[gmx-users] how to differentiate crystal water and explicit waters in gromacs ???

[Praveen Kumar Madala]

Hi,

I am new to GROMACS and I am trying to perform a MD run in PBC  
condition with water as solvent.


I want to keep the crystal water molecules different from explicit  
waters,  I believe this helps me in analysis of crystal waters.


Can someone help me wit this ???

Thanking you.

regards,
Praveen


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Re: [gmx-users] unit of surface tension, KJ/mol?

[Elisabeth]

Thanks Mark for the hints. I am using a pre equilibrated box for both runs.
Can you again explain how Can I interpret this from fluctuations from two
runs? Below is the resutls from two versions: Thanks!

4.0.7

Statistics over 733801 steps [ 0. thru 1467.6001 ps ], 1 data sets
All averages are exact over 733801 steps

Energy  Average   RMSD Fluct.  Drift
Tot-Drift
---
#Surf*SurfTen   203.7783623.993623.98 -0.00203751
-2.99026


Statistics over 483401 steps [ 500. thru 1466.8000 ps ], 1 data sets
All averages are exact over 483401 steps

Energy  Average   RMSD Fluct.  Drift
Tot-Drift
---
#Surf*SurfTen   203.1293612.583612.28   0.168686
163.086
-
4.5.3



Statistics over 732501 steps [ 1. through 1466. ps ], 1 data sets
All statistics are over 73251 points

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
#Surf*SurfTen   2374.4957021081.3   -3251.38  (bar
nm)

Statistics over 384501 steps [ 1000. through 1769. ps ], 1 data sets
All statistics are over 38451 points

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
#Surf*SurfTen   2610.25   100021109.94638.38  (bar
nm)

Statistics over 483001 steps [ 500. through 1466. ps ], 1 data sets
All statistics are over 48301 points

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
#Surf*SurfTen   1645.0739020288.3   -174.289  (bar
nm)





On 22 March 2011 23:56, Mark Abraham  wrote:

>
>
> On 23/03/11, *Elisabeth *  wrote:
>
>
>
> On 22 March 2011 22:46, Justin A. Lemkul  wrote:
>
>>
>>
>> Elisabeth wrote:
>>
>>
>>>
>>> On 22 March 2011 22:31, Justin A. Lemkul >> jalem...@vt.edu>> wrote:
>>>
>>>
>>>
>>>Elisabeth wrote:
>>>
>>>Hello,
>>> I did two simulations on the same system using versions 4.0.7
>>>and 4.5.3. It seems like the unit of surface tension is not the
>>>same in these versions because I am getting ~250 KJ/mol an in
>>>4.0.7 and ~ 5000bar nm in 4.5.3?! How KJ/mol can be converted
>>>into bar nm? Can anyone help please.
>>>
>>>
>>>Is this from g_energy output?  In past versions, everything was
>>>printed as "kJ/mol," even quantities that obviously weren't, like
>>>temperature, pressure, etc.
>>>
>>>
>>> Yes, so why are the results so different. I am using exactly the same mdp
>>> file.!
>>>
>>>
>> Any pressure-related quantity is going to be subject to enormous
>> fluctuations. This has been discussed within the last few days.  Without
>> seeing the .mdp file and a description of the system, it's hard for anyone
>> to comment on what the results might mean.
>>
>
> Thanks. I am working on a pure alkane system, in a box of 3X3X3 which is
> extended in Z to create liq/air interface. That is 3X3X6 . What could be
> reason for such a big difference in results from two version? Thanks alot!
>
>
>
> Look at the size of the fluctuations printed by g_energy. If they're
> comparable or larger than your differences, then you are not observing a
> statistically significant difference. Over just 2ns of a small system,
> that's likely to be the case. Damping such fluctuations requires large
> simulations or long times or both.
>
> You are also generating velocities at the start of this run, so probably
> you are including spurious measurements on non-equilibrated configurations
> in your statistics. If you'd thought to tell us your command lines, I
> wouldn't be guessing :-) You can fix this with g_energy -b, but really you
> should separate your equilibration from your production run, even if you
> don't really need to, so that all your workflows have similar properties.
> Then when you come back to repeat some analysis in a month's time, you don't
> have to remember to ignore the first 1ns of this simulation...
>
> Mark
>
>
> integrator  =  md
> dt  =  0.002
> nsteps  =  100
>
> nstenergy   =  100
> nstxout =  100
> nstlist =  10
> ns_type =  grid
> coulombtype =  PME
> vdw-type=  Shift
> rcoulomb-switch =  0
> rvdw-switch =  0
> rlist   =  1.1
> rcoulomb=  1.1
> rvdw=  1.0
>
> fourierspacing  =  0.12
> fourier_nx  =  0
> fourier_ny  =  0
> fourier_nz  =  0
> pme_order

Re: [gmx-users] unit of surface tension, KJ/mol?

[Mark Abraham]

On 23/03/11, Elisabeth   wrote:
> 
> 
> On 22 March 2011 22:46, Justin A. Lemkul  wrote:
> 
> > 
> > 
> > 
> > 
> > 
> > Elisabeth wrote:
> > 
> > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > On 22 March 2011 22:31, Justin A. Lemkul  > > > wrote:
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > >     Elisabeth wrote:
> > > 
> > > 
> > > 
> > >         Hello,
> > > 
> > >          I did two simulations on the same system using versions 4.0.7
> > > 
> > >         and 4.5.3. It seems like the unit of surface tension is not the
> > > 
> > >         same in these versions because I am getting ~250 KJ/mol an in
> > > 
> > >         4.0.7 and ~ 5000bar nm in 4.5.3?! How KJ/mol can be converted
> > > 
> > >         into bar nm? Can anyone help please.
> > > 
> > > 
> > > 
> > > 
> > > 
> > >     Is this from g_energy output?  In past versions, everything was
> > > 
> > >     printed as "kJ/mol," even quantities that obviously weren't, like
> > > 
> > >     temperature, pressure, etc.
> > > 
> > > 
> > > 
> > > 
> > > 
> > > Yes, so why are the results so different. I am using exactly the same mdp 
> > > file.! 
> > > 
> > > 
> > > 
> > > 
> > 
> > 
> > 
> > 
> > Any pressure-related quantity is going to be subject to enormous 
> > fluctuations. This has been discussed within the last few days.  Without 
> > seeing the .mdp file and a description of the system, it's hard for anyone 
> > to comment on what the results might mean.
> > 
> > 
> 
> Thanks. I am working on a pure alkane system, in a box of 3X3X3 which is 
> extended in Z to create liq/air interface. That is 3X3X6 . What could be 
> reason for such a big difference in results from two version? Thanks alot!   
> 
> 
> 

Look at the size of the fluctuations printed by g_energy. If they're comparable 
or larger than your differences, then you are not observing a statistically 
significant difference. Over just 2ns of a small system, that's likely to be 
the case. Damping such fluctuations requires large simulations or long times or 
both.

You are also generating velocities at the start of this run, so probably you 
are including spurious measurements on non-equilibrated configurations in your 
statistics. If you'd thought to tell us your command lines, I wouldn't be 
guessing :-) You can fix this with g_energy -b, but really you should separate 
your equilibration from your production run, even if you don't really need to, 
so that all your workflows have similar properties. Then when you come back to 
repeat some analysis in a month's time, you don't have to remember to ignore 
the first 1ns of this simulation...

Mark


> integrator  =  md         
> dt  =  0.002                 
> nsteps  =  100 
>         
> nstenergy   =  100                  
> 
> nstxout =  100                
> nstlist =  10                
> ns_type =  grid                
> coulombtype =  PME     
> vdw-type        =  Shift              
> 
> rcoulomb-switch =  0                    
> rvdw-switch =  0             
> rlist   =  1.1                
> rcoulomb    =  1.1             
> rvdw    =  1.0                
> 
> 
> fourierspacing      =  0.12                 
> fourier_nx          =  0
> fourier_ny          =  0
> fourier_nz          =  0
> pme_order          =  4              
> ewald_rtol  =  1e-5
> ;optimize_fft      =  yes
> 
>   
> Tcoupl  =  v-rescale            
> tc-grps =  System       
> tau_t   =  0.1        
> ref_t   =  300             
>   
> pbc              =  xyz       
> 
>        
> gen_vel =  yes                
> gen_temp    =  300.0                
> gen_seed    =  173529                
> 
> constraints         = all-bonds       
> constraint-algorithm = lincs
> 
>  
> 
> > 
> > 
> > 
> > -Justin
> > 
> > 
> > 
> > 
> > -- 
> > 
> > 
> > 
> > 
> > 
> > Justin A. Lemkul
> > 
> > Ph.D. Candidate
> > 
> > ICTAS Doctoral Scholar
> > 
> > MILES-IGERT Trainee
> > 
> > Department of Biochemistry
> > 
> > Virginia Tech
> > 
> > Blacksburg, VA
> > 
> > jalemkul[at]vt.edu(http://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
> > 
> > 
> > 
> > 
> 
> 
> 
> 
>
-- 
gmx-users maili

Re: [gmx-users] unit of surface tension, KJ/mol?

