[gmx-users] Reg: Unit Of Surface Tension

[vinothkumar mohanakrishnan]

Hi all

What is the unit of Surface tension that one obtains from Gromacs using the
g_energy command?. I searched the mailing list and i found two posts but the
answers seems to be contradictory. Because in one post it was said that mN/m
and in the other bar nm. below are the link of the two post. any help is
highly appreciated.

http://oldwww.gromacs.org/pipermail/gmx-users/2006-September/024028.html

http://www.mail-archive.com/gmx-users@gromacs.org/msg09748.html

Regards
Vinoth
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[gmx-users] Re: nve run of carbon nanotube

[Adwait Mevada]

Date: Wed, 17 Nov 2010 15:08:02 -0500

>>> From: Vitaly Chaban 
>>> Subject: [gmx-users] Re: nve run of carbon nanotube
>>> To: gmx-users@gromacs.org
>>> Message-ID:
>>> 
>>> Content-Type: text/plain; charset=3DISO-8859-1
>>>
>>> Also, as far as I understand, before NVE simulation, one should
>>> equilibrate the system in the  NVT ensemble (at the desired T) and
>>> only then switch off T-coupling (=3DNVE).
>> so are you suggesting that for the parameters I want to test I should
>> fix a temp say 300K, then simulate it (in vaccum) with NVT, see if the
>> physical variables equilibrate around experimental values and then go
>> switch of T-coupling?
>>> Vitaly Chaban
>>>
>>>
>> I would not say that you tube rotates so vigorously to be
>> suspicious... The tube is also very small. What about  
trying a bigger

>> one, e.g. with about 1 000 atoms? It should be more inert, if you'd
>> like it to be such.
> ok. I will do that and tell you what happens.
>>
>>> hope this might be useful:
>>> they are top and sideviews
>>> http://www.youtube.com/watch?v=3DaMMa4o0CzxU
>>> http://www.youtube.com/watch?v=3DUVksVaHcw8U
>>> http://www.youtube.com/watch?v=3DxJu3NSkA3gU
>>> http://www.youtube.com/watch?v=3DcdcyqnPY7D4
>>
>> So, now the problem becomes why NVE simulation does not preserve
>> system energy. I did not find above what method you used (MDP file)
>> for the LJ interactions. I believe the problem is someplace around
>> this point.
> I do not get you, surely the itp & top files will have the  
information

> regarding
> the LJ interactions. As far as i remember for C-C interactions I
> have C6
> and C12 interaction mentioned in [non_bond param] section  
and also whe=

n
> defining the atom type C I have used the same parameter values, is
> there
> anything else i have to take into consideration besides that?
> -Adwait

 You didn't set "vdwtype" in your .mdp file, but in this case it
 should default
 to "cutoff," which I don't think is a problem.  What might be an
 issue is your
 treatment of PBC.  If your box is somewhat small, your system will
 experience
 repulsion from forces derived from periodic copies of your  molecule.
  The proper
 approach for a vacuum simulation would be to set "pbc =3D no" and set
  all cutoffs
 to 0 to capture all intramolecular interactions.

 -Justin
>>>
>> Justin as you suggested I set pbc=3Dno, but i could not set  
cutoff's to 0
>> as grompp was giving an error saying rvdw>=3Drlist so i set  
cutoff for vd=

w
>> to 0.4 instead of 1 which resulted in greatly reduced perturbations in
>> the geometry to the extent that the carbon nanotube retained its
>> cylindrical structure. The temprature was 4K and T.E. of the  
system were

>> 11 as computed
>> by g_energy with LJ being -0.69. setting comm_mode =3D angular  
removed an=

y
>> rotation about x axis for the system
>>
>> I also tried the same thing with a large nanotube containing 1000 atoms
>> as suggested by Vitaly, and his suggestion also works out i do not find
>> distortions in the geometry except that being a long narrow tube it
>> flutuates
>> along its length, which is fine i suppose.
>>
>> What i wonder is why reduction in rvdw helps in reducing the fluction?
>> and also now if i want to put this carbon nanotube in water will using
>> this parameter set suffice or i will have to make changes so that it is
>> stable in
>> water either in NVT or NPT ensemble?
>>
>
> Making ad hoc changes to rvdw will break whatever force field  
parameter se=

t
> you're using.  For vacuum, you should set all cutoffs (rvdw,  
rcoulomb, rli=

st)
> equal to zero.  I suspect that the reduced rvdw is masking the real  =20
> underlying
> physical instability.
>

I set cutoffs to zero as you suggested but i find that the simulation =20
now just resembles the simulation of which videos i have uploaded on =20
youtube previously

> As for the condensed phase parameters, sensible non-zero values of  =20
> all cutoffs
> would be required, per whatever force field you're using.
>
> -Justin


-Adwait

-Adwait


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Re: [gmx-users] number of coordinates in pdb file does not match number of coordinates in topology file

[Justin A. Lemkul]

Taylor Kaplan wrote:

Hi all!

I have this protein GFP that I'm working and right now a co-worker 
of mine is fixing the parameterization of the chromophore which is the 
middle of the protein and so my research professor asked me to run a 
simulation with the chromophore cut out of the protein. So I took my pdb 
file of the GFP molecule and with the vi editor deleted all the 
chromophore atoms. I then used




Are you filling in the resulting gap with a reasonable "filler" residue?  If 
not, I guarantee your simulation will collapse instantly.



pdb2gmx -f gfp.pdb -ignh

which created my basic topol.top file among other basic files that the 
command produces.


I then used the command

editconf -f gfp.pdb -o gfp.pdb -c -d 5 -bt decahedron



A box-solute distance of 5 nm is overkill for most common applications.  I 
suspect this is related to your problem (see below).  If nothing else, you're 
certainly going to take a major performance hit simulating a few hundred 
thousand water molecules, most of which are completely unnecessary.


which created my box with no problems. I then proceeded to generate 
water molecules with this command...


genbox -cp gfp.pdb -o gfpW.pdb -p topol.top -cs spc216.gro

lastly I then used to try to minimize my GFP and thats where things went 
wrong.


grompp -f em.mdp -c gfpW.pdb -p topol.top -o gfpEM.tpr

The warning I received was

Fatal error:
number of coordinates in coordinate file (gfpW.pdb, 258012)
 does not match topology (topol.top, 344648)

I don't get this because I used the pdb file that was used to generate 
the topology file and then I continued to tell gromacs to modify the two 
files simultaneously after generating water for my box. I am new to 
gromacs and finding tutorials that give you all the information you need 
is near impossible. I've read the gromacs manual as well and its not 
very helpful. Please let me know what I'm doing wrong.




Commentary on what would make tutorials more user-friendly would be welcome, 
especially for those of us who work hard to write useful ones.  Just saying 
they're insufficient isn't going to make them any better ;)


I suspect there's a problem with the atom numbering that is allowed by the .pdb 
file.  Due to the huge number of atoms you've got, something might be breaking 
down, but this is a bit of a guess.  In principle, Gromacs should be able to 
deal with any number of atoms, but perhaps something is going wrong.  Try to 
re-build the system (back at the editconf step) with something like -d 1 to 
generate a substantially smaller box and a more suitable number of waters.


The one thing you can certainly check is whether or not the .pdb and .top should 
indeed match.  If you do:


grep -c OW gfpW.pdb

...it should match the number of SOL indicated in topol.top.  If it does, then 
you've probably run into some bizarre problem.  If it doesn't, then something 
else has gone wrong, though from the commands you've provided everything seems 
like it should work.


