date:20110629

[gmx-users] implicit solvent and generic interaction

2011-06-29 Thread Makoto Yoneya

Dear GROMACS experts:

I'm using a GB implicit solvent function in ver. 4.5.4.
When I switched on GMX_NB_GENERIC with implicit_solvent=GBSA,
I've got the message,
"Fatal error:
Death & horror! GB generic interaction not implemented".

I'm wondering that is it difficult to add some code to nb_generic.c
for the generic GB electrostatic interaction?
If it is not, I'd like to try.
I'd like to use GMX_NB_GENERIC for my own modified version of 
nb_generic.c to utilize Weeks-Chandler-Andersen (WCA) potential.
And I'd like to use the WCA potential with the GB implicit solvent.
Any info. will be welcome.

Thank you for advance.

Makoto Yoneya, Dr.
AIST, Tsukuba
JAPAN

Makoto Yoneya, Dr.
http://staff.aist.go.jp/makoto-yoneya/


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Re: [gmx-users] Running Lyz in water

2011-06-29 Thread Mark Abraham

On 06/29/2011 04:18 PM, Ravi Kumar Venkatraman wrote:

Dear all,
I have been running lyz in water. I have 20 ps
pre-equilibrated NVT and 200 ps NPT configuration of spce216 water. I
am following the instruction from gromacs tutorial. This is the link
for the tutorial,

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html

After editing the box for lyz and then I tried to solvate the box with
spce216 water. I followed the same instruction but it shows fatal I/O
error - topol.top.

That will usually mean you've followed the instructions incompletely.
However, we don't know what you actually did do, so we can't help other
than to suggest you go back and try afresh.

It was not able to find the input file topol.top. But in this tutorial
its an output command. Further it shows 6091 solvent instead of 10832
as per tutorial. Pls help me find the problem.

Something must be greatly different, and unless Justin's made an error
in his tutorial and you're the first to notice, it will be something
you've done.

Mark

Thank you

*With Regards,**
*
*
*
*Ravi Kumar Venkatraman,*
*c/o Prof. Siva Umapathy,**
*
*IPC Dept., IISc.,*
*Bangalore, INDIA.*
*Phone No: +91-9686933963*

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[gmx-users] Re:Re: Tabulated potential for metal-oxide (Mark Abraham)

2011-06-29 Thread manana koberidze

Thank you Mark, what puzzles me here is summation, if it was only one term
than it would be clear.

Generally, if there is no other way than changing the source code which
files must be modified?Is there any information about it anywhere? I found
just the list of files but for bonded interaction in the manual.

Thanks again


> On 28/06/2011 8:49 PM, manana koberidze wrote:
> > Dear All,
> >
> > I've just started using GROMACS, I've read the manual and searched the
> > mailing list but still confused. I'm trying to simulate metal
> > oxidation with GROMACS. As a first step, I'm trying to tabulate the
> > EAM (Embedded atom potential), which in addition to residual pair-pair
> > repulsion includes the energy required to embed atom i in a local
> > electron density rho, where rho is defined as:
> > rho_i=SUM{k_j*exp(-beta_j*(r_ij-r*_j)) }
> > k, beta, r*_j are known parameters and the sum runs over all other atoms.
> >
> > Is there any way to tabulate the energy functional of such local
> > electron density?
>
> Since it depends only on inter-atomic coordinates, it should be
> possible. Before that, get some experience with normal GROMACS simulations.
>
> Mark
> -- next part --
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>
> End of gmx-users Digest, Vol 86, Issue 188
> **
>



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Graduate Student
Department of Applied Physics
Aalto University School of Science
P.O.Box 11100
FI-00076 AALTO
Finland
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E-mail: manana.koberidze (at) aalto.fi
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Re: [gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27

2011-06-29 Thread Leonhard Henkes

Thanks for your reply,

my whole pdb file includes an equilibrated membrane bilayer, constructed with 
VMD for NAMD. I used the CHARMM27 FF while constructing it.
Now, I wanted to convert this system for a run in Gromacs. 
To solve my issus, I divided my system into four new pdb's (ion, water, lipids, 
protein). This was an advise I found in an older thread. In the end, all 
created *.gro files will be united again, to one big file.

I checked the POPE entry in the charmff folder and the lipid names are the same 
as in my pdb. So I assumed that my bilayer can be converted with pdb2gmx too. 
The occurring errors are attached. 