[Elisabeth]

On 22 March 2011 22:46, Justin A. Lemkul  wrote:

>
>
> Elisabeth wrote:
>
>
>>
>> On 22 March 2011 22:31, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Elisabeth wrote:
>>
>>Hello,
>> I did two simulations on the same system using versions 4.0.7
>>and 4.5.3. It seems like the unit of surface tension is not the
>>same in these versions because I am getting ~250 KJ/mol an in
>>4.0.7 and ~ 5000bar nm in 4.5.3?! How KJ/mol can be converted
>>into bar nm? Can anyone help please.
>>
>>
>>Is this from g_energy output?  In past versions, everything was
>>printed as "kJ/mol," even quantities that obviously weren't, like
>>temperature, pressure, etc.
>>
>>
>> Yes, so why are the results so different. I am using exactly the same mdp
>> file.!
>>
>>
> Any pressure-related quantity is going to be subject to enormous
> fluctuations. This has been discussed within the last few days.  Without
> seeing the .mdp file and a description of the system, it's hard for anyone
> to comment on what the results might mean.
>

Thanks. I am working on a pure alkane system, in a box of 3X3X3 which is
extended in Z to create liq/air interface. That is 3X3X6 . What could be
reason for such a big difference in results from two version? Thanks alot!


integrator  =  md
dt  =  0.002
nsteps  =  100

nstenergy   =  100
nstxout =  100
nstlist =  10
ns_type =  grid
coulombtype =  PME
vdw-type=  Shift
rcoulomb-switch =  0
rvdw-switch =  0
rlist   =  1.1
rcoulomb=  1.1
rvdw=  1.0

fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order  =  4
ewald_rtol  =  1e-5
;optimize_fft  =  yes

Tcoupl  =  v-rescale
tc-grps =  System
tau_t   =  0.1
ref_t   =  300

pbc  =  xyz

gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529

constraints = all-bonds
constraint-algorithm = lincs


>
> -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
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] unit of surface tension, KJ/mol?

[Justin A. Lemkul]

Elisabeth wrote:



On 22 March 2011 22:31, Justin A. Lemkul > wrote:




Elisabeth wrote:

Hello,
 I did two simulations on the same system using versions 4.0.7
and 4.5.3. It seems like the unit of surface tension is not the
same in these versions because I am getting ~250 KJ/mol an in
4.0.7 and ~ 5000bar nm in 4.5.3?! How KJ/mol can be converted
into bar nm? Can anyone help please.


Is this from g_energy output?  In past versions, everything was
printed as "kJ/mol," even quantities that obviously weren't, like
temperature, pressure, etc.


Yes, so why are the results so different. I am using exactly the same 
mdp file.! 





Any pressure-related quantity is going to be subject to enormous fluctuations. 
This has been discussed within the last few days.  Without seeing the .mdp file 
and a description of the system, it's hard for anyone to comment on what the 
results might mean.


-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] unit of surface tension, KJ/mol?

[Elisabeth]

On 22 March 2011 22:31, Justin A. Lemkul  wrote:

>
>
> Elisabeth wrote:
>
>> Hello,
>>  I did two simulations on the same system using versions 4.0.7 and 4.5.3.
>> It seems like the unit of surface tension is not the same in these versions
>> because I am getting ~250 KJ/mol an in 4.0.7 and ~ 5000bar nm in 4.5.3?! How
>> KJ/mol can be converted into bar nm? Can anyone help please.
>>
>>
> Is this from g_energy output?  In past versions, everything was printed as
> "kJ/mol," even quantities that obviously weren't, like temperature,
> pressure, etc.
>

Yes, so why are the results so different. I am using exactly the same mdp
file.!

>
> -Justin
>
>  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!
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>
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Re: [gmx-users] unit of surface tension, KJ/mol?

[Justin A. Lemkul]

Elisabeth wrote:

Hello,
 
I did two simulations on the same system using versions 4.0.7 and 4.5.3. 
It seems like the unit of surface tension is not the same in these 
versions because I am getting ~250 KJ/mol an in 4.0.7 and ~ 5000bar nm 
in 4.5.3?! How KJ/mol can be converted into bar nm? Can anyone help please.




Is this from g_energy output?  In past versions, everything was printed as 
"kJ/mol," even quantities that obviously weren't, like temperature, pressure, etc.


-Justin


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] unit of surface tension, KJ/mol?

[Elisabeth]

Hello,

I did two simulations on the same system using versions 4.0.7 and 4.5.3. It
seems like the unit of surface tension is not the same in these versions
because I am getting ~250 KJ/mol an in 4.0.7 and ~ 5000bar nm in 4.5.3?! How
KJ/mol can be converted into bar nm? Can anyone help please.

Thanks
-- 
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Re: [gmx-users] Parameterization of a molecule containing a radical (oxygen)

[Justin A. Lemkul]

Simone Cirri wrote:

Hi all,
I have a question regarding a new parameterization: actually, I'm 
wondering whether or not it is possible to do it.


The molecule is tempol; you cand find its PubChem entry 
here http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994&loc=ec_rcs 

As you can see, the problem of this molecule is its O radical; this, and 
the N belonging to the cycle too.
My lab would really benefit from the parameterization (for the AMBER 
force field) of tempol, since we commonly use it in our NMR experiments. 
We don't know how to treat the oxygen radical and the N bound to it, though.
If this parameterization is impossible to do we will give up, but we 
would like to be sure about it.

Thanks in advance for any answer you could provide.



This would not be a trivial molecule to parameterize.  You could start by using 
antechamber (available free as part of AmberTools), since it allows you to tune 
multiplicity (-m flag).  Otherwise, the existing force fields may not provide a 
suitable atom type for the O radical or its effects on the rest of the molecule. 
 I still don't know if parameterization would be possible for a standard MM 
force field (though it very well might), but this might get you started.


-Justin


--

Simone Cirri



--


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] Alcohol Dehydrogenase MD simulation....Reg

[Mark Abraham]

On 23/03/2011 4:38 AM, Kishore wrote:

Dear All,

I had been in the look out for someone who has a reasonable amount of 
expertise in dealing with the MD simulation of an Alcohol 
Dehydrogenase. I have a problem dealing with the NADPH. I was unable 
to maintain the planarity of the carboxamide of the nicotinamide 
moiety in the simulation as a result of which important sidechain 
hydrogen bonds are being lost in the simulation. Is such behaviour 
expected or is it because of the non quantum mechanical treatment of 
the NADPH molecule that these kind of situations occur? If anyone has 
some experience please share it.


Classical MD simulations use improper dihedrals to maintain such 
planarity. You can see this in the amide links in a peptide backbone, 
for example. Each set of four co-planar atoms (three arranged around a 
central one) needs an improper dihedral. So you need H-N-C-H, N-C-O-Cr4 
and C-Cr4-Cr5-Cr3 (where the ring carbons are named Cr and numbered 
clockwise from N) in order for the carboxamide to stay coplanar with the 
aromatic ring

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Re: [gmx-users] install problems cygwin

[Mark Abraham]

On 23/03/2011 4:10 AM, vijaya subramanian wrote:

Hi
I tried doing it from my home directory. It didn't work.  Also gcc 
hello.c and g77 hello.f don't produce

executables, though both seem to run-not a.out file is created.


The Cygwin linker package is not installed by default - you need the 
"binutils" package from Cygwin setup. Sometimes the system can try to 
fall back on the Windows ld.exe and that doesn't work.


Mark


> From: rol...@utk.edu
> Date: Tue, 22 Mar 2011 12:51:45 -0400
> Subject: Re: [gmx-users] install problems cygwin
> To: gmx-users@gromacs.org
>
> Hi,
>
> try to move your files into your cygwin home directory before
> compiling. If that doesn't work, try to first compile a hello world C
> program to see why the compiler doesn't work.
>
> Roland
>
> On Tue, Mar 22, 2011 at 12:13 PM, vijaya subramanian
>  wrote:
> >
> > Hi
> > I am trying to install gromacs on a windows laptop with rhcygwin.  
I am

> > doing it as administrator
> > and I ran into the same problem when I tried installing fftw-3.2.2.
> >
> > $ ./configure --enable-sse --enable-float
> > checking for a BSD-compatible install... /usr/bin/install -c
> > checking whether build environment is sane... yes
> > checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
> > checking for gawk... gawk
> > checking whether make sets $(MAKE)... yes
> > checking whether to enable maintainer-specific portions of 
Makefiles... no

> > checking build system type... i686-pc-cygwin
> > checking host system type... i686-pc-cygwin
> > checking for gcc... gcc
> > checking for C compiler default output file name...
> > configure: error: in `/cygdrive/c/fftw-3.2.2':
> > configure: error: C compiler cannot create executables
> > See `config.log' for more details.
> >
> > The config.log file is attached.
> > I read the config.log file but am unable to figure out what the 
problem is.