-Justin


Thanks!

(Gromacian in training) Taylor




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] number of coordinates in pdb file does not match number of coordinates in topology file

[Taylor Kaplan]

Hi all!

    I have this protein GFP that I'm working and right now a co-worker of mine 
is fixing the parameterization of the chromophore which is the middle of the 
protein and so my research professor asked me to run a simulation with the 
chromophore cut out of the protein. So I took my pdb file of the GFP molecule 
and with the vi editor deleted all the chromophore atoms. I then used 

pdb2gmx -f gfp.pdb -ignh

which created my basic topol.top file among other basic files that the command 
produces.

I then used the command

editconf -f gfp.pdb -o gfp.pdb -c -d 5 -bt decahedron

which created my box with no problems. I then proceeded to generate water 
molecules with this command...

genbox -cp gfp.pdb -o gfpW.pdb -p topol.top -cs spc216.gro

lastly I then used to try to minimize my GFP and thats where things went wrong.

grompp -f em.mdp -c gfpW.pdb -p topol.top -o gfpEM.tpr

The warning I received was 

Fatal error:
number of coordinates in coordinate file (gfpW.pdb, 258012)
 does not match topology (topol.top, 344648)

I don't get this because I used the pdb file that was used to generate the 
topology file and then I continued to tell gromacs to modify the two files 
simultaneously after generating water for my box. I am new to gromacs and 
finding tutorials that give you all the information you need is near 
impossible. I've read the gromacs manual as well and its not very helpful. 
Please let me know what I'm doing wrong.

Thanks!

(Gromacian in training) Taylor



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[gmx-users] clusters of conformations of a molecular structure using g_cluster

[段宝根]

Hi, gmx-users

I want to know whether the g_cluster is appropriate to analyze clusters of 
conformations of a structure from a trajectory, and how to use it correctly to 
attain the right results? 
I try to analyze the clusters of conformations of a structure using 
g_cluster. But the output *.pdb clusters file seemed not to be right.
g_cluster -f *.xtc -s *.tpr -wcl 10 -cutoff 0.1 -method -linkage; the only 
1 cluster was found. And the results are different when I add the option -
fit or -nofit.  The explanation of manual to the option -fit is using least 
squares fitting before RMSD calculation. what is the meaning about it in detail?
Thanks for great help.

Yours Sincerely

Duan baogen
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Re: [gmx-users] Re: nve run of carbon nanotube

[Justin A. Lemkul]

Adwait Mevada wrote:

Quoting gmx-users-requ...@gromacs.org:


Send gmx-users mailing list submissions to
gmx-users@gromacs.org

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Message: 4
Date: Wed, 17 Nov 2010 15:08:02 -0500
From: Vitaly Chaban 
Subject: [gmx-users] Re: nve run of carbon nanotube
To: gmx-users@gromacs.org
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1

Also, as far as I understand, before NVE simulation, one should
equilibrate the system in the  NVT ensemble (at the desired T) and
only then switch off T-coupling (=NVE).

so are you suggesting that for the parameters I want to test I should
fix a temp say 300K, then simulate it (in vaccum) with NVT, see if the
physical variables equilibrate around experimental values and then go
switch of T-coupling?

Vitaly Chaban



I would not say that you tube rotates so vigorously to be
suspicious... The tube is also very small. What about trying a bigger
one, e.g. with about 1 000 atoms? It should be more inert, if you'd
like it to be such.

ok. I will do that and tell you what happens.



hope this might be useful:
they are top and sideviews
http://www.youtube.com/watch?v=aMMa4o0CzxU
http://www.youtube.com/watch?v=UVksVaHcw8U
http://www.youtube.com/watch?v=xJu3NSkA3gU
http://www.youtube.com/watch?v=cdcyqnPY7D4


So, now the problem becomes why NVE simulation does not preserve
system energy. I did not find above what method you used (MDP file)
for the LJ interactions. I believe the problem is someplace around
this point.

I do not get you, surely the itp & top files will have the information
regarding
the LJ interactions. As far as i remember for C-C interactions I 
have C6

and C12 interaction mentioned in [non_bond param] section and also when
defining the atom type C I have used the same parameter values, is 
there

anything else i have to take into consideration besides that?
-Adwait


You didn't set "vdwtype" in your .mdp file, but in this case it  
should default
to "cutoff," which I don't think is a problem.  What might be an  
issue is your
treatment of PBC.  If your box is somewhat small, your system will  
experience
repulsion from forces derived from periodic copies of your  molecule. 
 The proper
approach for a vacuum simulation would be to set "pbc = no" and set 
 all cutoffs

to 0 to capture all intramolecular interactions.

-Justin



Justin as you suggested I set pbc=no, but i could not set cutoff's to 0
as grompp was giving an error saying rvdw>=rlist so i set cutoff for vdw
to 0.4 instead of 1 which resulted in greatly reduced perturbations in 
the geometry to the extent that the carbon nanotube retained its 
cylindrical structure. The temprature was 4K and T.E. of the system were 
11 as computed
by g_energy with LJ being -0.69. setting comm_mode = angular removed any 
rotation about x axis for the system


I also tried the same thing with a large nanotube containing 1000 atoms
as suggested by Vitaly, and his suggestion also works out i do not find
distortions in the geometry except that being a long narrow tube it 
flutuates

along its length, which is fine i suppose.

What i wonder is why reduction in rvdw helps in reducing the fluction?
and also now if i want to put this carbon nanotube in water will using 
this parameter set suffice or i will have to make changes so that it is 
stable in

water either in NVT or NPT ensemble?



Making ad hoc changes to rvdw will break whatever force field parameter set 
you're using.  For vacuum, you should set all cutoffs (rvdw, rcoulomb, rlist) 
equal to zero.  I suspect that the reduced rvdw is masking the real underlying 
physical instability.


As for the condensed phase parameters, sensible non-zero values of all cutoffs 
would be required, per whatever force field you're using.


-Justin



-Adwait


This message was sent using IMP, the Internet Messaging Program.



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Re: nve run of carbon nanotube

[Adwait Mevada]

Quoting gmx-users-requ...@gromacs.org:


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gmx-users@gromacs.org

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Message: 4
Date: Wed, 17 Nov 2010 15:08:02 -0500
From: Vitaly Chaban 
Subject: [gmx-users] Re: nve run of carbon nanotube
To: gmx-users@gromacs.org
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1

Also, as far as I understand, before NVE simulation, one should
equilibrate the system in the  NVT ensemble (at the desired T) and
only then switch off T-coupling (=NVE).

so are you suggesting that for the parameters I want to test I should
fix a temp say 300K, then simulate it (in vaccum) with NVT, see if the
physical variables equilibrate around experimental values and then go
switch of T-coupling?

Vitaly Chaban



I would not say that you tube rotates so vigorously to be
suspicious... The tube is also very small. What about trying a bigger
one, e.g. with about 1 000 atoms? It should be more inert, if you'd
like it to be such.

ok. I will do that and tell you what happens.



hope this might be useful:
they are top and sideviews
http://www.youtube.com/watch?v=aMMa4o0CzxU
http://www.youtube.com/watch?v=UVksVaHcw8U
http://www.youtube.com/watch?v=xJu3NSkA3gU
http://www.youtube.com/watch?v=cdcyqnPY7D4


So, now the problem becomes why NVE simulation does not preserve
system energy. I did not find above what method you used (MDP file)
for the LJ interactions. I believe the problem is someplace around
this point.