I don't understand these errors.
Thanks for your help,

M.Kalavera

...
Warning: Long Bond (232-234 = 0.547183 nm)
Warning: Long Bond (232-235 = 0.710465 nm)
Warning: Long Bond (235-236 = 0.514028 nm)
Warning: Long Bond (235-237 = 0.707876 nm)
Warning: Long Bond (235-238 = 0.341151 nm)
Warning: Long Bond (238-239 = 0.545028 nm)
Warning: Long Bond (238-240 = 0.538926 nm)
Warning: Long Bond (241-242 = 0.586707 nm)
Warning: Long Bond (241-243 = 0.360561 nm)
Warning: Long Bond (241-244 = 0.447081 nm)
Warning: Long Bond (244-245 = 0.57 nm)
Warning: Long Bond (244-246 = 0.412897 nm)
Warning: Long Bond (244-247 = 0.414759 nm)
Warning: Long Bond (247-248 = 0.785856 nm)
Warning: Long Bond (247-249 = 0.865684 nm)
Warning: Long Bond (247-250 = 0.447969 nm)

WARNING: atom P is missing in residue POPE 1 in the pdb file


WARNING: atom O13 is missing in residue POPE 1 in the pdb file


WARNING: atom O14 is missing in residue POPE 1 in the pdb file


WARNING: atom O11 is missing in residue POPE 1 in the pdb file


WARNING: atom O12 is missing in residue POPE 1 in the pdb file


WARNING: atom C1 is missing in residue POPE 1 in the pdb file


WARNING: atom HA is missing in residue POPE 1 in the pdb file
 You might need to add atom HA to the hydrogen database of building 
block POPE
 in the file lipids.hdb (see the manual)


WARNING: atom HB is missing in residue POPE 1 in the pdb file
 You might need to add atom HB to the hydrogen database of building 
block POPE
 in the file lipids.hdb (see the manual)


WARNING: atom C2 is missing in residue POPE 1 in the pdb file


WARNING: atom HS is missing in residue POPE 1 in the pdb file
 You might need to add atom HS to the hydrogen database of building 
block POPE
 in the file lipids.hdb (see the manual)


WARNING: atom O21 is missing in residue POPE 1 in the pdb file


WARNING: atom C21 is missing in residue POPE 1 in the pdb file


WARNING: atom O22 is missing in residue POPE 1 in the pdb file


WARNING: atom C22 is missing in residue POPE 1 in the pdb file


WARNING: atom H2R is missing in residue POPE 1 in the pdb file
 You might need to add atom H2R to the hydrogen database of building 
block POPE
 in the file lipids.hdb (see the manual)


WARNING: atom H2S is missing in residue POPE 1 in the pdb file
 You might need to add atom H2S to the hydrogen database of building 
block POPE
 in the file lipids.hdb (see the manual)


WARNING: atom C3 is missing in residue POPE 1 in the pdb file

...

---
Program pdb2gmx_mpi, VERSION 4.5.4
Source code file: /usr/people/../gromacs-4.5.4/src/kernel/pdb2top.c, line: 1463

Fatal error:
There were 250 missing atoms in molecule Lipids, if you want to use this 
incomplete topology anyhow, use the option -missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---



> 
> 
> kalav...@gmx.net wrote:
> > Dear gromacs users,
> > 
> > I constructed a small *.pdb file comprised of only lipids (POPE
> bilayer). If I try to convert this pdb file with pdb2gmx (gromacs 4.5.4) and 
> the
> included charmm27 forcefield, I get warnings for "missing hydrogen atoms" and
> "Long Bond" warnings.  
> > 
> 
> pdb2gmx is ill-suited for dealing with multiple molecules.  The better
> approach 
> is to work with a single POPE molecule with a suitably constructed .rtp
> entry 
> for it.  pdb2gmx should then generate a topology for one lipid, which can
> then 
> be modified to be used in an #include statement or extended to accommodate
> an 
> entire bilayer simply by altering the [molecules] directive.
> 
> The errors you are seeing are likely due to naming mismatch or poor
> starting 
> geometry, but since you haven't quoted the errors, I don't dare guess
> beyond that.
> 
> > In other threads, the lipids.hdb is discussed in this context. In my
> case, all hydrogen atoms are available. Do I need to proceed the lipids.hdb
> (like described in the manual), or can I leave it empty ?  
> 
> The .hdb file is only necessary to reconstruct missing H atoms.  If your 
> structure has all of them and they are correctly named, then an .hdb is
> not 
> necessary.
> 
> -Justin
> 
> > The resnam

[gmx-users] Re: Running Lyz in water

2011-06-29 Thread Ravi Kumar Venkatraman

   Dear all,
I am not finding mistake in that tutorial but I wanted to
know where did I go wrong. Until generation of topology for protein there
was no problem (I cross checked with the tutorial).
After that I edited the box of protein as such. After generating the
solvation box I having problem. At least let me know is there different
command for input /output *.top file in genbox. Please help me in this
regard.


Thank you.