> > It shows
> > the right version of gcc installed and configure appears to find it.
> >
> >
> > Thanks
> > Vijaya
> >
> > --
> > 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
> >
>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
> --
> gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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http://www.gromacs.org/Support/Mailing_Lists/Search before posting!

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Re: [gmx-users] Tables - two non-bonded interactions

[Gareth Tribello]

Hello

I think the easiest way to do this is to use multiple tables.  Look at:

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

There are some details there.

ciao
Gareth

2011/3/22 Vinícius Contessoto :
> hello!
> I trying to simulate a protein with C-alpha model (my protein have only 
> alpha-carbons) . I need two different interatomic interactions.
> 1 - Some interactions in a specific alpha-carbons, using a Lennard Jones  10 
> -12 potential (i'm determining the pairs in my topology file).
> 2 - All carbons in my system should to interact among themselves with a 
> Buckingham potential ( here is the problem - how can i use this potential for 
> all my atoms and a LJ 10-12 to just a few atoms?)
> I'm using a table for a LJ 10-12 and trying to use a table to Buckingham.
>
> Thank You!
>
>
>
> --
> 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
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> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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[gmx-users] Tables - two non-bonded interactions

[Vinícius Contessoto]

hello!
I trying to simulate a protein with C-alpha model (my protein have only 
alpha-carbons) . I need two different interatomic interactions.
1 - Some interactions in a specific alpha-carbons, using a Lennard Jones  10 
-12 potential (i'm determining the pairs in my topology file).
2 - All carbons in my system should to interact among themselves with a 
Buckingham potential ( here is the problem - how can i use this potential for 
all my atoms and a LJ 10-12 to just a few atoms?)
I'm using a table for a LJ 10-12 and trying to use a table to Buckingham.

Thank You!



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Re: [gmx-users] Hydroixde Ion

[Justin A. Lemkul]

SHIVANGI NANGIA wrote:

Hi,

Thanks so much for the prompt help.

Yes, I did realize that methanol as solvent was not updated in the .top 
file. I had to fix the .top file manually.


When I add ions using genion I replace methanol.

As a test I tried setting up the whole system with the change that 
instead of 8 hydroxide ions I added 8 chloride ions.

And everything works perfectly!

So, I think its something with the hyrdroxide ion.

I will try adding hydroxide ions using genbox.
I think then I need to treat it as a charged residue and have it 
included in the .rtp file, correct?




No.  Only pdb2gmx uses .rtp entries for polymeric materials (i.e. proteins and 
nucleic acids).  You already have a topology written for hydroxide, from what 
you've shown.  All you need to do is #include "hydroxide.itp" in your .top and 
add the 8 required molecules with genbox -ci -nmol.


-Justin


Thanks,
Shivangi

Shivangi Nangia
Garrison Group
Graduate Student
201A Chemistry Building
University Park PA 16802


SHIVANGI NANGIA wrote:
 > Hi again,
 >
 > I have the following:
 >
 > I have not changed anything in ffG53a6.atp and .rtp
 > As suggested by gmx users, I have the following in the ions,itp file
 >
 > [ moleculetype ]
 >   ; molname   nrexcl
 > OH1
 >
 > [ atoms ]
 > ; id  at type  res nr   residu name at name  cg nr charge
 >   1  OH 1  OHOH  1  0
 >   1  OW 1  OWOW  1 -1
 >
 >
 > I executed the following commands:
 >
 > (a) pdb2gmx -f his8.pdb -ignh -ter -his -p topol.top -o his8.gro
 > (b) editconf -f his8.gro -box 5 5 5 -o his8box.gro
 > (c) genbox -cp his8box.gro  -ci  1methanol.gro -nmol 1800 -o 
his8_meoh.gro -p topol.top


Were all 1800 methanol molecules properly inserted here?  Note that 
genbox does not update the topology automatically for any molecules 
other than water.


 > (d) grompp -f ions.mdp -c his8_meoh.gro -p topol.top -o ions.tpr -p 
topol.top
 > (e) genion -s ions.tpr -o added_ions.gro -p topol.top -pname NA 
-nname OH -nn 8


Per the genion help information, it is not well-suited to inserting 
polyatomic ions.  Also, what are you choosing to replace here?  genion 
is designed to replace water molecules with monoatomic ions, but you 
haven't added any water yet.  If you're simply replacing elements of the 
"System" group, you've probably got fractional species somewhere.  I 
would be willing to bet that this process is what is causing your 
problem.  Check the contents of the coordinate file and topology before 
and after genion, and you will probably find the problem. Solution: 
don't use genion.  Use genbox -ci -nmol to add your 8 OH molecules.


-Justin

 > (f)  genbox -cp added_ions.gro  -cs tip4p.gro  -o his8_meohi_wat.gro 
-p topol.top

 >  Commands (a)-(f), all goes smooth.
 >
 > When I do the following
 >  grompp -f minim.mdp -c his8_meohi_wat.gro -p topol.top -o em.tpr
 >
 > I run into error which says moleculetype OH not found.
 >
 >
 > Added the following specifically in .top file
 >  [ moleculetype ]
 >   ; molname   nrexcl
 >   OH1
 >
 >   [atoms]
 >   1 OH  1   OH OH  1   0.21 1.008 ;
 >   2 OW  1   OH OW  1  -1.2115.4   ;
 >   [ bonds ]
 > OW   HW1gb_38
 >
 > Going back to the command
 > grompp -f minim.mdp -c his8_meohi_wat.gro -p topol.top -o em.tpr
 >
 > runs into different error as mentioned earlier : Fatal error: number 
of coordinates in coordinate file (5his8_meohi_wat.gro, 12487) does not 
match topology (topol.top, 12519)

 >
 > The .top file includes tip4p.itp, methanol.itp and ions.itp.
 >
 > So I am totally confused as to where I am going wrong.
 > Please guide.
 >
 > Thanks,
 > Shivangi
 >
 >
 >
 > Shivangi Nangia
 > Garrison Group
 > Graduate Student
 > 201A Chemistry Building
 > University Park PA 16802
 >
 >  >
 >
 >
 >
 >
 >
 > Hello,
 >  >
 >  > Thanks a lot for the suggestion.
 >  >
 >  > I think I made some progress but I am not there yet.
 >  >
 >  > I added the following in the ions.itp file
 >  >
 >  > [ moleculetype ]
 >  > ; molname   nrexcl
 >  > OH1
 >  >
 >  > [ atoms ]
 >  > ; id  at type  res nr   residu name at name  cg nr charge
 >  > 1  OH 1  OHOH  1  0
 >  > 1  OW 1  OWOW  1 -1
 >  >
 >  >
 >  > Still I ran into the same error that it could not find 
moleculetype OH.

 >  >
 >  > Than I specifically added the following to the .top file
 >  >
 >  > [ moleculetype ]
 >  > ; molname   nrexcl
 >  > OH1
 >  >
 >  > [atoms]
 >  >  1 OH  1   OH OH  1   0.21 1.008 ;
 >  >  2 OW  1   OH OW  1  -1.2115.4   ;
 >  > [ bonds ]
 >  >OW   HW1gb_38
 >  >
 >  > This helped.
 >  > However, there is new error I am running into which says:
 >  > Fatal error: number of coordinates in coordinate file 
(5his8_meohi_wat.gro, 12487) does not match topology (topol.top, 12519)

 >  >
 >  > I am trying to add 8 hydroxide ions in my methanol-water system.
 >  >
 >
 > And how are

Re: Re: Re: Re: [gmx-users] Hydroixde Ion

[SHIVANGI NANGIA]

Hi,

Thanks so much for the prompt help.

Yes, I did realize that methanol as solvent was not updated in the .top file. I
had to fix the .top file manually.

When I add ions using genion I replace methanol.

As a test I tried setting up the whole system with the change that instead of 8
hydroxide ions I added 8 chloride ions.
And everything works perfectly!

So, I think its something with the hyrdroxide ion.

I will try adding hydroxide ions using genbox.
I think then I need to treat it as a charged residue and have it included in
the .rtp file, correct?

