grompp is just enumerating the possible combinations of parameters

given

your inputs. Whether any of those will be used in the simulation

will

depend on whether atoms of given types are close enough and not

excluded.


Mark



I understand...but why for 60 mer polypeptide there are 1830

nonbonded

interactions ?




On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann <

s.neuman...@gmail.com

wrote:



I got it. However,

I have 60  atoms in my chain all with given C6 and C12 with a

combination

rule 1. When running grompp:

Generated 1830 of the 1830 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 1830 of the 1830 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_X'
Analysing residue names:
There are: 1Protein residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 118.00
This run will generate roughly 2 Mb of data

when changing nrexcl in my topology to 0:


Generated 1830 of the 1830 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 1830 of the 1830 1-4 parameter combinations
Excluding 0 bonded neighbours molecule type 'Protein_chain_X'
Analysing residue names:
There are: 1Protein residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 118.00
This run will generate roughly 2 Mb of data

So if I exclude 1-3 interactions I have the same number of

nonbonded

parameters as well as 1-4 interactions. Can someone explain me

this

please?




On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann <

s.neuman...@gmail.com

wrote:






On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul <

jalem...@vt.edu>

wrote:





On 6/12/13 6:00 AM, Steven Neumann wrote:


Thank you. That means that e.g. when two LJ atoms of a

different

type

approaching each other the non bonded LJ potential energy

is a

sum

of

two

potentials of those atoms?



No, please refer to the Gromacs manual for discussion on

"combination

rules" and how they fit into the Lennard-Jones equation.

-Justin



I read it.
I used combination rule 1 in which C=4epsSig^6 and

A=4epsSig^12

-

So

that

means that when you provide in [atomtypes] in ffnonbonded

your C

and

A

values each atom has a specific LJ potential shape. Right?
So two of them approaching each other in my system will have

have

the

sum

of it.

Steven







On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul <

jalem...@vt.edu>

wrote:





On 6/12/13 5:30 AM, Steven Neumann wrote:

  Dear Gmx Users,


Please, correct me if I am wrong. In ffnonbonded.itp

[ atomtypes ] - these are nonbonded parameters between

atoms

of

the

same
type



No, these are the nonbonded parameters that are used when

applying

combination rules between any atoms.


   [ nonbond_params ] these are nonbonded parameters between

atoms

of



different type



No, these override combination rules.


   [ pairtypes ] - 1-4 interactions



If that is correct why amber force filed has only

[atomtypes]

column?

How
nonbonded parameters are calculated between atoms of a

different

type?

The same with charmm - only [atomtypes ] and [pairtypes ]

are

provided.

Would you please explain?


  Gromos force fields, for instance, have complex ways of

generating

nonbonded interactions that are not always the same for a

given

atomtype.
   Other force fields just use straight combination rules

and

thus

never

need
[nonbond_params].

-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

<

http://vt.edu/Pages/Personal/justin>




http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>




====

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gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Nonbonded parameters

So how come 1830 1-4 interaction? There should be 57 of 1-4 interactions
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Re: [gmx-users] Nonbonded parameters




On 6/12/13 8:16 AM, Steven Neumann wrote:

So how come 1830 1-4 interaction? There should be 57 of 1-4 interactions



Mark already told you this - interactions that exist are different from possible 
interactions.  You may have 57 interactions, but that's specific to your system 
because of how many atoms there are (which is also independent of how many atom 
types are used therein).  grompp generates a bunch of information (a matrix of 
possible interactions that could theoretically occur with N atom types); whether 
or not it uses that information is not necessarily relevant.


-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] Re: gromacs 4.6.2 MPI distribution location problems

On Wed, Jun 12, 2013 at 12:42 AM, sirishkaushik  wrote:

> Note that this works fine with 4.5.5.
>
> when I installed using:
>
> ./configure CPPFLAGS="-I/home/kaushik/fftw-new/include"
> LDFLAGS="-L/home/kaushik/fftw-new/lib" --enable-mpi --prefix
> /home/kaushik/gromacs_executable/gromacs-old
>
> ldd mdrun on the 4.5.5 version correctly points to the fftw and the mpi
> locations:
>
>
> linux-vdso.so.1 =>  (0x7fff6a302000)
> libfftw3f.so.3 => /home/kaushik/fftw-new/lib/libfftw3f.so.3
> (0x7f2e7a6e2000)
> libmpi.so.1 => /usr/local/lib/libmpi.so.1 (0x7f2e7a34)
> libnsl.so.1 => /lib/libnsl.so.1 (0x7f2e7a11b000)
> libm.so.6 => /lib/libm.so.6 (0x7f2e79e99000)
> libdl.so.2 => /lib/libdl.so.2 (0x7f2e79c95000)
> libnuma.so.1 => /usr/lib/libnuma.so.1 (0x7f2e79a8c000)
> librt.so.1 => /lib/librt.so.1 (0x7f2e79884000)
> libutil.so.1 => /lib/libutil.so.1 (0x7f2e79681000)
> libpthread.so.0 => /lib/libpthread.so.0 (0x7f2e79464000)
> libc.so.6 => /lib/libc.so.6 (0x7f2e79102000)
> libmpi.so.0 => /usr/lib/libmpi.so.0 (0x7f2e78e52000)
> /lib64/ld-linux-x86-64.so.2 (0x7f2e7a9f4000)
> libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x7f2e78c05000)
> libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x7f2e789b)
>
>
> However, with 4.6.2, when I install using:
>
> cmake -DCMAKE_INSTALL_PREFIX=/home/kaushik/gromacs_executable/gromacs-mpi
> -DGMX_THREADS=DGMX_X11=OFF -DGMX_MPI=ON
> -DCMAKE_PREFIX_PATH=/home/kaushik/fftw-new -DGMX_DEFAULT_SUFFIX=OFF
> -DMPI_INCLUDE_PATH=/usr/local/include -DMPI_COMPILER=/usr/local/bin/mpicxx
>

cmake -DCMAKE_C_COMPILER=/usr/local/bin/mpicc should Just Work.

its now pointing to the wrong MPI libraries causing the crash with the
> mpirun:
>
> ldd mdrun:
> linux-vdso.so.1 =>  (0x7fffba9ff000)
> libfftw3f.so.3 => /home/kaushik/fftw-new/lib/libfftw3f.so.3
> (0x7f32c6785000)
> libmpi_cxx.so.0 => /usr/lib/libmpi_cxx.so.0 (0x7f32c655e000)
> libmpi.so.0 => /usr/lib/libmpi.so.0 (0x7f32c62ae000)
> libdl.so.2 => /lib/libdl.so.2 (0x7f32c60aa000)
> libm.so.6 => /lib/libm.so.6 (0x7f32c5e27000)
> libnuma.so.1 => /usr/lib/libnuma.so.1 (0x7f32c5c1f000)
> librt.so.1 => /lib/librt.so.1 (0x7f32c5a17000)
> libnsl.so.1 => /lib/libnsl.so.1 (0x7f32c57fe000)
> libutil.so.1 => /lib/libutil.so.1 (0x7f32c55fb000)
> libpthread.so.0 => /lib/libpthread.so.0 (0x7f32c53df000)
> libgomp.so.1 => /usr/local/lib64/libgomp.so.1 (0x7f32c51d)
> libc.so.6 => /lib/libc.so.6 (0x7f32c4e6e000)
> libstdc++.so.6 => /usr/local/lib64/libstdc++.so.6
> (0x7f32c4b67000)
> libgcc_s.so.1 => /usr/local/lib64/libgcc_s.so.1
> (0x7f32c4951000)
> libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x7f32c4705000)
> /lib64/ld-linux-x86-64.so.2 (0x7f32c6a97000)
> libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x7f32c44af000)
>
>
> Is this a potential bug, as in the gromacs compilation is picking up the
> /usr/lib/ and /usr/include (old MPI locations) despite manually specifying
> it using -DMPI_INCLUDE, etc?
>

Perhaps, but it is not yet clear where the problem lies. In cmake, we try
to compile an MPI test program with the compiler you've made available, and
just use that compiler if it works. This combines nicely with modern MPI
wrapper compilers, hence the above suggestion. Otherwise, in cmake we try
to do some detection, and that presumably leads to your symptoms. It might
be possible to work around that by setting CMAKE_PREFIX_PATH=/usr/local, so
that the detection finds the version you want.