Dear all,
> I have been running lyz in water. I have 20 ps pre-equilibrated
> NVT and 200 ps NPT configuration of spce216 water. I am following the
> instruction from gromacs tutorial. This is the link for the tutorial,
>
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
>
> After editing the box for lyz and then I tried to solvate the box with
> spce216 water. I followed the same instruction but it shows fatal I/O error
> - topol.top. It was not able to find the input file topol.top. But in this
> tutorial its an output command. Further it shows 6091 solvent instead of
> 10832 as per tutorial. Pls help me find the problem.
>
> Thank you
>
> *With Regards,**
> *
> *
> *
> *Ravi Kumar Venkatraman,*
> *c/o Prof. Siva Umapathy,**
> *
> *IPC Dept., IISc.,*
> *Bangalore, INDIA.*
> *Phone No: +91-9686933963*
>
>


-- 
*With Regards,**
*
*
*
*Ravi Kumar Venkatraman,*
*c/o Prof. Siva Umapathy,**
*
*IPC Dept., IISc.,*
*Bangalore, INDIA.*
*Phone No: +91-9686933963*
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Re: [gmx-users] Re: Running Lyz in water

2011-06-29 Thread Justin A. Lemkul

Ravi Kumar Venkatraman wrote:

Dear all,
I am not finding mistake in that tutorial but I wanted
to know where did I go wrong. Until generation of topology for protein
there was no problem (I cross checked with the tutorial).
After that I edited the box of protein as such. After generating the
solvation box I having problem. At least let me know is there different
command for input /output *.top file in genbox. Please help me in this
regard.

In the genbox step, the topology is both input and output, since it is modified
by the program. You still haven't posted the exact command you tried, but if
you did what the tutorial said, it would have worked. I know because several
hundred people have gone through the tutorial successfully.

Either you named the file differently or perhaps placed it in a different
directory such that genbox can't find it, but if you did indeed follow the
tutorial exactly, this should not happen.

-Justin

Thank you.

Dear all,
I have been running lyz in water. I have 20 ps
pre-equilibrated NVT and 200 ps NPT configuration of spce216 water.
I am following the instruction from gromacs tutorial. This is the
link for the tutorial,

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html

After editing the box for lyz and then I tried to solvate the box
with spce216 water. I followed the same instruction but it shows
fatal I/O error - topol.top. It was not able to find the input file
topol.top. But in this tutorial its an output command. Further it
shows 6091 solvent instead of 10832 as per tutorial. Pls help me
find the problem.

Thank you

*With Regards,**
*
*
*
*Ravi Kumar Venkatraman,*
*c/o Prof. Siva Umapathy,**
*
*IPC Dept., IISc.,*
*Bangalore, INDIA.*
*Phone No: +91-9686933963*

--
*With Regards,**
*
*
*
*Ravi Kumar Venkatraman,*
*c/o Prof. Siva Umapathy,**
*
*IPC Dept., IISc.,*
*Bangalore, INDIA.*
*Phone No: +91-9686933963*

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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27

2011-06-29 Thread Justin A. Lemkul




Leonhard Henkes wrote:

Thanks for your reply,

my whole pdb file includes an equilibrated membrane bilayer, constructed with 
VMD for NAMD. I used the CHARMM27 FF while constructing it.
Now, I wanted to convert this system for a run in Gromacs. 
To solve my issus, I divided my system into four new pdb's (ion, water, lipids, protein). This was an advise I found in an older thread. In the end, all created *.gro files will be united again, to one big file.




The only species you have to explicitly deal with are the protein and lipids. 
The water and ions do not need to be processed by pdb2gmx.  Their topologies are 
handled by #include statements later.


I checked the POPE entry in the charmff folder and the lipid names are the same as in my pdb. So I assumed that my bilayer can be converted with pdb2gmx too. The occurring errors are attached. 


I don't understand these errors.


The combination of long bond warnings and mismatching names suggests that the 
.pdb file is misformatted.  Gromacs requires that the exact PDB standard be 
upheld, and a quick look at your file indicates that at the very least, your 
coordinate columns are shifted left, which leads to incorrect interpretation of 
the values and gives the long bond warnings.  This may also have a side effect 
related to the atom names.  Start over with a correctly formatted .pdb file.


-Justin


Thanks for your help,

M.Kalavera

...
Warning: Long Bond (232-234 = 0.547183 nm)
Warning: Long Bond (232-235 = 0.710465 nm)
Warning: Long Bond (235-236 = 0.514028 nm)
Warning: Long Bond (235-237 = 0.707876 nm)
Warning: Long Bond (235-238 = 0.341151 nm)
Warning: Long Bond (238-239 = 0.545028 nm)
Warning: Long Bond (238-240 = 0.538926 nm)
Warning: Long Bond (241-242 = 0.586707 nm)
Warning: Long Bond (241-243 = 0.360561 nm)
Warning: Long Bond (241-244 = 0.447081 nm)
Warning: Long Bond (244-245 = 0.57 nm)
Warning: Long Bond (244-246 = 0.412897 nm)
Warning: Long Bond (244-247 = 0.414759 nm)
Warning: Long Bond (247-248 = 0.785856 nm)
Warning: Long Bond (247-249 = 0.865684 nm)
Warning: Long Bond (247-250 = 0.447969 nm)