I do not get you, surely the itp & top files will have the information
regarding
the LJ interactions. As far as i remember for C-C interactions I have C6
and C12 interaction mentioned in [non_bond param] section and also when
defining the atom type C I have used the same parameter values, is there
anything else i have to take into consideration besides that?
-Adwait


You didn't set "vdwtype" in your .mdp file, but in this case it   
should default
to "cutoff," which I don't think is a problem.  What might be an   
issue is your
treatment of PBC.  If your box is somewhat small, your system will   
experience
repulsion from forces derived from periodic copies of your   
molecule.  The proper
approach for a vacuum simulation would be to set "pbc = no" and set  
 all cutoffs

to 0 to capture all intramolecular interactions.

-Justin



Justin as you suggested I set pbc=no, but i could not set cutoff's to 0
as grompp was giving an error saying rvdw>=rlist so i set cutoff for vdw
to 0.4 instead of 1 which resulted in greatly reduced perturbations in  
the geometry to the extent that the carbon nanotube retained its  
cylindrical structure. The temprature was 4K and T.E. of the system  
were 11 as computed
by g_energy with LJ being -0.69. setting comm_mode = angular removed  
any rotation about x axis for the system


I also tried the same thing with a large nanotube containing 1000 atoms
as suggested by Vitaly, and his suggestion also works out i do not find
distortions in the geometry except that being a long narrow tube it flutuates
along its length, which is fine i suppose.

What i wonder is why reduction in rvdw helps in reducing the fluction?
and also now if i want to put this carbon nanotube in water will using  
this parameter set suffice or i will have to make changes so that it  
is stable in

water either in NVT or NPT ensemble?


-Adwait


This message was sent using IMP, the Internet Messaging Program.

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Re: [gmx-users] domain decomposition error

[Mark Abraham]

On 18/11/2010 12:07 AM, Fabio Affinito wrote:

Hi,
I'm trying to run a simulation with 4.5.3 (double precision) on bluegene.


Double precision comes with a big performance penalty, particularly on 
BlueGene. Don't use it unless you know you need it.



I get this error:



NOTE: Turning on dynamic load balancing

vol 0.35! imb F 54% pme/F 2.06 step 100, remaining runtime: 3 s
vol 0.33! imb F 48% pme/F 2.09 step 200, remaining runtime: 2 s
vol 0.35! imb F 28% pme/F 2.42 step 300, remaining runtime: 1 s
vol 0.34! imb F 26% pme/F 2.46 step 400, remaining runtime: 0 s

---
Program mdrun_mpi_bg_d, VERSION 4.5.3
Source code file: domdec.c, line: 3581

Fatal error:
Step 490: The X-size (0.78) times the triclinic skew factor (1.00) is 
smaller than the smallest allowed cell size (0.80) for domain decomposition 
grid cell 4 2 2
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"Everything's formed from particles" (Van der Graaf Generator)

Error on node 188, will try to stop all the nodes
Halting parallel program mdrun_mpi_bg_d on CPU 188 out of 256


I guess that your system is too small for 256 processors, or that if 
it's large enough, that it's 
www.gromacs.org/Documentation/Terminology/Blowing_Up


The nature of the interactions in your system sets a minimum domain 
decomposition cell size, of which GROMACS reports the calculation in the 
.log file before the simulation proper starts. Each processor must have 
at least one of those cells, so your system needs to be large enough 
that you can have 256 such cells. Basically, the engineering in GROMACS 
parallelism is not able to run small systems on large numbers of 
processors - which would be inefficient to use anyway. If your BlueGene 
can't offer fewer processors, then you need to change the simulation 
system or the machine.


Mark
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Re: [gmx-users] RE: Temperature Fluctuations

[Mark Abraham]

On 18/11/2010 3:28 AM, Nimesh Jain wrote:

Hi,

I am doing Replica Exchange (RE) simulations with 8 replicas 10 degree 
apart. My system has implicit solvent and there is only one molecule 
in the system (around 270 atoms). I am using Nose-Hover thermostat and 
tabulated potentials.
When I do simulations with exchange frequency of 1 ns, the system 
blows up and the temperature goes to a few 10,000K. When I remove RE, 
the temperature fluctuations are +/- 20 degrees and they increase with 
time.
Does anyone know what the problem is ? Let me know if you need any 
other info about the system I am simulating.


If one of your simulations is not stable on its own, then you've not 
equilibrated under your thermostat properly. What was your preparation 
protocol and final .mdp?


Mark
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Re: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

[Justin A. Lemkul]

X Rules wrote:


 >
 > There was a bug in an early 4.0.x feature that box vectors were not 
properly
 > written to .pdb files (CRYST line), but this was obviously fixed 
months, if not
 > a year or more, ago. Gromacs tools are expected to handle numerous 
file types
 > effortlessly, so using .gro is certainly not required. If you have 
direct
 > evidence that some tool has written or interpreted the box 
incorrectly, then

 > please file a bugzilla, but otherwise something else likely went wrong.
 >
 > -Justin

well I will check a bit more and submit it to bugzila as there is no 
cryst line if you write a pdb with genion .. so that might be the root 
cause to my problems.


I would investigate that very thoroughly and be very sure it's reproducible 
before submitting a bugzilla.  I've run through an entire workflow (pdb2gmx, 
editconf, genbox, genion, grompp, mdrun) with lysozyme using both .gro and .pdb 
files and everything works fine either way.  That doesn't preclude the 
possibility of a bug somewhere, but I would think it very unlikely that a bug 
exists in something so fundamental that was fixed a very long time ago.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

[X Rules]

> 
> There was a bug in an early 4.0.x feature that box vectors were not properly 
> written to .pdb files (CRYST line), but this was obviously fixed months, if 
> not 
> a year or more, ago.  Gromacs tools are expected to handle numerous file 
> types 
> effortlessly, so using .gro is certainly not required.  If you have direct 
> evidence that some tool has written or interpreted the box incorrectly, then 
> please file a bugzilla, but otherwise something else likely went wrong.
> 
> -Justin

well I will check a bit more and submit it to bugzila as there is no cryst line 
if you write a pdb with genion .. so that might be the root cause to my 
problems. 
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[gmx-users] Re: nve run of carbon nanotube

[Vitaly Chaban]

Also, as far as I understand, before NVE simulation, one should
equilibrate the system in the  NVT ensemble (at the desired T) and
only then switch off T-coupling (=NVE).

Vitaly Chaban


>>> I would not say that you tube rotates so vigorously to be
>>> suspicious... The tube is also very small. What about trying a bigger
>>> one, e.g. with about 1 000 atoms? It should be more inert, if you'd
>>> like it to be such.
>> ok. I will do that and tell you what happens.
>>>
 hope this might be useful:
 they are top and sideviews
 http://www.youtube.com/watch?v=aMMa4o0CzxU
 http://www.youtube.com/watch?v=UVksVaHcw8U
 http://www.youtube.com/watch?v=xJu3NSkA3gU
 http://www.youtube.com/watch?v=cdcyqnPY7D4
>>>
>>> So, now the problem becomes why NVE simulation does not preserve
>>> system energy. I did not find above what method you used (MDP file)
>>> for the LJ interactions. I believe the problem is someplace around
>>> this point.
>> I do not get you, surely the itp & top files will have the information
>> regarding
>> the LJ interactions. As far as i remember for C-C interactions I have C6
>> and C12 interaction mentioned in [non_bond param] section and also when
>> defining the atom type C I have used the same parameter values, is there
>> anything else i have to take into consideration besides that?
>> -Adwait
>
> You didn't set "vdwtype" in your .mdp file, but in this case it should default
> to "cutoff," which I don't think is a problem.  What might be an issue is your
> treatment of PBC.  If your box is somewhat small, your system will experience
> repulsion from forces derived from periodic copies of your molecule.  The 
> proper
> approach for a vacuum simulation would be to set "pbc = no" and set all 
> cutoffs
> to 0 to capture all intramolecular interactions.
>
> -Justin
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Re: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

[Justin A. Lemkul]

X Rules wrote:


 > The error would imply that the box you have set up is < 2.0 nm, given 
the
 > cutoffs here. How did you define the box (editconf command)? What is 
your box

 > size (last line of the .gro file or in the header of a .pdb)?
 >
 > -Justin

okey.. I got it under control. The problem was.