Mark
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[gmx-users] charmm27 in gromacs- grompp error

2013-06-12 Thread Revthi Sanker

Dear all,
I am using charmm27 forcefield in gromacs for performing all atom simulations 
(system comprising of DOPC, cholesteryl ester and protein) .I got the itp file 
for dopc from the lipid book in which they have mentioned #include 
"charmm27.ff/ffbonded.itp" and  "charmm27.ff/ffnonbonded.itp" to source to 
these for the parameters of each bond, angle dihedral etc based on the atom 
types instead of mentioning explicitly each numerical value from the gromacs 
directory.But it could not read the file and displayed:

Syntax error - File ffbonded.itp, line 2 Last line read: '[ atomtypes ]' 
Invalid order for directive defaults

 When I commented those lines and again ran grompp, it generated the following 
error:
  No default Angle types
No default Ryckaert-Bell. types.

Kindly suggest me in this issue.

Earnestly awaiting a reply,

Revathi
M.S. Research Scholar
Indian Institute Of Technology, Madras
India

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Re: [gmx-users] charmm27 in gromacs- grompp error

Sounds like either you're following wrong instructions, or not following
them correctly. Please double check and/or take up the issue with the
author.

Mark


On Wed, Jun 12, 2013 at 3:03 PM, Revthi Sanker wrote:

> Dear all,
> I am using charmm27 forcefield in gromacs for performing all atom
> simulations (system comprising of DOPC, cholesteryl ester and protein) .I
> got the itp file for dopc from the lipid book in which they have mentioned
> #include "charmm27.ff/ffbonded.itp" and  "charmm27.ff/ffnonbonded.itp" to
> source to these for the parameters of each bond, angle dihedral etc based
> on the atom types instead of mentioning explicitly each numerical value
> from the gromacs directory.But it could not read the file and displayed:
>
> Syntax error - File ffbonded.itp, line 2 Last line read: '[ atomtypes ]'
> Invalid order for directive defaults
>
>  When I commented those lines and again ran grompp, it generated the
> following error:
>   No default Angle types
> No default Ryckaert-Bell. types.
>
> Kindly suggest me in this issue.
>
> Earnestly awaiting a reply,
>
> Revathi
> M.S. Research Scholar
> Indian Institute Of Technology, Madras
> India
>
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[gmx-users] Details of umbrella sampling simulation

2013-06-12 Thread Kieu Thu Nguyen

Dear users,

What is the algorithm of umbrella sampling simulation ? And can anyone who
had experience in this explain pulling force to me  ?

Thankul and regards,

~Thu
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[gmx-users] Quartic Angle

Dear Gmx Users,

I run a simulation with quartic angle potential. These function has two
minima at 100 at 120 degrees. However, seems from my simulation that it is
not applied... all angles are around 180 degrees and my chain is a line
chain (straight).

I have in my topology

[ angles ]
; i  j  k funct th0  C0  C1  C2  C3  C4
123601389.5-46.90530.59033  -0.00328291
0.0680894

in the log file the quartic potential is shown every time. Can it be the
reason of th0 to be zero?

Steven
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[gmx-users] Re: Free Energy Calculations in Gromacs

2013-06-12 Thread JW Gibbs

Thanks Justin and Professor Shirts. The gmxdump on the resulting tpr did
indeed solve a lot of my problems. Thanks again.




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[gmx-users] Re: Details of umbrella sampling simulation

2013-06-12 Thread JW Gibbs

Hi,

Please see the following links:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/

http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WCMS66.html

I think you will understand the concept of the pulling force once you go
through either of the links. 
It's basically the force to restraint a particular collective variable
around a certain value for sampling around that region in phase space.



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Re: [gmx-users] stay at some temperature during annealing

2013-06-12 Thread mu xiaojia

Hi Guys, sorry I replay so late,
the annealing_npoints should be 4 4 4, which I incorrectly defined to 3 3 3.
the problem solved.

Thanks! Justin


On Tue, Jun 11, 2013 at 6:36 AM, Dr. Vitaly Chaban wrote:

> On Tue, Jun 11, 2013 at 12:52 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 6/11/13 1:11 AM, mu xiaojia wrote:
> >
> >> Hi guys,
> >>
> >> I am using simulated annealing for my protein+water+Ion system, I tried
> to
> >> let the system stay at some temperature for a while, e.g.: stay at 600k
> >> from 3000ps to 1 ps, then gradually cool it down to 298k, so my mdp
> is
> >> like:
> >>
> >> annealing_time = 0 3000 1 2 0 3000 1 2 0 3000 1
> 2
> >> annealing_temp = 298 600 600 298 298 600 600 298  298 600 600 298
> >>
> >>
> >> however, error message is:
> >>
> >> Found 12 annealing_time values, wanter 9
> >>
> >> apparently, the "600 600" does not work, does anyone have any
> suggestion,
> >> or I could only separate the simulation? Thanks very much!
> >>
> >>
>
>
> There is a problem with the number of temperature coupling groups. You have
> defined less than you expect, as the program requests only 9 values. So,
> refer to the number of points to T annealing, which you do not list here.
>
>
> Dr. Vitaly Chaban
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Re: [gmx-users] Re: Enthalpy Confusion

2013-06-12 Thread David van der Spoel


On 2013-06-11 23:31, Jeffery Perkins wrote:

or should i be doing < U+*ref_p > = ?



More specifically,  + *ref_p = H



 isn't really meaningful thing.  I mean, you can define something
such that  = H, but that's not really thermodynamics.


sorry I always have issues deciding how to talk about this stuff, so thanks
for putting up with my terrible notation =)


example system gives  = -1168 kJ/mol and i find  = -725 kJ/mol
either



Interesting.  What material at what phase conditions?  For liquids,
the PV contribution should be very small.


I hadn't really thought about that... but the system is a monatomic
Lennard-Jones particle (uncharged sigma = 0.35 nm epsilon = 2 kJ/mol mass =
40 amu) which should be a liquid at the conditions I was looking at, P=1000
bar, T = 300 K using phase diagram in: Equation of state for the
Lennard-Jones fluid, J. J. Nicolas et al., MOLECULAR PHYSICS, 1979, VOL. 37,
No. 5, 1429-1454

the  is -1600 and the p is 880 when manually done, around 400 from
g_energy

Here's the code:
/* This is pV (in kJ/mol).  The pressure is the reference 
pressure,

   not the instantaneous pressure */
pv = vol*md->ref_p/PRESFAC;

add_ebin(md->ebin, md->ipv, 1, &pv, bSum);
enthalpy = pv + enerd->term[F_ETOT];

What is your volume?
What is Etot?

PRESFAC  ~ 16.6










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Re: [gmx-users] Quartic Angle




On 6/12/13 10:01 AM, Steven Neumann wrote:

Dear Gmx Users,

I run a simulation with quartic angle potential. These function has two
minima at 100 at 120 degrees. However, seems from my simulation that it is
not applied... all angles are around 180 degrees and my chain is a line
chain (straight).

I have in my topology

[ angles ]
; i  j  k funct th0  C0  C1  C2  C3  C4
123601389.5-46.90530.59033  -0.00328291
0.0680894

in the log file the quartic potential is shown every time. Can it be the
reason of th0 to be zero?



That's what I'd suspect.

-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] Re: Details of umbrella sampling simulation

2013-06-12 Thread Kieu Thu Nguyen

Thank JW so much :-)


On Wed, Jun 12, 2013 at 10:30 PM, JW Gibbs wrote:

> Hi,
>
> Please see the following links:
>
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/
>
> http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WCMS66.html
>
> I think you will understand the concept of the pulling force once you go
> through either of the links.
> It's basically the force to restraint a particular collective variable
> around a certain value for sampling around that region in phase space.
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Details-of-umbrella-sampling-simulation-tp5009113p5009116.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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[gmx-users] Fw: charmm27 in gromacs- grompp error

2013-06-12 Thread Revthi Sanker




Dear all,
I am using charmm27 forcefield in gromacs for performing all atom simulations 
(system comprising of DOPC, cholesteryl ester and protein) .I got the itp file 
for dopc from the lipid book in which they have mentioned #include 
"charmm27.ff/ffbonded.itp" and  "charmm27.ff/ffnonbonded.itp" to source to 
these for the parameters of each bond, angle dihedral etc based on the atom 
types instead of mentioning explicitly each numerical value from the gromacs 
directory.But it could not read the file and displayed:

Syntax error - File ffbonded.itp, line 2 Last line read: '[ atomtypes ]' 
Invalid order for directive defaults

 When I commented those lines and again ran grompp, it generated the following 
error:
  No default Angle types
No default Ryckaert-Bell. types.

Kindly suggest me in this
 issue.

Earnestly awaiting a reply,

Revathi
M.S. Research Scholar
Indian Institute Of Technology, Madras
India
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Re: [gmx-users] Quartic Angle