WARNING: atom P is missing in residue POPE 1 in the pdb file


WARNING: atom O13 is missing in residue POPE 1 in the pdb file


WARNING: atom O14 is missing in residue POPE 1 in the pdb file


WARNING: atom O11 is missing in residue POPE 1 in the pdb file


WARNING: atom O12 is missing in residue POPE 1 in the pdb file


WARNING: atom C1 is missing in residue POPE 1 in the pdb file


WARNING: atom HA is missing in residue POPE 1 in the pdb file
 You might need to add atom HA to the hydrogen database of building 
block POPE
 in the file lipids.hdb (see the manual)


WARNING: atom HB is missing in residue POPE 1 in the pdb file
 You might need to add atom HB to the hydrogen database of building 
block POPE
 in the file lipids.hdb (see the manual)


WARNING: atom C2 is missing in residue POPE 1 in the pdb file


WARNING: atom HS is missing in residue POPE 1 in the pdb file
 You might need to add atom HS to the hydrogen database of building 
block POPE
 in the file lipids.hdb (see the manual)


WARNING: atom O21 is missing in residue POPE 1 in the pdb file


WARNING: atom C21 is missing in residue POPE 1 in the pdb file


WARNING: atom O22 is missing in residue POPE 1 in the pdb file


WARNING: atom C22 is missing in residue POPE 1 in the pdb file


WARNING: atom H2R is missing in residue POPE 1 in the pdb file
 You might need to add atom H2R to the hydrogen database of building 
block POPE
 in the file lipids.hdb (see the manual)


WARNING: atom H2S is missing in residue POPE 1 in the pdb file
 You might need to add atom H2S to the hydrogen database of building 
block POPE
 in the file lipids.hdb (see the manual)


WARNING: atom C3 is missing in residue POPE 1 in the pdb file

...

---
Program pdb2gmx_mpi, VERSION 4.5.4
Source code file: /usr/people/../gromacs-4.5.4/src/kernel/pdb2top.c, line: 1463

Fatal error:
There were 250 missing atoms in molecule Lipids, if you want to use this 
incomplete topology anyhow, use the option -missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---





kalav...@gmx.net wrote:

Dear gromacs users,

I constructed a small *.pdb file comprised of only lipids (POPE

bilayer). If I try to convert this pdb file with pdb2gmx (gromacs 4.5.4) and the
included charmm27 forcefield, I get warnings for "missing hydrogen atoms" and
"Long Bond" warnings.  
pdb2gmx is ill-suited for dealing with multiple molecules.  The better
approach 
is to work with a single POPE molecule with a suitably constructed .rtp
entry 
for it.  pdb2gmx should then generate a topology for one lipid, which can
then 
be modified to be used in an #include statement or extended to accom

[gmx-users] error in running pdb2gmx command

2011-06-29 Thread rashi parihar

HI all ..while running pdb2gmx command .I am getting error "Fatal error:
Atom CT in residue TYR 314 was not found in rtp entry TYR with 20 atoms
while sorting atoms" .what this error mean and how can I rectify this
problem?plz help me.

-- 

[image: images[12]]

“Many Smiles Begin Because Of Another Smile . . . ."

Regards,
Rashi
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Re: [gmx-users] error in running pdb2gmx command

2011-06-29 Thread Justin A. Lemkul




rashi parihar wrote:


HI all ..while running pdb2gmx command .I am getting error "Fatal error:
Atom CT in residue TYR 314 was not found in rtp entry TYR with 20 atoms
while sorting atoms" .what this error mean and how can I rectify this 
problem?plz help me.


Please search the mailing list archive and Gromacs website before posting. 
Nearly all common errors are explained on the website or within a few seconds of 
searching.  For instance:


http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry

-Justin



--
 
images[12]
 
“Many Smiles Begin Because Of Another Smile . . . ."
 
Regards,

Rashi



--


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] minimization problem (Martini simulation)

2011-06-29 Thread politr


Thank you very much. It worked.
Regina
Quoting "Justin A. Lemkul" :




pol...@fh.huji.ac.il wrote:

Dear Justin,
Thank you very much for your answer.
Can you please explain me what do you mean by saying "EM wasn't  
sufficient". What information do you need in order be able to help?

I run EM with emtol=60 and I got the following energies:
Steepest Descents converged to Fmax < 60 in 2256 steps
Potential Energy = -1.2244622e+07
Maximum force = 4.7755444e+01 on atom 1659
Norm of force = 6.3245118e-01


This was the information I wanted to see.  Without it, no one had  
any idea if your EM converged reasonably.



Everything seems ok.


Indeed it does.


After that I run MD using mdp file attached and I got the following error:
Started mdrun on node 0 Tue Jun 28 00:10:12 2011

Step Time Lambda
0 0.0 0.0

Energies (kJ/mol)
Bond G96Angle Improper Dih. LJ (SR) Coulomb (SR)
6.39093e+03 9.79589e+03 3.77765e+02 -1.22386e+07 -1.82773e+03
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-1.22239e+07 1.25745e+00 -1.22239e+07 2.55766e-04 -1.14611e+03


Here's your problem.  The initial temperature is ridiculously small,  
indicating something has gone wrong.