1. created a good box widths.. went upto 30nm with editconf and box vector
2. (Made a mistake while adding ions with genion): *saved the file as 
pdb instead of gro!!*
3. was trying grompp with the pdb file (So I have no idea what grommp 
found different in a file with/witout ions)


Thanks for hinting on the last line of gro. (still I think it is 
probably a bug or feature)





There was a bug in an early 4.0.x feature that box vectors were not properly 
written to .pdb files (CRYST line), but this was obviously fixed months, if not 
a year or more, ago.  Gromacs tools are expected to handle numerous file types 
effortlessly, so using .gro is certainly not required.  If you have direct 
evidence that some tool has written or interpreted the box incorrectly, then 
please file a bugzilla, but otherwise something else likely went wrong.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

[X Rules]

> The error would imply that the box you have set up is < 2.0 nm, given the 
> cutoffs here.  How did you define the box (editconf command)?  What is your 
> box 
> size (last line of the .gro file or in the header of a .pdb)?
> 
> -Justin

okey.. I got it under control. The problem was.

1. created a good box widths.. went upto 30nm with editconf and box vector
2. (Made a mistake while adding ions with genion): saved the file as pdb 
instead of gro!!
3. was trying grompp with the pdb file (So I have no idea what grommp found 
different in a file with/witout ions)

Thanks for hinting on the last line of gro. (still I think it is probably a bug 
or feature)


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Re: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

[Justin A. Lemkul]

X Rules wrote:

Thanks Justin.
Here is the quoted error:


/processing topology...
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'CL'
processing coordinates...
double-checking input for internal consistency...

ERROR 1 [file protein.top, line 9279]:
  ERROR: One of the box lengths is smaller than twice the cut-off length.
  Increase the box size or decrease rlist.


---
Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 1104

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"Three Little Fonzies" (Pulp Fiction)/

and the mdp

/; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment

title   = Energy Minimization   ; Title of run

; The following line tell the program the standard locations where to 
find certain files

cpp = /usr/bin/cpp  ; Preprocessor

; Define can be used to control processes
define  = -DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 1.0   ; Stop minimization when the maximum 
force < 1.0 kJ/mol
nsteps  = 5000  ; Maximum number of (minimization) steps 
to perform
nstenergy   = 1 ; Write energies to disk every nstenergy 
steps

energygrps  = System; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how 
to calculate the interactions
ns_type = simple; Method to determine neighbor list 
(simple, grid)

coulombtype = PME   ; Treatment of long range electrostatic interactions
rcoulomb= 1.0   ; long range electrostatic cut-off
rvdw= 1.0   ; long range Van der Waals cut-off
constraints = none  ; Bond types to replace by constraints
pbc = xyz   ; Periodic Boundary Conditions (yes/no)/

Hope you can locate my error here!!



The error would imply that the box you have set up is < 2.0 nm, given the 
cutoffs here.  How did you define the box (editconf command)?  What is your box 
size (last line of the .gro file or in the header of a .pdb)?


-Justin




 > Date: Wed, 17 Nov 2010 13:09:32 -0500
 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] Error on Box Length when adding ions 
(gromacs 4.5.3/Charmm27/Tip3p)

 >
 >
 >
 > X Rules wrote:
 > > I am having problems with grompp with my system.
 > >
 > > I am using Gromacs 4.5.3
 > > FF = Charmm27 beta
 > > WT = TIP3P (recommended and its claimed its not too different than
 > > Charmms TIP3P)
 > >
 > > during minimization with pbc, I get the error about box length being
 > > small if I add neutralizing ions (I do not get this error in just
 > > water+protein system).
 > >
 >
 > Providing your actual sequence of commands, .mdp file(s), and the actual
 > (quoted) error message is the only way to diagnose what's going on.
 >
 > > Also I have tried increasing my box length upto a cube of 40 Angstroms
 > > and still get the error ( I have a tiny 50 residue protein).
 > >
 > > IS IT A BUG or I am doing something wrong.
 > >
 >
 > You're probably doing something wrong, but it's impossible to say 
what. Please

 > provide more detail.
 >
 > -Justin
 >
 > >
 > > I can add more information if needed.
 > >
 > > Thanks,
 > >
 >
 > --
 > 
 >
 > Justin A. Lemkul
 > Ph.D. Candidate
 > ICTAS Doctoral Scholar
 > MILES-IGERT Trainee
 > 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 list gmx-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


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral 

[gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

[X Rules]

 Thanks Justin. 
Here is the quoted error:

processing topology...
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'CL'
processing coordinates...
double-checking input for internal consistency...

ERROR 1 [file protein.top, line 9279]:
  ERROR: One of the box lengths is smaller than twice the cut-off length.
  Increase the box size or decrease rlist.


---
Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 1104

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"Three Little Fonzies" (Pulp Fiction)
and the mdp
; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment

title   = Energy Minimization   ; Title of run

; The following line tell the program the standard locations where to find 
certain files
cpp = /usr/bin/cpp  ; Preprocessor

; Define can be used to control processes
define  = -DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 1.0   ; Stop minimization when the maximum force < 
1.0 kJ/mol
nsteps  = 5000  ; Maximum number of (minimization) steps to 
perform
nstenergy   = 1 ; Write energies to disk every nstenergy steps
energygrps  = System; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
ns_type = simple; Method to determine neighbor list (simple, 
grid)
coulombtype = PME   ; Treatment of long range electrostatic interactions
rcoulomb= 1.0   ; long range electrostatic cut-off
rvdw= 1.0   ; long range Van der Waals cut-off
constraints = none  ; Bond types to replace by constraints
pbc = xyz   ; Periodic Boundary Conditions (yes/no)
Hope you can locate my error here!!



> Date: Wed, 17 Nov 2010 13:09:32 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Error on Box Length when adding ions (gromacs
> 4.5.3/Charmm27/Tip3p)
> 
> 
> 
> X Rules wrote:
> > I am having problems with grompp with my system.
> > 
> > I am using Gromacs 4.5.3
> > FF  = Charmm27 beta
> > WT = TIP3P (recommended and its claimed its not too different than 
> > Charmms TIP3P)
> > 
> > during minimization with pbc, I get the error about box length being 
> > small if I add neutralizing ions (I do not get this error in just 
> > water+protein system).
> > 
> 
> Providing your actual sequence of commands, .mdp file(s), and the actual 
> (quoted) error message is the only way to diagnose what's going on.
> 
> > Also I have tried increasing my box length upto a cube of 40 Angstroms 
> > and still get the error ( I have a tiny 50 residue protein).
> > 
> > IS IT A BUG or I am doing something wrong.
> > 
> 
> You're probably doing something wrong, but it's impossible to say what.  
> Please 
> provide more detail.
> 
> -Justin
> 
> > 
> > I can add more information if needed.
> > 
> > Thanks,
> > 
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
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Re: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

[Justin A. Lemkul]

X Rules wrote:

I am having problems with grompp with my system.