Thanks,
Shivangi

Shivangi Nangia
Garrison Group
Graduate Student
201A Chemistry Building
University Park PA 16802


SHIVANGI NANGIA wrote:
> Hi again,
>
> I have the following:
>
> I have not changed anything in ffG53a6.atp and .rtp
> As suggested by gmx users, I have the following in the ions,itp file
>
> [ moleculetype ]
>   ; molname   nrexcl
> OH1
>
> [ atoms ]
> ; id  at type  res nr   residu name at name  cg nr charge
>   1  OH 1  OHOH  1  0
>   1  OW 1  OWOW  1 -1
>
>
> I executed the following commands:
>
> (a) pdb2gmx -f his8.pdb -ignh -ter -his -p topol.top -o his8.gro
> (b) editconf -f his8.gro -box 5 5 5 -o his8box.gro
> (c) genbox -cp his8box.gro  -ci  1methanol.gro -nmol 1800 -o his8_meoh.gro -p
topol.top

Were all 1800 methanol molecules properly inserted here?  Note that genbox does
not update the topology automatically for any molecules other than water.

> (d) grompp -f ions.mdp -c his8_meoh.gro -p topol.top -o ions.tpr -p topol.top
> (e) genion -s ions.tpr -o added_ions.gro -p topol.top -pname NA -nname OH -nn
8

Per the genion help information, it is not well-suited to inserting polyatomic
ions.  Also, what are you choosing to replace here?  genion is designed to
replace water molecules with monoatomic ions, but you haven't added any water
yet.  If you're simply replacing elements of the "System" group, you've
probably got fractional species somewhere.  I would be willing to bet that this
process is what is causing your problem.  Check the contents of the coordinate
file and topology before and after genion, and you will probably find the
problem. Solution: don't use genion.  Use genbox -ci -nmol to add your 8 OH
molecules.

-Justin

> (f)  genbox -cp added_ions.gro  -cs tip4p.gro  -o his8_meohi_wat.gro -p
topol.top
>  Commands (a)-(f), all goes smooth.
>
> When I do the following
>  grompp -f minim.mdp -c his8_meohi_wat.gro -p topol.top -o em.tpr
>
> I run into error which says moleculetype OH not found.
>
>
> Added the following specifically in .top file
>  [ moleculetype ]
>   ; molname   nrexcl
>   OH1
>
>   [atoms]
>   1 OH  1   OH OH  1   0.21 1.008 ;
>   2 OW  1   OH OW  1  -1.2115.4   ;
>   [ bonds ]
> OW   HW1gb_38
>
> Going back to the command
> grompp -f minim.mdp -c his8_meohi_wat.gro -p topol.top -o em.tpr
>
> runs into different error as mentioned earlier : Fatal error: number of
coordinates in coordinate file (5his8_meohi_wat.gro, 12487) does not match
topology (topol.top, 12519)
>
> The .top file includes tip4p.itp, methanol.itp and ions.itp.
>
> So I am totally confused as to where I am going wrong.
> Please guide.
>
> Thanks,
> Shivangi
>
>
>
> Shivangi Nangia
> Garrison Group
> Graduate Student
> 201A Chemistry Building
> University Park PA 16802
>
>  >
>
>
>
>
>
> Hello,
>  >
>  > Thanks a lot for the suggestion.
>  >
>  > I think I made some progress but I am not there yet.
>  >
>  > I added the following in the ions.itp file
>  >
>  > [ moleculetype ]
>  > ; molname   nrexcl
>  > OH1
>  >
>  > [ atoms ]
>  > ; id  at type  res nr   residu name at name  cg nr charge
>  > 1  OH 1  OHOH  1  0
>  > 1  OW 1  OWOW  1 -1
>  >
>  >
>  > Still I ran into the same error that it could not find moleculetype OH.
>  >
>  > Than I specifically added the following to the .top file
>  >
>  > [ moleculetype ]
>  > ; molname   nrexcl
>  > OH1
>  >
>  > [atoms]
>  >  1 OH  1   OH OH  1   0.21 1.008 ;
>  >  2 OW  1   OH OW  1  -1.2115.4   ;
>  > [ bonds ]
>  >OW   HW1gb_38
>  >
>  > This helped.
>  > However, there is new error I am running into which says:
>  > Fatal error: number of coordinates in coordinate file
(5his8_meohi_wat.gro, 12487) does not match topology (topol.top, 12519)
>  >
>  > I am trying to add 8 hydroxide ions in my methanol-water system.
>  >
>
> And how are you attempting this?  What command(s) did you give?  What
subsequent modifications to your topology did you make?
>
> The generic solution to your problem can be found here:
>
>
http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>
>  > The confusion I have is:
>  > The .gro file has OH but is gromacs really accounting OH as 2 atoms?
>
> Gromacs assigns parameters to the molecules it finds based on the entries in 

Re: [gmx-users] Hydroixde Ion

[Justin A. Lemkul]

SHIVANGI NANGIA wrote:

Hi again,

I have the following:

I have not changed anything in ffG53a6.atp and .rtp
As suggested by gmx users, I have the following in the ions,itp file

[ moleculetype ]
  ; molname   nrexcl
OH1

[ atoms ]
; id  at type  res nr   residu name at name  cg nr charge
  1  OH 1  OHOH  1  0
  1  OW 1  OWOW  1 -1


I executed the following commands:

(a) pdb2gmx -f his8.pdb -ignh -ter -his -p topol.top -o his8.gro
(b) editconf -f his8.gro -box 5 5 5 -o his8box.gro
(c) genbox -cp his8box.gro  -ci  1methanol.gro -nmol 1800 -o 
his8_meoh.gro -p topol.top


Were all 1800 methanol molecules properly inserted here?  Note that genbox does 
not update the topology automatically for any molecules other than water.


(d) grompp -f ions.mdp -c his8_meoh.gro -p topol.top -o ions.tpr -p 
topol.top
(e) genion -s ions.tpr -o added_ions.gro -p topol.top -pname NA -nname 
OH -nn 8


Per the genion help information, it is not well-suited to inserting polyatomic 
ions.  Also, what are you choosing to replace here?  genion is designed to 
replace water molecules with monoatomic ions, but you haven't added any water 
yet.  If you're simply replacing elements of the "System" group, you've probably 
got fractional species somewhere.  I would be willing to bet that this process 
is what is causing your problem.  Check the contents of the coordinate file and 
topology before and after genion, and you will probably find the problem. 
Solution: don't use genion.  Use genbox -ci -nmol to add your 8 OH molecules.


-Justin

(f)  genbox -cp added_ions.gro  -cs tip4p.gro  -o his8_meohi_wat.gro -p 
topol.top
 
Commands (a)-(f), all goes smooth.


When I do the following
 grompp -f minim.mdp -c his8_meohi_wat.gro -p topol.top -o em.tpr

I run into error which says moleculetype OH not found.


Added the following specifically in .top file
 [ moleculetype ]
  ; molname   nrexcl
  OH1

  [atoms]
  1 OH  1   OH OH  1   0.21 1.008 ;
  2 OW  1   OH OW  1  -1.2115.4   ;
  [ bonds ]
OW   HW1gb_38

Going back to the command
grompp -f minim.mdp -c his8_meohi_wat.gro -p topol.top -o em.tpr

runs into different error as mentioned earlier : Fatal error: number of 
coordinates in coordinate file (5his8_meohi_wat.gro, 12487) does not 
match topology (topol.top, 12519)


The .top file includes tip4p.itp, methanol.itp and ions.itp.

So I am totally confused as to where I am going wrong.
Please guide.

Thanks,
Shivangi



Shivangi Nangia
Garrison Group
Graduate Student
201A Chemistry Building
University Park PA 16802

 >





Hello,
 >
 > Thanks a lot for the suggestion.
 >
 > I think I made some progress but I am not there yet.
 >
 > I added the following in the ions.itp file
 >
 > [ moleculetype ]
 > ; molname   nrexcl
 > OH1
 >
 > [ atoms ]
 > ; id  at type  res nr   residu name at name  cg nr charge
 > 1  OH 1  OHOH  1  0
 > 1  OW 1  OWOW  1 -1
 >
 >
 > Still I ran into the same error that it could not find moleculetype OH.
 >
 > Than I specifically added the following to the .top file
 >
 > [ moleculetype ]
 > ; molname   nrexcl
 > OH1
 >
 > [atoms]
 >  1 OH  1   OH OH  1   0.21 1.008 ;
 >  2 OW  1   OH OW  1  -1.2115.4   ;
 > [ bonds ]
 >OW   HW1gb_38
 >
 > This helped.
 > However, there is new error I am running into which says:
 > Fatal error: number of coordinates in coordinate file 
(5his8_meohi_wat.gro, 12487) does not match topology (topol.top, 12519)

 >
 > I am trying to add 8 hydroxide ions in my methanol-water system.
 >

And how are you attempting this?  What command(s) did you give?  What 
subsequent modifications to your topology did you make?


The generic solution to your problem can be found here:

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

 > The confusion I have is:
 > The .gro file has OH but is gromacs really accounting OH as 2 atoms?