Cons. rmsd ()
4.25390e-06

DD step 9 load imb.: force 3.0%

---
Program mdrun_mpi, VERSION 4.0.3


Any reason you're using a really old version of Gromacs?



Here's your problem.  The combination of:


tcoupl   = Berendsen


and


gen_vel  = no


is generally not stable.  You should set "gen_vel = yes" to start a  
reasonable equilibration period.


-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] protonated histidine with Martini

2011-06-29 Thread politr


Dear gromacs users,
I want to use Martini force field for my simulation. The simulation is  
supposed to be performed at acidic environment (pH2.6). In this  
environment His is protonated. I want to add protonate Hisidine in itp  
file. Where exactly should I put the charge on S2c or on S3c? Maybe I  
should put 0.5 on each CG bead?

Thank you in advance.
Regina


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Re: [gmx-users] Re:Re: Tabulated potential for metal-oxide (Mark Abraham)

2011-06-29 Thread Mark Abraham

On 29/06/2011 7:08 PM, manana koberidze wrote:
Thank you Mark, what puzzles me here is summation, if it was only one 
term than it would be clear.

But a normal Coulomb interaction has the form E_i = q_i * SUM{q_j / 
r_ij} summing over the other atoms j. If you can cast the electrostatic 
component of the energy into a form dependent only on the inter-atomic 
distance and atomic charge (as above) then using the tabulated 
non-bonded interactions already implemented in GROMACS is 
straightforward. See manual. If you need a different interaction for 
each pair of atom types, then that is doable, but you'll have to make a 
lot of energy groups and corresponding table files and accept 
not-very-good performance - but I don't think you need this.

Mark

Generally, if there is no other way than changing the source code 
which files must be modified?Is there any information about it 
anywhere? I found just the list of files but for bonded interaction in 
the manual.

Thanks again

On 28/06/2011 8:49 PM, manana koberidze wrote:
> Dear All,
>
> I've just started using GROMACS, I've read the manual and
searched the
> mailing list but still confused. I'm trying to simulate metal
> oxidation with GROMACS. As a first step, I'm trying to tabulate the
> EAM (Embedded atom potential), which in addition to residual
pair-pair
> repulsion includes the energy required to embed atom i in a local
> electron density rho, where rho is defined as:
>
rho_i=SUM{k_j*exp(-beta_j*(r_ij-r*_j)) }

> k, beta, r*_j are known parameters and the sum runs over all
other atoms.
>
> Is there any way to tabulate the energy functional of such local
> electron density?

Since it depends only on inter-atomic coordinates, it should be
possible. Before that, get some experience with normal GROMACS
simulations.

Mark
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Manana Koberidze

Graduate Student
Department of Applied Physics
Aalto University School of Science
P.O.Box 11100
FI-00076 AALTO
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Re: [gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27

2011-06-29 Thread Leonhard Henkes

One of my issues is now solved.
As you guessed, the PBD was in an improper format. 

After solving this small issues, I read about the need for an lipids.itp and 
pope.itp file. I found these tutorial (link below) for the itp file 
construction. Can I adept these steps for the construction of correct itp files 
for POPE lipids? In a last step , I would exchange all parameters with the 
right ones from a CHARMM FF.
Right now, I in fear of conduction terrible mistakes. Is there a much more 
common way to solve this task ? 

Thanks for your kind help,
M.Kalavera

Tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html
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[gmx-users] Question about g_bar output

2011-06-29 Thread Warren Gallin

Hi,

I've just run g_bar on data from a simulation, and I am having trouble 
reconciling the graphical output with the numerical output.  The units seem to 
be inconsistent.

In particular the numbers under detailed results are in units of kT, 
followed by final results in kJ/mole (see below).

However, the graphical output from -o and -oi seem to numerically be 
from the kT units list, but the y-axis is labelled in kJ/mole (see atached PDF 
files.

Am I missing something here, or is this a bug in the output code?

Warren Gallin



md_0.05.xvg: 0.0 - 2000.0; lambda = 0.050
foreign lambdas: 0.050 (11 pts) 0.000 (11 pts) 0.100 (11 pts)

md_0.1.xvg: 0.0 - 2000.0; lambda = 0.100
foreign lambdas: 0.100 (11 pts) 0.050 (11 pts) 0.150 (11 pts)

md_0.15.xvg: 0.0 - 2000.0; lambda = 0.150
foreign lambdas: 0.150 (11 pts) 0.100 (11 pts) 0.200 (11 pts)

md_0.2.xvg: 0.0 - 2000.0; lambda = 0.200
foreign lambdas: 0.200 (11 pts) 0.150 (11 pts) 0.250 (11 pts)

md_0.25.xvg: 0.0 - 2000.0; lambda = 0.250
foreign lambdas: 0.250 (11 pts) 0.200 (11 pts) 0.300 (11 pts)