I am using Gromacs 4.5.3
FF  = Charmm27 beta
WT = TIP3P (recommended and its claimed its not too different than 
Charmms TIP3P)


during minimization with pbc, I get the error about box length being 
small if I add neutralizing ions (I do not get this error in just 
water+protein system).




Providing your actual sequence of commands, .mdp file(s), and the actual 
(quoted) error message is the only way to diagnose what's going on.


Also I have tried increasing my box length upto a cube of 40 Angstroms 
and still get the error ( I have a tiny 50 residue protein).


IS IT A BUG or I am doing something wrong.



You're probably doing something wrong, but it's impossible to say what.  Please 
provide more detail.


-Justin



I can add more information if needed.

Thanks,



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

[X Rules]

I am having problems with grompp with my system. 

I am using Gromacs 4.5.3
FF  = Charmm27 beta
WT = TIP3P (recommended and its claimed its not too different than Charmms 
TIP3P)

during minimization with pbc, I get the error about box length being small if I 
add neutralizing ions (I do not get this error in just water+protein system). 

Also I have tried increasing my box length upto a cube of 40 Angstroms and 
still get the error ( I have a tiny 50 residue protein). 

IS IT A BUG or I am doing something wrong. 


I can add more information if needed.

Thanks,

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[gmx-users] (no subject)

[Daniel Adriano Silva M]

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[gmx-users] RE: Temperature Fluctuations

[Nimesh Jain]

Hi,

I am doing Replica Exchange (RE) simulations with 8 replicas 10 degree
apart. My system has implicit solvent and there is only one molecule in the
system (around 270 atoms). I am using Nose-Hover thermostat and tabulated
potentials.
When I do simulations with exchange frequency of 1 ns, the system blows up
and the temperature goes to a few 10,000K. When I remove RE, the temperature
fluctuations are +/- 20 degrees and they increase with time.
Does anyone know what the problem is ? Let me know if you need any other
info about the system I am simulating.

Thanks,
Nimesh
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[gmx-users] Re: gmx-users Digest, Vol 79, Issue 124

[Stephane Abel]

OK thank you all, I give up  :-(

a bientot





Stephane Abel wrote:
  

OK thank you for your help justin

With the change you have suggested, grompp starts but an other error 
come quickly with the first line of the gb.itp:


ERROR 1 [file /home/cont003/abel01/charmm27.ff//gb.itp, line 1]:
Invalid directive implicit_genborn_params


---
Program grompp_mpi, VERSION 4.0.7
Source code file: toppush.c, line: 756

Fatal error:
Unknown bond_atomtype 0.155
---

"Pump Up the Volume Along With the Tempo" (Jazzy Jeff)

Here the head of my gb.itp file

[ implicit_genborn_params ]
; Atom type sar st pi gbr hct

NH1 0.155 1 1.028 0.17063 0.79 ; N

I have tried to pass this error by commenting the #include "gb.itp" 
statements in the forcefield.itp file with no success.


Do you have any other (good) suggestion ?




I would echo what Mark has said - the only clean way to make this work is to use 
a compatible version of Gromacs (4.5.3 preferably).  There have been significant 
changes between 4.0.7 and 4.5, and anything you might hack to "make work" would 
be questionable.


-Justin

  

Stefane






--

Message: 3
Date: Wed, 17 Nov 2010 07:59:20 -0500
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] [Fwd: Use an altenative folder for itp files]
To: Discussion list for GROMACS users 
Message-ID: <4ce3d1a8.9070...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Stephane Abel wrote:
 
  

Dear all,


I have a little question about the use of a alternative localization 
of the ff librairy in GMX4.0.7. These (old) version of GMX is 
installed in a big cluster and i would like to use it for testing 
some CHARMM27 parameters. Since the charmm27.ff is not given this 
distribution, i would like to use my own ff lib, so i have placed my 
home directory the charmm27.ff directory with all the necessary 
files. As expected, when i use grompp, i have an error :



Fatal error:
Library file ffnonbonded.itp not found in current dir nor in default 
directories.

(You can set the directories to search with the GMXLIB path variable)


How to indicate to grompp that the charmm27.ff is my directory say 
/home/cont003/stefane/charmm27.ff/



I have read that the include directive can do the job, so i placed 
the path of the charmm27.ff like this in my mdp file



include = = -I /home/cont003/stefane/charmm27.ff/forcefield.itp


but the program hangs:

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.13#
checking input for internal consistency...
processing topology...


have I missed something ?



The "include" keyword should point to a directory in which your .itp 
files reside, not an .itp file itself.


-Justin

 
  

Thanks in advance for your help


Stefane





  
  


  


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Re: [gmx-users] Re: nve run of carbon nanotube

[Justin A. Lemkul]

Adwait Mevada wrote:




I would not say that you tube rotates so vigorously to be
suspicious... The tube is also very small. What about trying a bigger
one, e.g. with about 1 000 atoms? It should be more inert, if you'd
like it to be such.

ok. I will do that and tell you what happens.



hope this might be useful:
they are top and sideviews
http://www.youtube.com/watch?v=aMMa4o0CzxU
http://www.youtube.com/watch?v=UVksVaHcw8U
http://www.youtube.com/watch?v=xJu3NSkA3gU
http://www.youtube.com/watch?v=cdcyqnPY7D4


So, now the problem becomes why NVE simulation does not preserve
system energy. I did not find above what method you used (MDP file)
for the LJ interactions. I believe the problem is someplace around
this point.
I do not get you, surely the itp & top files will have the information 
regarding
the LJ interactions. As far as i remember for C-C interactions I have C6 
and C12 interaction mentioned in [non_bond param] section and also when 
defining the atom type C I have used the same parameter values, is there 
anything else i have to take into consideration besides that?

-Adwait


You didn't set "vdwtype" in your .mdp file, but in this case it should default 
to "cutoff," which I don't think is a problem.  What might be an issue is your 
treatment of PBC.  If your box is somewhat small, your system will experience 
repulsion from forces derived from periodic copies of your molecule.  The proper 
approach for a vacuum simulation would be to set "pbc = no" and set all cutoffs 
to 0 to capture all intramolecular interactions.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Re: nve run of carbon nanotube

[Adwait Mevada]

Quoting gmx-users-requ...@gromacs.org:


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Today's Topics:

   1. Re: nve run of carbon nanotube (Vitaly Chaban)
   2. question (Raymond)
   3. Re: question (Mark Abraham)
   4. Reg: pcoupling and ref_p (vinothkumar mohanakrishnan)


--

Message: 1
Date: Tue, 16 Nov 2010 23:48:39 -0500
From: Vitaly Chaban 
Subject: [gmx-users] Re: nve run of carbon nanotube
To: gmx-users@gromacs.org
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1

I would not say that you tube rotates so vigorously to be
suspicious... The tube is also very small. What about trying a bigger
one, e.g. with about 1 000 atoms? It should be more inert, if you'd
like it to be such.

ok. I will do that and tell you what happens.



hope this might be useful:
they are top and sideviews
http://www.youtube.com/watch?v=aMMa4o0CzxU
http://www.youtube.com/watch?v=UVksVaHcw8U
http://www.youtube.com/watch?v=xJu3NSkA3gU
http://www.youtube.com/watch?v=cdcyqnPY7D4


So, now the problem becomes why NVE simulation does not preserve
system energy. I did not find above what method you used (MDP file)
for the LJ interactions. I believe the problem is someplace around
this point.
I do not get you, surely the itp & top files will have the information  
regarding
the LJ interactions. As far as i remember for C-C interactions I have  
C6 and C12 interaction mentioned in [non_bond param] section and also  
when defining the atom type C I have used the same parameter values,  
is there anything else i have to take into consideration besides that?