Gromacs assigns parameters to the molecules it finds based on the 
entries in the respective [moleculetypes].  If you tell grompp or any 
other program that the [moleculetype] "OH" is comprised of two atoms, 
then there's no reason to believe  anything is wrong.


 > Also, the difference (12519-12487) is greater than 8.
 >

Without some context as to what you're doing and what you've done up to 
this point, this information does not lead to any useful solution.  The 
number of molecules (either methanol or OH) in your topology does not 
match the contents of your coordinate file.


-Justin

 > Kindly help.
 >
 > Thanks,
 > Shivangi
 >
 >
 >
 > Shivangi Nangia
! > Garrison Group
 > Graduate Student
 > 201A Chemistry Building
 > University Park PA 16802
 >
 > On 22/03/2011 7:44 AM, SHIVANGI NANGIA wrote:
 >  > Hello,
 >  >
 >  > I am new gromacs user.
 >  > I am trying to set up a water-methanol system with few hyrdroxide 
i

Re: Re: Re: [gmx-users] Hydroixde Ion

[SHIVANGI NANGIA]

Hi again,

I have the following:

I have not changed anything in ffG53a6.atp and .rtp
As suggested by gmx users, I have the following in the ions,itp file

[ moleculetype ]
 
; molname   nrexcl

OH1



[ atoms ]

; id  at type  res nr   residu name at name  cg nr charge
 
1  OH 1  OHOH  1  0
 
1  OW 1  OWOW  1 -1


I executed the following commands:

(a) pdb2gmx -f his8.pdb -ignh -ter -his -p topol.top -o his8.gro
(b) editconf -f his8.gro -box 5 5 5 -o his8box.gro
(c) genbox -cp his8box.gro  -ci  1methanol.gro -nmol 1800 -o his8_meoh.gro -p
topol.top
(d) grompp -f ions.mdp -c his8_meoh.gro -p topol.top -o ions.tpr -p topol.top
(e) genion -s ions.tpr -o added_ions.gro -p topol.top -pname NA -nname OH -nn 8
(f)  genbox -cp added_ions.gro  -cs tip4p.gro  -o his8_meohi_wat.gro -p
topol.top
 
Commands (a)-(f), all goes smooth.

When I do the following
 grompp -f minim.mdp -c his8_meohi_wat.gro -p topol.top -o em.tpr

I run into error which says moleculetype OH not found.


Added the following specifically in .top file 
 [ moleculetype ]
 
; molname   nrexcl
 
OH1


 
[atoms]

  1 OH  1   OH OH  1   0.21 
1.008 ;

  2 OW  1   OH OW  1  -1.21
15.4   ;
 
[ bonds ]

OW   HW1gb_38

Going back to the command
grompp -f minim.mdp -c his8_meohi_wat.gro -p topol.top -o em.tpr

runs into different error as mentioned earlier : Fatal error: number of
coordinates in coordinate file 
(5his8_meohi_wat.gro, 12487) does not match topology (topol.top, 12519)

The .top file includes tip4p.itp, methanol.itp and ions.itp.

So I am totally confused as to where I am going wrong. 
Please guide.

Thanks,
Shivangi



Shivangi Nangia
Garrison Group
Graduate Student
201A Chemistry Building
University Park PA 16802

> 





Hello,
>
> Thanks a lot for the suggestion.
>
> I think I made some progress but I am not there yet.
>
> I added the following in the ions.itp file
>
> [ moleculetype ]
> ; molname   nrexcl
> OH1
>
> [ atoms ]
> ; id  at type  res nr   residu name at name  cg nr charge
> 1  OH 1  OHOH  1  0
> 1  OW 1  OWOW  1 -1
>
>
> Still I ran into the same error that it could not find moleculetype OH.
>
> Than I specifically added the following to the .top file
>
> [ moleculetype ]
> ; molname   nrexcl
> OH1
>
> [atoms]
>  1 OH  1   OH OH  1   0.21 1.008 ;
>  2 OW  1   OH OW  1  -1.2115.4   ;
> [ bonds ]
>OW   HW1gb_38
>
> This helped.
> However, there is new error I am running into which says:
> Fatal error: number of coordinates in coordinate file (5his8_meohi_wat.gro,
12487) does not match topology (topol.top, 12519)
>
> I am trying to add 8 hydroxide ions in my methanol-water system.
>

And how are you attempting this?  What command(s) did you give?  What
subsequent modifications to your topology did you make?

The generic solution to your problem can be found here:

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

> The confusion I have is:
> The .gro file has OH but is gromacs really accounting OH as 2 atoms?

Gromacs assigns parameters to the molecules it finds based on the entries in 
the respective [moleculetypes].  If you tell grompp or any other program that 
the [moleculetype] "OH" is comprised of two atoms, then there's no reason to 
believe  anything is wrong.

> Also, the difference (12519-12487) is greater than 8.
>

Without some context as to what you're doing and what you've done up to this 
point, this information does not lead to any useful solution.  The number of 
molecules (either methanol or OH) in your topology does not match the contents 
of your coordinate file.

-Justin

> Kindly help.
>
> Thanks,
> Shivangi
>
>
>
> Shivangi Nangia
> Garrison Group
> Graduate Student
> 201A Chemistry Building
> University Park PA 16802
>
> On 22/03/2011 7:44 AM, SHIVANGI NANGIA wrote:
>  > Hello,
>  >
>  > I am new gromacs user.
>  > I am trying to set up a water-methanol system with few hyrdroxide ions.
>  >
>  > Since hyrdroxide ion does not already exist in gromacs database, I defined 
> the following in the .rtp file ( I am using ffG53a6)
>  >
>  > [ OH ]
>  >  [ atoms ]
>  >OWOW-1.41000 0
>  >   HW1 H 0.41000 0
>  >  [ bonds ]
>  >OW   HW1gb_38
>  >  [ angles ]
>  > ;  aiajak   gromos typpe
>  >  [ impropers ]
>  > ;  aiajakal   gromos type
>  >  [ dihedrals ]
>  > ;  aiajakal   gromos type
>
> That's only useful for pdb2gmx when generating .top files.
>
>  > I also included OH in the .atp file ( I realise that hydroxide ion is NOT 
> an atom, its a diatomic anion, I was just trying!)
>
> Don't. The .atp defines *atom* types.
>
>  > I ran into the error: No such moleculetype OH
>  >
>  > I further included information in the ions.itp as follows:
>  >
>  > [ moleculetype ]
>  > ; molname   nrexcl
>  > OH

Re: [gmx-users] Various web issues

[Justin A. Lemkul]

Thanks for the fix!

-Justin

Rossen Apostolov wrote:

Hi again,

On 3/22/11 6:57 PM, Justin A. Lemkul wrote:
I posted this a few days ago, but the problem persists - the "search" 
feature on the Gromacs site either returns an error or completely 
nonsensical content.  Can someone please look into why this is so?  
Manual navigation is very tedious. 
The search works again. The search index cache was corrupted and 
rebuilding it fixed the issue.


Cheers,
Rossen


--


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] Various web issues

[Rossen Apostolov]

Hi again,

On 3/22/11 6:57 PM, Justin A. Lemkul wrote:
I posted this a few days ago, but the problem persists - the "search" 
feature on the Gromacs site either returns an error or completely 
nonsensical content.  Can someone please look into why this is so?  
Manual navigation is very tedious. 
The search works again. The search index cache was corrupted and 
rebuilding it fixed the issue.


Cheers,
Rossen
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Re: [gmx-users] Various web issues

[Rossen Apostolov]

Hi Justin,

On 3/22/11 6:57 PM, Justin A. Lemkul wrote:


Hi,

I posted this a few days ago, but the problem persists - the "search" 
feature on the Gromacs site either returns an error or completely 
nonsensical content.  Can someone please look into why this is so?  
Manual navigation is very tedious.

Right, the search returns total crap. I'll look into that.



A couple of other things:

1. manual.gromacs.org no longer has any useful content.  The site 
comes up with "syrah.cbr.su.se" and nothing else.  Are there changes 
going on with this site?


We changed the universities and I moved the www.gromacs.org server along 
with us, but manual.gromacs.org stayed at the old host (syrah). I'll 
look put a new one.


2. Sorting features of the mailing list search no longer work.  
Clicking on the title of any column has no effect.



Now it does:)

Cheers,
Rossen


-Justin



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[gmx-users] Various web issues

[Justin A. Lemkul]

Hi,

I posted this a few days ago, but the problem persists - the "search" feature on 
the Gromacs site either returns an error or completely nonsensical content.  Can 
someone please look into why this is so?  Manual navigation is very tedious.


A couple of other things:

1. manual.gromacs.org no longer has any useful content.  The site comes up with 
"syrah.cbr.su.se" and nothing else.  Are there changes going on with this site?