md_0.3.xvg: 0.0 - 2000.0; lambda = 0.300
foreign lambdas: 0.300 (11 pts) 0.250 (11 pts) 0.350 (11 pts)

md_0.35.xvg: 0.0 - 2000.0; lambda = 0.350
foreign lambdas: 0.350 (11 pts) 0.300 (11 pts) 0.400 (11 pts)

md_0.4.xvg: 0.0 - 2000.0; lambda = 0.400
foreign lambdas: 0.400 (11 pts) 0.350 (11 pts) 0.450 (11 pts)

md_0.45.xvg: 0.0 - 2000.0; lambda = 0.450
foreign lambdas: 0.450 (11 pts) 0.400 (11 pts) 0.500 (11 pts)

md_0.5.xvg: 0.0 - 2000.0; lambda = 0.500
foreign lambdas: 0.500 (11 pts) 0.450 (11 pts) 0.550 (11 pts)

md_0.55.xvg: 0.0 - 2000.0; lambda = 0.550
foreign lambdas: 0.550 (11 pts) 0.500 (11 pts) 0.600 (11 pts)

md_0.6.xvg: 0.0 - 2000.0; lambda = 0.600
foreign lambdas: 0.600 (11 pts) 0.550 (11 pts) 0.650 (11 pts)

md_0.65.xvg: 0.0 - 2000.0; lambda = 0.650
foreign lambdas: 0.650 (11 pts) 0.600 (11 pts) 0.700 (11 pts)

md_0.7.xvg: 0.0 - 2000.0; lambda = 0.700
foreign lambdas: 0.700 (11 pts) 0.650 (11 pts) 0.750 (11 pts)

md_0.75.xvg: 0.0 - 2000.0; lambda = 0.750
foreign lambdas: 0.750 (11 pts) 0.700 (11 pts) 0.800 (11 pts)

md_0.8.xvg: 0.0 - 2000.0; lambda = 0.800
foreign lambdas: 0.800 (11 pts) 0.750 (11 pts) 0.850 (11 pts)

md_0.85.xvg: 0.0 - 2000.0; lambda = 0.850
foreign lambdas: 0.850 (11 pts) 0.800 (11 pts) 0.900 (11 pts)

md_0.9.xvg: 0.0 - 2000.0; lambda = 0.900
foreign lambdas: 0.900 (11 pts) 0.850 (11 pts) 0.950 (11 pts)

md_0.95.xvg: 0.0 - 2000.0; lambda = 0.950
foreign lambdas: 0.950 (11 pts) 0.900 (11 pts) 1.000 (11 pts)

md_0.xvg: 0.0 - 2000.0; lambda = 0.000
foreign lambdas: 0.000 (11 pts) 0.050 (11 pts)

md_1.xvg: 0.0 - 2000.0; lambda = 1.000
foreign lambdas: 1.000 (11 pts) 0.950 (11 pts)


Writing histogram to histogram.xvg

Temperature: 300 K

Detailed results in kT (see help for explanation):

 lam_A  lam_B  DG   +/- s_A   +/- s_B   +/-   stdev   +/- 
 0.000  0.050   -1.47  0.397.65  0.728.37  0.647.31  1.41
 0.050  0.100   -1.34  0.277.53  0.487.30  0.145.98  0.42
 0.100  0.150   -0.65  0.268.04  0.277.71  0.257.15  0.36
 0.150  0.200   -0.30  0.447.98  0.278.13  0.207.55  0.30
 0.200  0.250   -1.01  0.368.61  0.278.50  0.188.56  0.36
 0.250  0.300   -0.47  0.196.99  0.217.48  0.266.26  0.31
 0.300  0.350   -0.22  0.248.31  0.208.43  0.227.93  0.22
 0.350  0.4000.05  0.447.34  0.307.87  0.146.66  0.40
 0.400  0.4500.19  0.188.03  0.387.94  0.177.16  0.46
 0.450  0.500   -0.11  0.118.40  0.168.34  0.207.99  0.26
 0.500  0.550   -0.14  0.097.73  0.137.77  0.197.04  0.18
 0.550  0.600   -0.05  0.298.18  0.158.06  0.277.51  0.17
 0.600  0.650   -0.03  0.167.95  0.158.05  0.107.31  0.17
 0.650  0.7000.42  0.217.54  0.227.53  0.136.70  0.23
 0.700  0.7500.85  0.378.07  0.108.36  0.217.60  0.11
 0.750  0.8000.85  0.137.67  0.327.78  0.306.86  0.51
 0.800  0.8500.80  0.208.30  0.288.05  0.187.63  0.35
 0.850  0.9000.78  0.288.00  0.147.87  0.157.44  0.31
 0.900  0.9501.09  0.417.86  0.488.16  0.327.60  0.62
 0.950  1.0001.09  0.397.87  0.317.40  0.427.09  0.74