-Adwait


--
Dr. Vitaly Chaban


--

Message: 2
Date: Wed, 17 Nov 2010 14:52:48 +0800
From: "Raymond" <3609...@sina.com>
Subject: [gmx-users] question
To: "gmx-users" 
Message-ID: <201011171452473369...@sina.com>
Content-Type: text/plain; charset="us-ascii"

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Message: 3
Date: Wed, 17 Nov 2010 19:26:46 +1100
From: Mark Abraham 
Subject: Re: [gmx-users] question
To: Discussion list for GROMACS users 
Message-ID: <4ce391c6.1020...@anu.edu.au>
Content-Type: text/plain; charset="iso-8859-1"

On 17/11/2010 5:52 PM, Raymond wrote:

Why my rdf is larger than 1 in the long range
2010-11-17

Raymond


Probably because you did not measure what you thought you measured :-)

Mark
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Message: 4
Date: Wed, 17 Nov 2010 14:08:54 +0530
From: vinothkumar mohanakrishnan 
Subject: [gmx-users] Reg: pcoupling and ref_p
To: Discussion list for GROMACS users 
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Hi Gromacians

I have created two liquid-liquid interfaces by combining three
(DCE-Water-DCE) boxes. I want to calculate the Interfacial surface tension
by using the surface tension option in Gromacs.
I know that I need to give two values for ref_p one for xy and other for z.
it was said in the manual that the "first value should be reference surface
tension times the number of surfaces".what does it mean? what is this
reference surface tension and what value i should put to calculate the
surface tension? i know that the ref_p for z should be 1 bar (correct me if
i am wrong) Further more how come ref_p unit will be bar nm for xy and for z
it will be bar? any help is highly appreciated.

Regards
Vinoth
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End of gmx-users Digest, Vol 79, Issue 121
**





-Adwait

Re: [gmx-users] PGI link error: unknown switch --rpath & attempted static link of dynamic object fftw/lib/libfftw3.so

[Justin A. Lemkul]

Yudong Sun wrote:

Hi Roland,

CMake works fine for the installation.

There may be minor typos in the online installation instructions using 
CMake here http://www.gromacs.org/Developer_Zone/Cmake


To use single precision FFTW, the two FFTW3 flags should be:

cmake -D FFTW3F_INCLUDE_DIR=... -D FFTW3F_LIBRARIES=...

instead of FFTW3_INCLUDE_DIR and FFTW3_LIBRARIES. Otherwise cmake will 
complain fftw library not found when building single precision libraries.




Fixed on the wiki.  Thanks.

-Justin


Thanks,

Yudong


Hi,

this is a bug in the autoconf version GROMACS is using. Since we are 
moving
to cmake we are not updating it thus this is an issue which won't be 
fixed.


There are two options:
- Create a folder. Copy (or symlink) the static library into that folder.
Point the linker (-L) to that folder. Because your folder only has the
static libraries it will work.
- Use cmake. For cmake this issue is solved.



The Numerical Algorithms Group Ltd is a company registered in England
and Wales with company number 1249803. The registered office is:
Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.

This e-mail has been scanned for all viruses by Star. The service is
powered by MessageLabs. 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] PGI link error: unknown switch --rpath & attempted static link of dynamic object fftw/lib/libfftw3.so

[Yudong Sun]

Hi Roland,

CMake works fine for the installation.

There may be minor typos in the online installation instructions using 
CMake here http://www.gromacs.org/Developer_Zone/Cmake


To use single precision FFTW, the two FFTW3 flags should be:

cmake -D FFTW3F_INCLUDE_DIR=... -D FFTW3F_LIBRARIES=...

instead of FFTW3_INCLUDE_DIR and FFTW3_LIBRARIES. Otherwise cmake will 
complain fftw library not found when building single precision libraries.


Thanks,

Yudong


Hi,

this is a bug in the autoconf version GROMACS is using. Since we are moving
to cmake we are not updating it thus this is an issue which won't be fixed.

There are two options:
- Create a folder. Copy (or symlink) the static library into that folder.
Point the linker (-L) to that folder. Because your folder only has the
static libraries it will work.
- Use cmake. For cmake this issue is solved.



The Numerical Algorithms Group Ltd is a company registered in England
and Wales with company number 1249803. The registered office is:
Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.

This e-mail has been scanned for all viruses by Star. The service is
powered by MessageLabs. 


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Re: [gmx-users] Use an altenative folder for itp files

[Justin A. Lemkul]

Stephane Abel wrote:

OK thank you for your help justin

With the change you have suggested, grompp starts but an other error 
come quickly with the first line of the gb.itp:


ERROR 1 [file /home/cont003/abel01/charmm27.ff//gb.itp, line 1]:
Invalid directive implicit_genborn_params


---
Program grompp_mpi, VERSION 4.0.7
Source code file: toppush.c, line: 756

Fatal error:
Unknown bond_atomtype 0.155
---

"Pump Up the Volume Along With the Tempo" (Jazzy Jeff)

Here the head of my gb.itp file

[ implicit_genborn_params ]
; Atom type sar st pi gbr hct

NH1 0.155 1 1.028 0.17063 0.79 ; N

I have tried to pass this error by commenting the #include "gb.itp" 
statements in the forcefield.itp file with no success.


Do you have any other (good) suggestion ?



I would echo what Mark has said - the only clean way to make this work is to use 
a compatible version of Gromacs (4.5.3 preferably).  There have been significant 
changes between 4.0.7 and 4.5, and anything you might hack to "make work" would 
be questionable.


-Justin


Stefane






--

Message: 3
Date: Wed, 17 Nov 2010 07:59:20 -0500
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] [Fwd: Use an altenative folder for itp files]
To: Discussion list for GROMACS users 
Message-ID: <4ce3d1a8.9070...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Stephane Abel wrote:
 

Dear all,


I have a little question about the use of a alternative localization 
of the ff librairy in GMX4.0.7. These (old) version of GMX is 
installed in a big cluster and i would like to use it for testing 
some CHARMM27 parameters. Since the charmm27.ff is not given this 
distribution, i would like to use my own ff lib, so i have placed my 
home directory the charmm27.ff directory with all the necessary 
files. As expected, when i use grompp, i have an error :



Fatal error:
Library file ffnonbonded.itp not found in current dir nor in default 
directories.

(You can set the directories to search with the GMXLIB path variable)


How to indicate to grompp that the charmm27.ff is my directory say 
/home/cont003/stefane/charmm27.ff/



I have read that the include directive can do the job, so i placed 
the path of the charmm27.ff like this in my mdp file



include = = -I /home/cont003/stefane/charmm27.ff/forcefield.itp


but the program hangs:

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.13#
checking input for internal consistency...
processing topology...


have I missed something ?




The "include" keyword should point to a directory in which your .itp 
files reside, not an .itp file itself.