2. Sorting features of the mailing list search no longer work.  Clicking on the 
title of any column has no effect.


-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] Hydroixde Ion

[Justin A. Lemkul]

SHIVANGI NANGIA wrote:

Hello,

Thanks a lot for the suggestion.

I think I made some progress but I am not there yet.

I added the following in the ions.itp file

[ moleculetype ]
; molname   nrexcl
OH1

[ atoms ]
; id  at type  res nr   residu name at name  cg nr charge
1  OH 1  OHOH  1  0
1  OW 1  OWOW  1 -1


Still I ran into the same error that it could not find moleculetype OH.

Than I specifically added the following to the .top file

[ moleculetype ]
; molname   nrexcl
OH1

[atoms]
 1 OH  1   OH OH  1   0.21 1.008 ;
 2 OW  1   OH OW  1  -1.2115.4   ;
[ bonds ]
   OW   HW1gb_38

This helped.
However, there is new error I am running into which says:
Fatal error: number of coordinates in coordinate file 
(5his8_meohi_wat.gro, 12487) does not match topology (topol.top, 12519)


I am trying to add 8 hydroxide ions in my methanol-water system.



And how are you attempting this?  What command(s) did you give?  What subsequent 
modifications to your topology did you make?


The generic solution to your problem can be found here:

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


The confusion I have is:
The .gro file has OH but is gromacs really accounting OH as 2 atoms? 


Gromacs assigns parameters to the molecules it finds based on the entries in the 
respective [moleculetypes].  If you tell grompp or any other program that the 
[moleculetype] "OH" is comprised of two atoms, then there's no reason to believe 
 anything is wrong.



Also, the difference (12519-12487) is greater than 8.



Without some context as to what you're doing and what you've done up to this 
point, this information does not lead to any useful solution.  The number of 
molecules (either methanol or OH) in your topology does not match the contents 
of your coordinate file.


-Justin


Kindly help.

Thanks,
Shivangi



Shivangi Nangia
Garrison Group
Graduate Student
201A Chemistry Building
University Park PA 16802

On 22/03/2011 7:44 AM, SHIVANGI NANGIA wrote:
 > Hello,
 >
 > I am new gromacs user.
 > I am trying to set up a water-methanol system with few hyrdroxide ions.
 >
 > Since hyrdroxide ion does not already exist in gromacs database, I 
defined the following in the .rtp file ( I am using ffG53a6)

 >
 > [ OH ]
 >  [ atoms ]
 >OWOW-1.41000 0
 >   HW1 H 0.41000 0
 >  [ bonds ]
 >OW   HW1gb_38
 >  [ angles ]
 > ;  aiajak   gromos typpe
 >  [ impropers ]
 > ;  aiajakal   gromos type
 >  [ dihedrals ]
 > ;  aiajakal   gromos type

That's only useful for pdb2gmx when generating .top files.

 > I also included OH in the .atp file ( I realise that hydroxide ion is 
NOT an atom, its a diatomic anion, I was just trying!)


Don't. The .atp defines *atom* types.

 > I ran into the error: No such moleculetype OH
 >
 > I further included information in the ions.itp as follows:
 >
 > [ moleculetype ]
 > ; molname   nrexcl
 > OH1
 >
 > [ atoms ]
 > ; id  at type  res nr   residu name at name  cg nr charge
 > 1  OH 1  OHOH  1 -1

Use two atoms, like you did for your .rtp entry.

 > The genion adds the "OH"  in the .gro file and also the topol.top but 
when I try to minimize the system using

 > grompp -f minim.mdp -c 5his8_meohi_wat.gro -p topol.top -o em.tpr
 > I am still running into the same error, No such moleculetype OH.

Your .top still does not have a functional [ moleculetype ] OH. You're 
probably not using the #include "ions.itp"  mechanism correctly.


Mark



--


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] Alcohol Dehydrogenase MD simulation....Reg

[Kishore]

Dear All,

I had been in the look out for someone who has a reasonable amount of
expertise in dealing with the MD simulation of an Alcohol Dehydrogenase. I
have a problem dealing with the NADPH. I was unable to maintain the
planarity of the carboxamide of the nicotinamide moiety in the simulation as
a result of which important sidechain hydrogen bonds are being lost in the
simulation. Is such behaviour expected or is it because of the non quantum
mechanical treatment of the NADPH molecule that these kind of situations
occur? If anyone has some experience please share it.

-- 
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Re: Re: [gmx-users] Hydroixde Ion

[SHIVANGI NANGIA]

Hello,

Thanks a lot for the suggestion.

I think I made some progress but I am not there yet.

I added the following in the ions.itp file

[ moleculetype ]
; molname   nrexcl
OH1

[ atoms ]
; id  at type  res nr   residu name at name  cg nr charge
1  OH 1  OHOH  1  0
1  OW 1  OWOW  1 -1


Still I ran into the same error that it could not find moleculetype OH.

Than I specifically added the following to the .top file

[ moleculetype ]
; molname   nrexcl
OH1

[atoms]
 1 OH  1   OH OH  1   0.21 1.008 ;
 2 OW  1   OH OW  1  -1.2115.4   ;
[ bonds ]
   OW   HW1gb_38

This helped. 
However, there is new error I am running into which says: 
Fatal error: number of coordinates in coordinate file (5his8_meohi_wat.gro,
12487) does not match topology (topol.top, 12519)

I am trying to add 8 hydroxide ions in my methanol-water system.

The confusion I have is: 
The .gro file has OH but is gromacs really accounting OH as 2 atoms?  
Also, the difference (12519-12487) is greater than 8. 

Kindly help.

Thanks,
Shivangi



Shivangi Nangia
Garrison Group
Graduate Student
201A Chemistry Building
University Park PA 16802

On 22/03/2011 7:44 AM, SHIVANGI NANGIA wrote:
> Hello,
> 
>
 I am new gromacs user.
> I am trying to set up a water-methanol 
system with few hyrdroxide ions.
> 
> Since hyrdroxide ion 
does not already exist in gromacs database, I defined the following in 
the .rtp file ( I am using ffG53a6)
> 
> [ OH ]
>  [ 
atoms ]
>OWOW-1.41000 0
>   HW1 H  
   0.41000 0
>  [ bonds ]
>OW   HW1gb_38
> 
 [ angles ]
> ;  aiajak   gromos typpe
>  [ 
impropers ]
> ;  aiajakal   gromos type
>  [ 
dihedrals ]
> ;  aiajakal   gromos type

That's 
only useful for pdb2gmx when generating .top files.

> I also 
included OH in the .atp file ( I realise that hydroxide ion is NOT an 
atom, its a diatomic anion, I was just trying!)

Don't. The .atp 
defines *atom* types.

> I ran into the error: No such 
moleculetype OH
> 
> I further included information in the 
ions.itp as follows:
> 
> [ moleculetype ]
> ; 
molname   nrexcl
> OH1
> 
> [ atoms ]
> ; 
id  at type  res nr   residu name at name  cg nr charge
> 1  OH 1 
 OHOH  1 -1

Use two atoms, like you did for your .rtp entry.

>
 The genion adds the "OH"  in the .gro file and also the topol.top but 
when I try to minimize the system using
> grompp -f minim.mdp -c 
5his8_meohi_wat.gro -p topol.top -o em.tpr
> I am still running 
into the same error, No such moleculetype OH.

Your .top still 
does not have a functional [ moleculetype ] OH. You're probably not 
using the #include "ions.itp"  mechanism correctly.

Mark

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RE: [gmx-users] install problems cygwin

[vijaya subramanian]

Hi
I tried doing it from my home directory. It didn't work.  Also gcc hello.c and 
g77 hello.f don't produce 
executables, though both seem to run-not a.out file is created.
Vijaya

> From: rol...@utk.edu
> Date: Tue, 22 Mar 2011 12:51:45 -0400
> Subject: Re: [gmx-users] install problems cygwin
> To: gmx-users@gromacs.org
> 
> Hi,
> 
> try to move your files into your cygwin home directory before
> compiling. If that doesn't work, try to first compile a hello world C
> program to see why the compiler doesn't work.
> 
> Roland
> 
> On Tue, Mar 22, 2011 at 12:13 PM, vijaya subramanian
>  wrote:
> >
> > Hi
> > I am trying to install gromacs on a windows laptop with rhcygwin.  I am
> > doing it as administrator
> > and I ran into the same problem when I tried installing fftw-3.2.2.
> >
> > $ ./configure --enable-sse --enable-float
> > checking for a BSD-compatible install... /usr/bin/install -c
> > checking whether build environment is sane... yes
> > checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
> > checking for gawk... gawk
> > checking whether make sets $(MAKE)... yes
> > checking whether to enable maintainer-specific portions of Makefiles... no
> > checking build system type... i686-pc-cygwin
> > checking host system type... i686-pc-cygwin
> > checking for gcc... gcc
> > checking for C compiler default output file name...
> > configure: error: in `/cygdrive/c/fftw-3.2.2':
> > configure: error: C compiler cannot create executables
> > See `config.log' for more details.
> >
> > The config.log file is attached.
> > I read the config.log file but am unable to figure out what the problem is.
> > It shows
> > the right version of gcc installed and configure appears to find it.
> >
> >
> > Thanks
> > Vijaya
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
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> >
> 
> 
> 
> -- 
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> 865-241-1537, ORNL PO BOX 2008 MS6309
> -- 
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] New maintenance release: gromacs-4.5.4

[Carsten Kutzner]

Hi,

try to add the --disable-shared flag to your invocation of .configure.