Final results in kJ/mol:

lambda  0.000 -  0.050,   DG -3.67 +/-  0.98
lambda  0.050 -  0.100,   DG -3.34 +/-  0.68
lambda  0.100 -  0.150,   DG -1.62 +/-  0.64
lambda  0.150 -  0.200,   DG -0.76 +/-  1.09
lambda  0.200 -  0.250,   DG -2.52 +/-  0.90
lambda  0.250 -  0.300,   DG -1.16 +/-  0.48
lambda  0.300 -  0.350,   DG -0.55 +/-  0.60
lambda  0.350 -  0

Re: [gmx-users] Question about g_bar output

2011-06-29 Thread Justin A. Lemkul




Warren Gallin wrote:

Hi,

I've just run g_bar on data from a simulation, and I am having trouble 
reconciling the graphical output with the numerical output.  The units seem to 
be inconsistent.

In particular the numbers under detailed results are in units of kT, 
followed by final results in kJ/mole (see below).

However, the graphical output from -o and -oi seem to numerically be 
from the kT units list, but the y-axis is labelled in kJ/mole (see atached PDF 
files.

Am I missing something here, or is this a bug in the output code?



There is a bug.  Proper output is discussed in the BAR tutorial:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/07_analysis.html

-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] Question about g_bar output

2011-06-29 Thread Warren Gallin

Justin,

OK, this makes sense to me, and I can do the interconversion of units 
easily enough outside of the GROMACS tools.

Should I file a bug report?

Warren Gallin

On 2011-06-29, at 12:48 PM, Justin A. Lemkul wrote:

> 
> 
> Warren Gallin wrote:
>> Hi,
>>  I've just run g_bar on data from a simulation, and I am having trouble 
>> reconciling the graphical output with the numerical output.  The units seem 
>> to be inconsistent.
>>  In particular the numbers under detailed results are in units of kT, 
>> followed by final results in kJ/mole (see below).
>>  However, the graphical output from -o and -oi seem to numerically be 
>> from the kT units list, but the y-axis is labelled in kJ/mole (see atached 
>> PDF files.
>>  Am I missing something here, or is this a bug in the output code?
> 
> There is a bug.  Proper output is discussed in the BAR tutorial:
> 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/07_analysis.html
> 
> -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 mailing listgmx-users@gromacs.org
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Re: [gmx-users] Question about g_bar output

2011-06-29 Thread Justin A. Lemkul

Warren Gallin wrote:

Justin,

OK, this makes sense to me, and I can do the interconversion of units
easily enough outside of the GROMACS tools.

Should I file a bug report?

No need. I've fixed this in the release-4-5-patches branch so the output will
be correct whenever version 4.5.5 is released.

-Justin

Warren Gallin

On 2011-06-29, at 12:48 PM, Justin A. Lemkul wrote:

Warren Gallin wrote:

Hi,
I've just run g_bar on data from a simulation, and I am having trouble
reconciling the graphical output with the numerical output. The units seem to
be inconsistent.
In particular the numbers under detailed results are in units of kT,
followed by final results in kJ/mole (see below).
However, the graphical output from -o and -oi seem to numerically be
from the kT units list, but the y-axis is labelled in kJ/mole (see atached PDF
files.
Am I missing something here, or is this a bug in the output code?

There is a bug. Proper output is discussed in the BAR tutorial:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/07_analysis.html

-Justin

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Re: [gmx-users] error in running pdb2gmx command

2011-06-29 Thread rashi parihar

thanx @justin..I have seen gromacs web site before posting..the solution of
my problem was written in gromacs website was " the atom names are expected
to match those found in the .rtp
file that
define the building block(s) in your structure". Now my question is that how
can i see or open the .rtp file of particular force field?

On Wed, Jun 29, 2011 at 5:24 PM, Justin A. Lemkul  wrote:

>
>
> rashi parihar wrote:
>
>>
>> HI all ..while running pdb2gmx command .I am getting error "Fatal error:
>> Atom CT in residue TYR 314 was not found in rtp entry TYR with 20 atoms
>> while sorting atoms" .what this error mean and how can I rectify this
>> problem?plz help me.
>>
>
> Please search the mailing list archive and Gromacs website before posting.
> Nearly all common errors are explained on the website or within a few
> seconds of searching.  For instance:
>
> http://www.gromacs.org/**Documentation/Errors#Atom_X_**
> in_residue_YYY_not_found_in_**rtp_entry
>
> -Justin
>
>
>> --
>>  images[12]
>>  “Many Smiles Begin Because Of Another Smile . . . ."
>>  Regards,
>> Rashi
>>
>>
> --
> ==**==
>
> 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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> Support/Mailing_Lists/Searchbefore
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> Can't post? Read 
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>

-- 

[image: images[12]]

“Many Smiles Begin Because Of Another Smile . . . ."