-Justin

 

Thanks in advance for your help


Stefane






  




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Use an altenative folder for itp files

[Stephane Abel]

OK thank you for your help justin

With the change you have suggested, grompp starts but an other error 
come quickly with the first line of the gb.itp:


ERROR 1 [file /home/cont003/abel01/charmm27.ff//gb.itp, line 1]:
Invalid directive implicit_genborn_params


---
Program grompp_mpi, VERSION 4.0.7
Source code file: toppush.c, line: 756

Fatal error:
Unknown bond_atomtype 0.155
---

"Pump Up the Volume Along With the Tempo" (Jazzy Jeff)

Here the head of my gb.itp file

[ implicit_genborn_params ]
; Atom type sar st pi gbr hct

NH1 0.155 1 1.028 0.17063 0.79 ; N

I have tried to pass this error by commenting the #include "gb.itp" 
statements in the forcefield.itp file with no success.


Do you have any other (good) suggestion ?

Stefane






--

Message: 3
Date: Wed, 17 Nov 2010 07:59:20 -0500
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] [Fwd: Use an altenative folder for itp files]
To: Discussion list for GROMACS users 
Message-ID: <4ce3d1a8.9070...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Stephane Abel wrote:
  

Dear all,


I have a little question about the use of a alternative localization of 
the ff librairy in GMX4.0.7. These (old) version of GMX is installed in 
a big cluster and i would like to use it for testing some CHARMM27 
parameters. Since the charmm27.ff is not given this distribution, i 
would like to use my own ff lib, so i have placed my home directory the 
charmm27.ff directory with all the necessary files. As expected, when i 
use grompp, i have an error :



Fatal error:
Library file ffnonbonded.itp not found in current dir nor in default 
directories.

(You can set the directories to search with the GMXLIB path variable)


How to indicate to grompp that the charmm27.ff is my directory say 
/home/cont003/stefane/charmm27.ff/



I have read that the include directive can do the job, so i placed the 
path of the charmm27.ff like this in my mdp file



include = = -I /home/cont003/stefane/charmm27.ff/forcefield.itp


but the program hangs:

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.13#
checking input for internal consistency...
processing topology...


have I missed something ?




The "include" keyword should point to a directory in which your .itp files 
reside, not an .itp file itself.


-Justin

  

Thanks in advance for your help


Stefane






  


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Re: [gmx-users] [Fwd: Use an altenative folder for itp files]

[Mark Abraham]

On 17/11/2010 10:59 PM, Stephane Abel wrote:


Dear all,


I have a little question about the use of a alternative localization 
of the ff librairy in GMX4.0.7. These (old) version of GMX is 
installed in a big cluster and i would like to use it for testing some 
CHARMM27 parameters. Since the charmm27.ff is not given this 
distribution, i would like to use my own ff lib, so i have placed my 
home directory the charmm27.ff directory with all the necessary files. 
As expected, when i use grompp, i have an error :



Fatal error:
Library file ffnonbonded.itp not found in current dir nor in default 
directories.

(You can set the directories to search with the GMXLIB path variable)


How to indicate to grompp that the charmm27.ff is my directory say 
/home/cont003/stefane/charmm27.ff/



I have read that the include directive can do the job, so i placed the 
path of the charmm27.ff like this in my mdp file



include = = -I /home/cont003/stefane/charmm27.ff/forcefield.itp


That line has too many "=" symbols. Also the force field organization 
changed between 4.0.7 and current, so this approach will not be fully 
functional. Get 4.5.3 installed and do things properly :-)


Mark




but the program hangs:

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.13#
checking input for internal consistency...
processing topology...


have I missed something ?


Thanks in advance for your help


Stefane





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[gmx-users] domain decomposition error

[Fabio Affinito]

Hi,
I'm trying to run a simulation with 4.5.3 (double precision) on bluegene.
I get this error:


> NOTE: Turning on dynamic load balancing
> 
> vol 0.35! imb F 54% pme/F 2.06 step 100, remaining runtime: 3 s
> vol 0.33! imb F 48% pme/F 2.09 step 200, remaining runtime: 2 s
> vol 0.35! imb F 28% pme/F 2.42 step 300, remaining runtime: 1 s
> vol 0.34! imb F 26% pme/F 2.46 step 400, remaining runtime: 0 s
> 
> ---
> Program mdrun_mpi_bg_d, VERSION 4.5.3
> Source code file: domdec.c, line: 3581
> 
> Fatal error:
> Step 490: The X-size (0.78) times the triclinic skew factor (1.00) is 
> smaller than the smallest allowed cell size (0.80) for domain 
> decomposition grid cell 4 2 2
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> "Everything's formed from particles" (Van der Graaf Generator)
> 
> Error on node 188, will try to stop all the nodes
> Halting parallel program mdrun_mpi_bg_d on CPU 188 out of 256
> 

Can anybody give me some hint about that?

Thanks in advance,

Fabio
-- 
*
Fabio Affinito, PhD
CINECA
SuperComputing Applications and Innovation Department - SCAI
Via Magnanelli, 6/3
40033 Casalecchio di Reno (Bologna) ITALY
+39/051/6171794 (Phone)
-- 
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[gmx-users] Re: Can I have the mdp file?

[Pär Bjelkmar]

Hi,

I forward this discussion to the mailing list now because I think that it might 
be of interest to some people at least. Please find the mdp file of the GROMACS 
runs attached. To get the energies between GROMACS and CHARMM to match one has 
to do at least two things:
* make sure the molecular conformation is _exactly_ the same. I.e. the 
coordinates of the atoms should be identical (inclusive correct number of 
significant figures)
* run without cut-offs 

Regards,
Pär Bjelkmar



md.mdp
Description: Binary data


17 nov 2010 kl. 13.16 skrev Xin Chen:

> yes, I have done. But the potential calculated by these two methods differs 
> greatly. And the difference between the two is more than 10kj/mol. The CHARMM 
> calculation seems fine. 
> I guess that I set the parameters wrong in the mdp file during the GROMACS 
> calculation...
> 
> 
> 
> 
>> -Original E-mail-
>> From: "Pär Bjelkmar" 
>> Sent Time: 2010-11-17 16:18:18
>> To: "Xin Chen" 
>> Cc: 
>> Subject: Re: Can I have the mdp file?
>> 
>> Hi,
>> 
>> I do not fully understand what you're trying to do. To reproduce Table 1 you 
>> need to run the program CHARMM as well as GROMACS, have you already done 
>> that?
>> 
>> /Pär
>> 
>> 17 nov 2010 kl. 03.24 skrev Xin Chen:
>> 
>>> 
>>> Professor Bjelkmar:
>>>   hello, I've finished the article that you referred to me in your last 
>>> mail. It's quite helpful and thank you. But I have some trouble when I test 
>>> some amoni acid. The results couldn't get well with the table1 in the 
>>> article. I considered whether I caculated in the same way as you did, 
>>> especially the mdp options for Gromacs. 
>>>   So, can I have the mdp file when you make the table? The table is also 
>>> sent as an attachment.
>>>   Thank you and Best Wishes!
>>> Xin Chen
>>>   2010.11.17
>>> 
>> 
> 

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Re: [gmx-users] [Fwd: Use an altenative folder for itp files]

[Justin A. Lemkul]

Stephane Abel wrote:


Dear all,


I have a little question about the use of a alternative localization of 
the ff librairy in GMX4.0.7. These (old) version of GMX is installed in 
a big cluster and i would like to use it for testing some CHARMM27 
parameters. Since the charmm27.ff is not given this distribution, i 
would like to use my own ff lib, so i have placed my home directory the 
charmm27.ff directory with all the necessary files. As expected, when i 
use grompp, i have an error :



Fatal error:
Library file ffnonbonded.itp not found in current dir nor in default 
directories.