Carsten


On Mar 22, 2011, at 3:26 PM, Ye MEI wrote:

> Thank you for the new version of gromacs.
> But the compilation of gromacs failed on my computer. The commands are as 
> follows:
> make distclean
> export CC=icc
> export F77=ifort
> export CXX=icc
> export CFLAGS="-xS -I/apps/fftw3/include"
> export FFLAGS="-xS -I/apps/fftw3/include"
> export CXXFLAGS="-I/apps/fftw3/include"
> export LDFLAGS="-L/apps/fftw3/lib -lfftw3f"
> ./configure --prefix=/apps/gromacs4.5 --with-fft=fftw3 --with-x 
> --with-qmmm-gaussian
> make
> 
> and the error message is
> icc  -shared  .libs/calcmu.o .libs/calcvir.o .libs/constr.o .libs/coupling.o 
> .libs/domdec.o .libs/domdec_box.o .libs/domdec_con.o .libs/domdec_network.o 
> .libs/domdec_setup.o .libs/domdec_top.o .libs/ebin.o .libs/edsam.o 
> .libs/ewald.o .libs/force.o .libs/forcerec.o .libs/ghat.o .libs/init.o 
> .libs/mdatom.o .libs/mdebin.o .libs/minimize.o .libs/mvxvf.o .libs/ns.o 
> .libs/nsgrid.o .libs/perf_est.o .libs/genborn.o .libs/genborn_sse2_single.o 
> .libs/genborn_sse2_double.o .libs/genborn_allvsall.o 
> .libs/genborn_allvsall_sse2_single.o .libs/genborn_allvsall_sse2_double.o 
> .libs/gmx_qhop_parm.o .libs/gmx_qhop_xml.o .libs/groupcoord.o .libs/pme.o 
> .libs/pme_pp.o .libs/pppm.o .libs/partdec.o .libs/pull.o .libs/pullutil.o 
> .libs/rf_util.o .libs/shakef.o .libs/sim_util.o .libs/shellfc.o .libs/stat.o 
> .libs/tables.o .libs/tgroup.o .libs/tpi.o .libs/update.o .libs/vcm.o 
> .libs/vsite.o .libs/wall.o .libs/wnblist.o .libs/csettle.o .libs/clincs.o 
> .libs/qmmm.o .libs/gmx_fft.o .libs/gmx_parallel_3dfft.o .libs/fft5d.o 
> .libs/gmx_wallcycle.o .libs/qm_gaussian.o .libs/qm_mopac.o .libs/qm_gamess.o 
> .libs/gmx_fft_fftw2.o .libs/gmx_fft_fftw3.o .libs/gmx_fft_fftpack.o 
> .libs/gmx_fft_mkl.o .libs/qm_orca.o .libs/mdebin_bar.o  -Wl,--rpath 
> -Wl,/home/ymei/gromacs-4.5.4/src/gmxlib/.libs -Wl,--rpath 
> -Wl,/apps/gromacs4.5/lib -lxml2 -L/apps/fftw3/lib /apps/fftw3/lib/libfftw3f.a 
> ../gmxlib/.libs/libgmx.so -lnsl  -pthread -Wl,-soname -Wl,libmd.so.6 -o 
> .libs/libmd.so.6.0.0
> ld: /apps/fftw3/lib/libfftw3f.a(problem.o): relocation R_X86_64_32 against `a 
> local symbol' can not be used when making a shared object; recompile with 
> -fPIC
> /apps/fftw3/lib/libfftw3f.a: could not read symbols: Bad value
> 
> However, it works fine for gromacs 4.5.3. Can anyone help?
> 
> Ye MEI
> 
> 2011-03-22 
> 
> 
> 
> From： Rossen Apostolov 
> Date： 2011-03-22  03:24:55 
> To： Discussion list for GROMACS development; Discussion list for GROMACS 
> users; gmx-announce 
> CC： 
> Subject： [gmx-users] New maintenance release: gromacs-4.5.4 
> 
> Dear Gromacs community,
> A new maintenance release of Gromacs is available for download at 
> ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz.
> Some notable updates in this release:
> * Fixed pdb2gmx picking up force field from local instead of library 
> directory
> * Made pdb2gmx vsite generation work again for certain His namings.
> * Fixed incorrect virial and pressure averages with certain nst... 
> values (instantaneous values correct)
> * Fixed incorrect cosine viscosity output
> * New -multidir alternative for mdrun -multi option
> * Several minor fixes in analysis tools
> * Several updates to the program documentation
> Big thanks to all developers and users!
> Happy simulating!
> Rossen
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] install problems cygwin

[Roland Schulz]

Hi,

try to move your files into your cygwin home directory before
compiling. If that doesn't work, try to first compile a hello world C
program to see why the compiler doesn't work.

Roland

On Tue, Mar 22, 2011 at 12:13 PM, vijaya subramanian
 wrote:
>
> Hi
> I am trying to install gromacs on a windows laptop with rhcygwin.  I am
> doing it as administrator
> and I ran into the same problem when I tried installing fftw-3.2.2.
>
> $ ./configure --enable-sse --enable-float
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> checking whether to enable maintainer-specific portions of Makefiles... no
> checking build system type... i686-pc-cygwin
> checking host system type... i686-pc-cygwin
> checking for gcc... gcc
> checking for C compiler default output file name...
> configure: error: in `/cygdrive/c/fftw-3.2.2':
> configure: error: C compiler cannot create executables
> See `config.log' for more details.
>
> The config.log file is attached.
> I read the config.log file but am unable to figure out what the problem is.
> It shows
> the right version of gcc installed and configure appears to find it.
>
>
> Thanks
> Vijaya
>
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Re: [gmx-users] New maintenance release: gromacs-4.5.4

[Roland Schulz]

On Tue, Mar 22, 2011 at 10:26 AM, Ye MEI  wrote:
> Thank you for the new version of gromacs.
> But the compilation of gromacs failed on my computer. The commands are as 
> follows:
> make distclean
> export CC=icc
> export F77=ifort
> export CXX=icc
> export CFLAGS="-xS -I/apps/fftw3/include"
> export FFLAGS="-xS -I/apps/fftw3/include"
> export CXXFLAGS="-I/apps/fftw3/include"
> export LDFLAGS="-L/apps/fftw3/lib -lfftw3f"
> ./configure --prefix=/apps/gromacs4.5 --with-fft=fftw3 --with-x 
> --with-qmmm-gaussian
> make
>
> and the error message is
> icc  -shared  .libs/calcmu.o .libs/calcvir.o .libs/constr.o .libs/coupling.o 
> .libs/domdec.o .libs/domdec_box.o .libs/domdec_con.o .libs/domdec_network.o 
> .libs/domdec_setup.o .libs/domdec_top.o .libs/ebin.o .libs/edsam.o 
> .libs/ewald.o .libs/force.o .libs/forcerec.o .libs/ghat.o .libs/init.o 
> .libs/mdatom.o .libs/mdebin.o .libs/minimize.o .libs/mvxvf.o .libs/ns.o 
> .libs/nsgrid.o .libs/perf_est.o .libs/genborn.o .libs/genborn_sse2_single.o 
> .libs/genborn_sse2_double.o .libs/genborn_allvsall.o 
> .libs/genborn_allvsall_sse2_single.o .libs/genborn_allvsall_sse2_double.o 
> .libs/gmx_qhop_parm.o .libs/gmx_qhop_xml.o .libs/groupcoord.o .libs/pme.o 
> .libs/pme_pp.o .libs/pppm.o .libs/partdec.o .libs/pull.o .libs/pullutil.o 
> .libs/rf_util.o .libs/shakef.o .libs/sim_util.o .libs/shellfc.o .libs/stat.o 
> .libs/tables.o .libs/tgroup.o .libs/tpi.o .libs/update.o .libs/vcm.o 
> .libs/vsite.o .libs/wall.o .libs/wnblist.o .libs/csettle.o .libs/clincs.o 
> .libs/qmmm.o .libs/gmx_fft.o .libs/gmx_parallel_3dfft.o .libs/fft5d.o 
> .libs/gmx_wallcycle.o .libs/qm_gaussian.o .libs/qm_mopac.o .libs/qm_gamess.o 
> .libs/gmx_fft_fftw2.o .libs/gmx_fft_fftw3.o .libs/gmx_fft_fftpack.o 
> .libs/gmx_fft_mkl.o .libs/qm_orca.o .libs/mdebin_bar.o  -Wl,--rpath 
> -Wl,/home/ymei/gromacs-4.5.4/src/gmxlib/.libs -Wl,--rpath 
> -Wl,/apps/gromacs4.5/lib -lxml2 -L/apps/fftw3/lib /apps/fftw3/lib/libfftw3f.a 
> ../gmxlib/.libs/libgmx.so -lnsl  -pthread -Wl,-soname -Wl,libmd.so.6 -o 
> .libs/libmd.so.6.0.0
> ld: /apps/fftw3/lib/libfftw3f.a(problem.o): relocation R_X86_64_32 against `a 
> local symbol' can not be used when making a shared object; recompile with 
> -fPIC
> /apps/fftw3/lib/libfftw3f.a: could not read symbols: Bad value