Regards,
Rashi
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Re: [gmx-users] error in running pdb2gmx command

2011-06-29 Thread Mark Abraham

On 30/06/2011 1:48 PM, rashi parihar wrote:
thanx @justin..I have seen gromacs web site before
posting..the solution of my problem was written in gromacs website
was " the atom names are
expected to match those found in the .rtp
file that define the
building block(s) in your structure". Now my question is
that how can i see or open the .rtp file of particular force
field?

Yes, it's somewhere under share/top of your GROMACS installation
directory - and probably pdb2gmx prints which one it is trying to
use.

Mark

On Wed, Jun 29, 2011 at 5:24 PM, Justin
A. Lemkul
wrote:

rashi parihar wrote:

HI all ..while running pdb2gmx command .I am getting error
"Fatal error:
Atom CT in residue TYR 314 was not found in rtp entry TYR
with 20 atoms
while sorting atoms" .what this error mean and how can I
rectify this problem?plz help me.

Please search the mailing list archive and Gromacs website
before posting. Nearly all common errors are explained on the
website or within a few seconds of searching. For instance:

http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry

-Justin

images[12]
“Many Smiles Begin Because Of Another Smile . . . ."
Regards,
Rashi

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“Many Smiles Begin Because Of Another Smile . . . ."
Regards,
Rashi

[gmx-users] CPHMD in GROMACS4.5

2011-06-29 Thread Anirban Ghosh

Hi ALL,

Is it possible to run constant pH MD simulation (CPHMD) in Gromacs4.5?
Any suggestion is welcome.


Thanks,

Anirban
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Re: [gmx-users] CPHMD in GROMACS4.5

2011-06-29 Thread Mark Abraham


On 30/06/2011 3:55 PM, Anirban Ghosh wrote:

Hi ALL,

Is it possible to run constant pH MD simulation (CPHMD) in Gromacs4.5?
Any suggestion is welcome.


Thanks,

Anirban


See http://www.gromacs.org/Documentation/FAQs

Mark
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[gmx-users] micelle clustering

2011-06-29 Thread sulatha M. S

Hi all,

I have simulated a system of randomly dispersed surfactants in water using
gromacs (4.0.7) for about 100 ns MD. Micelles are formed after around 40 ns.
 I am using a time step of 0.002 fs with xtc files written every 500 steps.
For analyzing the micellar properties, I tried the commands given in

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

and also looked at the various posts given on this topic, (specifically
Chris Neale’s and Tsjerk’s mails).

As posted by Chris Neale, I tried using the commands,

1. trjconv -f a.xtc -o b.gro -pbc cluster -e 0.001 (make sure to just

get one frame)

2. grompp -f a.mdp -c b.gro -p a.top -o b.tpr

3. trjconv -f a.xtc -o b.xtc -s b.tpr -pbc nojump



Also mentioned in Tsjerk’ post that

“When doing so, be sure to use a frame which is close enough to the

starting frame in terms of the coordinates. -pbc nojump works based on

the coordinates and if you use a reference which doesn't match the

starting frame close enough everything can get really messed up”.





I tried the command 1 with

 trjconv -f a.xtc -o b.gro -pbc cluster -e 0.002

and also

 trjconv -f a.xtc -o b.gro -pbc cluster –dump X (where x=2, 4, 6, 8 etc..)

The program gets into a never ending loop.

I also tried the command 1 on a later part of the trajectory (after 40 ns),
there also the program enters in a indefinite loop.

I will greatly appreciate any help on how to go about doing this
specifically which frame (for dump or –e argument) .  Please guide me on
this.

I also downloaded the modified trjconv.c  by Tsjerk (in one of his posts on
micelle clustering), but do not know where to incorporate this. I need some
help on how to use this modified trjconv code.


Thanks for any help or clue,

Sulatha
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[gmx-users] umbrella sampling pull_group0 adn pull_group1

2011-06-29 Thread sreelakshmi ramesh

Dear all,
   i wanted to do umbrella sampling on petide which is
completely folded.now in mdp file there is  a option  pull_group0 and
pull_group1  i just know the ref group and the one to which pulling
force has to be applied in pdb file their atom numbers are 201 adn 61
.how should i mention this in mdp file. for  pull_group0 and
pull_group1 .

regards,
sree.
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Re: [gmx-users] umbrella sampling pull_group0 adn pull_group1

2011-06-29 Thread Shay Teaching

You should define the proper groups in your index file. Then put their names
into pull_group0 and pull_group1 of the mdp file.

On Thu, Jun 30, 2011 at 9:21 AM, sreelakshmi ramesh <
sree.laks...@research.iiit.ac.in> wrote:

> Dear all,
>   i wanted to do umbrella sampling on petide which is
> completely folded.now in mdp file there is  a option  pull_group0 and
> pull_group1  i just know the ref group and the one to which pulling
> force has to be applied in pdb file their atom numbers are 201 adn 61
> .how should i mention this in mdp file. for  pull_group0 and
> pull_group1 .
>
> regards,
> sree.
> --
> 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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