(You can set the directories to search with the GMXLIB path variable)


How to indicate to grompp that the charmm27.ff is my directory say 
/home/cont003/stefane/charmm27.ff/



I have read that the include directive can do the job, so i placed the 
path of the charmm27.ff like this in my mdp file



include = = -I /home/cont003/stefane/charmm27.ff/forcefield.itp


but the program hangs:

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.13#
checking input for internal consistency...
processing topology...


have I missed something ?



The "include" keyword should point to a directory in which your .itp files 
reside, not an .itp file itself.


-Justin



Thanks in advance for your help


Stefane





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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Please search the archive at 
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[gmx-users] [Fwd: Use an altenative folder for itp files]

[Stephane Abel]

Dear all,


I have a little question about the use of a alternative localization of 
the ff librairy in GMX4.0.7. These (old) version of GMX is installed in 
a big cluster and i would like to use it for testing some CHARMM27 
parameters. Since the charmm27.ff is not given this distribution, i 
would like to use my own ff lib, so i have placed my home directory the 
charmm27.ff directory with all the necessary files. As expected, when i 
use grompp, i have an error :



Fatal error:
Library file ffnonbonded.itp not found in current dir nor in default 
directories.

(You can set the directories to search with the GMXLIB path variable)


How to indicate to grompp that the charmm27.ff is my directory say 
/home/cont003/stefane/charmm27.ff/



I have read that the include directive can do the job, so i placed the 
path of the charmm27.ff like this in my mdp file



include = = -I /home/cont003/stefane/charmm27.ff/forcefield.itp


but the program hangs: 



Back Off! I just backed up mdout.mdp to ./#mdout.mdp.13#
checking input for internal consistency...
processing topology...


have I missed something ?


Thanks in advance for your help


Stefane



--
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[gmx-users] problem linking fftw2 with gromacs 4.5.3

[Fabio Affinito]

Hi folks,
I'm experiencing some problem when I try to compile gromacs 4.5.3
linking fftw.
This is the configure:
> ./configure --prefix=/bgp/userinternal/cin0644a/gromacs.453 \
>   --host=ppc --build=ppc64 --enable-ppc-sqrt=1 \
>   --disable-ppc-altivec \
>   --enable-bluegene --enable-mpi --with-fft=fftw2 \
>   --program-suffix=_mpi_bg_dp \
>   --without-x \
>  CC=mpixlc_r \
>  CFLAGS="-O3 -qarch=450d -qtune=450" \
>  MPICC=mpixlc_r CXX=mpixlC_r \
>  CXXFLAGS="-O3 -qarch=450d -qtune=450" \
>  CPPFLAGS="-I/bgp/userinternal/cin0644a/fftw2/include" \
>  F77=mpixlf77_r FFLAGS="-O3 -qarch=auto -qtune=auto" \
>  LDFLAGS="-L/bgp/userinternal/cin0644a/fftw2/lib" 

This is the error during the make
> mkdir .libs
> libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled 
> argument `../mdlib/libmd_mpi.la'
> make[1]: *** [libgmxpreprocess_mpi.la] Error 1
> make[1]: Leaving directory 
> `/bgp/userinternal/cin0644a/gromacs-4.5.3/src/kernel'

The directory /lib:

> libfftw.a   libfftw_threads.a   librfftw.a   librfftw_threads.a
> libfftw.la  libfftw_threads.la  librfftw.la  librfftw_threads.la

The directory /include:

> fftw.h  fftw_threads.h  rfftw.h  rfftw_threads.h

Do you have any hint?

Thanks in advance,

Fabio



-- 
*
Fabio Affinito, PhD
CINECA
SuperComputing Applications and Innovation Department - SCAI
Via Magnanelli, 6/3
40033 Casalecchio di Reno (Bologna) ITALY
+39/051/6171794 (Phone)
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Re: [gmx-users] rdf wrong convergence

[Mark Abraham]

On 17/11/2010 8:07 PM, Raymond wrote:

I built a system with 2 bulks .left side is liquid side  right is gas .
But the convergence of the rdf only liquid I calculated is more than 
1(about 1.3) .
I make a comparison with the Previously work I did (liquid only 
without gas ) the trend is totally same but the convergence is at 1.3

I don't know  what's wrong with it
did the problem lie on the .mdp file(maybe the cutoff? my cutoff is 
1.9 and the X range of left bulk is 4,the right is 4 too ) or -RDF 
command or something other


Your description makes it very hard for anyone to help you - they have 
to spend so much time organizing the information that they're just going 
to walk away. In order to do science effectively, you need to be 
methodical, and that has to show in your description of what you've 
done, in order that other people can believe they can actually help you. 
Also consider some of the points here 
http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette and 
http://www.gromacs.org/Support about constructing help requests. :-) 
More information about your system preparation and simulation protocol 
is required, and your g_rdf command lines are necessary :-)


Mark
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Re: Re: [gmx-users] question

[Raymond]

I'm very sorry that  last Email was just a test ~~~ I don't know how to use 
this . here is my problem ~~ Thanks very much 

I built a system with 2 bulks .left side is liquid side  right is gas .
But the convergence of the rdf only liquid I calculated is more than 1(about 
1.3) .
I make a comparison with the Previously work I did (liquid only without gas ) 
the trend is totally same but the convergence is at 1.3

I don't know  what's wrong with it

did the problem lie on the .mdp file(maybe the cutoff? my cutoff is 1.9 and the 
X range of left bulk is 4,the right is 4 too ) or -RDF command or something 
other 

Thanks very much for giving me advice .  


2010-11-17 



Raymond 



发件人： Mark Abraham 
发送时间： 2010-11-17  16:27:39 
收件人： Discussion list for GROMACS users 
抄送： 
主题： Re: [gmx-users] question 
 
On 17/11/2010 5:52 PM, Raymond wrote: 

Why my rdf is larger than 1 in the long range
2010-11-17 



Raymond 

Probably because you did not measure what you thought you measured :-)

Mark
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[gmx-users] rdf wrong convergence

[Raymond]

I built a system with 2 bulks .left side is liquid side  right is gas .
But the convergence of the rdf only liquid I calculated is more than 1(about 
1.3) .
I make a comparison with the Previously work I did (liquid only without gas ) 
the trend is totally same but the convergence is at 1.3

I don't know  what's wrong with it

did the problem lie on the .mdp file(maybe the cutoff? my cutoff is 1.9 and the 
X range of left bulk is 4,the right is 4 too ) or -RDF command or something 
other 

Thanks very much for giving me advice .  

2010-11-17 



Raymond 
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[gmx-users] Reg: pcoupling and ref_p

[vinothkumar mohanakrishnan]

Hi Gromacians

I have created two liquid-liquid interfaces by combining three
(DCE-Water-DCE) boxes. I want to calculate the Interfacial surface tension
by using the surface tension option in Gromacs.
I know that I need to give two values for ref_p one for xy and other for z.
it was said in the manual that the "first value should be reference surface
tension times the number of surfaces".what does it mean? what is this
reference surface tension and what value i should put to calculate the
surface tension? i know that the ref_p for z should be 1 bar (correct me if
i am wrong) Further more how come ref_p unit will be bar nm for xy and for z
it will be bar? any help is highly appreciated.

Regards
Vinoth
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Re: [gmx-users] question

[Mark Abraham]

On 17/11/2010 5:52 PM, Raymond wrote:

Why my rdf is larger than 1 in the long range
2010-11-17

Raymond


Probably because you did not measure what you thought you measured :-)

Mark
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