Either recompile fftw with additional flag --with-pic or recompile
GROMACS with --disable-shared.

Roland
>
> However, it works fine for gromacs 4.5.3. Can anyone help?
>
> Ye MEI
>
> 2011-03-22
>
>
>
> From： Rossen Apostolov
> Date： 2011-03-22  03:24:55
> To： Discussion list for GROMACS development; Discussion list for GROMACS 
> users; gmx-announce
> CC：
> Subject： [gmx-users] New maintenance release: gromacs-4.5.4
>
> Dear Gromacs community,
> A new maintenance release of Gromacs is available for download at
> ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz.
> Some notable updates in this release:
> * Fixed pdb2gmx picking up force field from local instead of library
> directory
> * Made pdb2gmx vsite generation work again for certain His namings.
> * Fixed incorrect virial and pressure averages with certain nst...
> values (instantaneous values correct)
> * Fixed incorrect cosine viscosity output
> * New -multidir alternative for mdrun -multi option
> * Several minor fixes in analysis tools
> * Several updates to the program documentation
> Big thanks to all developers and users!
> Happy simulating!
> Rossen
> --
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[gmx-users] install problems cygwin

[vijaya subramanian]

Hi
I am trying to install gromacs on a windows laptop with rhcygwin.  I am doing 
it as administrator
and I ran into the same problem when I tried installing fftw-3.2.2.  

$ ./configure --enable-sse --enable-float
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... i686-pc-cygwin
checking host system type... i686-pc-cygwin
checking for gcc... gcc
checking for C compiler default output file name...
configure: error: in `/cygdrive/c/fftw-3.2.2':
configure: error: C compiler cannot create executables
See `config.log' for more details.

The config.log file is attached.  
I read the config.log file but am unable to figure out what the problem is.  It 
shows 
the right version of gcc installed and configure appears to find it. 


Thanks
Vijaya
  This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by fftw configure 3.2.2, which was
generated by GNU Autoconf 2.63.  Invocation command line was

  $ ./configure --enable-sse --enable-float

## - ##
## Platform. ##
## - ##

hostname = himalaya
uname -m = i686
uname -r = 1.8.2(0.230/5/3)
uname -s = CYGWIN_NT-6.1-WOW64
uname -v = 2010-09-01 14:47

/usr/bin/uname -p = unknown
/bin/uname -X = unknown

/bin/arch  = i686
/usr/bin/arch -k   = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo  = unknown
/bin/machine   = unknown
/usr/bin/oslevel   = unknown
/bin/universe  = unknown

PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bin
PATH: /cygdrive/c/Program Files/Common Files/Microsoft Shared/Windows Live
PATH: /cygdrive/c/Windows/system32
PATH: /cygdrive/c/Windows
PATH: /cygdrive/c/Windows/System32/Wbem
PATH: /cygdrive/c/Windows/System32/WindowsPowerShell/v1.0/
PATH: /cygdrive/c/Program Files/Intel/WiFi/bin/
PATH: /cygdrive/c/Program Files/Common Files/Intel/WirelessCommon/
PATH: /cygdrive/c/Program Files/WIDCOMM/Bluetooth Software/
PATH: /cygdrive/c/Program Files/WIDCOMM/Bluetooth Software/syswow64
PATH: /cygdrive/c/Program Files (x86)/Common Files/Roxio Shared/DLLShared/
PATH: /cygdrive/c/Program Files (x86)/Common Files/Roxio Shared/DLLShared/
PATH: /cygdrive/c/Program Files (x86)/Common Files/Roxio Shared/12.0/DLLShared/
PATH: /cygdrive/c/Program Files (x86)/Hewlett-Packard/HP SimplePass Identity 
Protection/x64
PATH: /cygdrive/c/Program Files (x86)/Hewlett-Packard/HP SimplePass Identity 
Protection/
PATH: /cygdrive/c/Program Files/MATLAB/R2010bSP1/runtime/win64
PATH: /cygdrive/c/Program Files/MATLAB/R2010bSP1/bin
PATH: /usr/lib/lapack


## --- ##
## Core tests. ##
## --- ##

configure:2188: checking for a BSD-compatible install
configure:2256: result: /usr/bin/install -c
configure:2267: checking whether build environment is sane
configure:2310: result: yes
configure:2335: checking for a thread-safe mkdir -p
configure:2374: result: /usr/bin/mkdir -p
configure:2387: checking for gawk
configure:2403: found /usr/bin/gawk
configure:2414: result: gawk
configure:2425: checking whether make sets $(MAKE)
configure:2447: result: yes
configure:2634: checking whether to enable maintainer-specific portions of 
Makefiles
configure:2643: result: no
configure:2693: checking build system type
configure:2711: result: i686-pc-cygwin
configure:2733: checking host system type
configure:2748: result: i686-pc-cygwin
configure:3181: checking for gcc
configure:3197: found /usr/bin/gcc
configure:3208: result: gcc
configure:3440: checking for C compiler version
configure:3448: gcc --version >&5
gcc (GCC) 4.3.4 20090804 (release) 1
Copyright (C) 2008 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:3452: $? = 0
configure:3459: gcc -v >&5
Using built-in specs.
Target: i686-pc-cygwin
Configured with: 
/gnu/gcc/releases/respins/4.3.4-3a/gcc4-4.3.4-3/src/gcc-4.3.4/configure 
--srcdir=/gnu/gcc/releases/respins/4.3.4-3a/gcc4-4.3.4-3/src/gcc-4.3.4 
--prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin 
--libexecdir=/usr/lib --datadir=/usr/share --localstatedir=/var 
--sysconfdir=/etc --infodir=/usr/share/info --mandir=/usr/share/man 
--datadir=/usr/share --infodir=/usr/share/info --mandir=/usr/share/man -v 
--with-gmp=/usr --with-mpfr=/usr --enable-bootstrap 
--enable-version-specific-runtime-libs --with-slibdir=/usr/bin 
--libexecdir=/usr/lib --enable-static --enable-shared --enable-shared-libgcc 
--disable-__cxa_atexit --with-gnu-ld --with-gnu-as --with-dwarf2 
--disable-sjlj-exceptions 
--enable-languages=ada,c,c++,fortran,java,objc,obj-c++ --disable

RE: [gmx-users] AFM pulling simulations

[X Rules]

too eager to send an email.. 
I think playing with editconf with princ flag should do the trick .. 

sorry folks and thanks for the help !! 

From: xru...@live.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] AFM pulling simulations
Date: Tue, 22 Mar 2011 15:47:41 +








Thanks Justin, 

 That is pretty much the only tutorial one can found.
 I have one question now, how do I force a particular orientation of my protein 
during genbox (for example if i need to pull along N->C vector, i need my 
protein oriented that way, i.e in Z direction for example to later apply the 
force in that direction).



> Date: Tue, 22 Mar 2011 11:15:54 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] AFM pulling simulations
> 
> 
> 
> X Rules wrote:
> > Hello All,
> > 
> >  I am looking for a very simple (step-by-step) tutorial on AFM pulling 
> > simulations (constant force/ constant velocity) with gromacs.
> > 
> >  Can someone point me to a simple tutorial to perform these simulations 
> > with gromacs?
> > 
> > Thanks,
> > 
> 
> http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling
> 
> -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
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
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> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
  

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RE: [gmx-users] AFM pulling simulations

[X Rules]

Thanks Justin, 

 That is pretty much the only tutorial one can found.
 I have one question now, how do I force a particular orientation of my protein 
during genbox (for example if i need to pull along N->C vector, i need my 
protein oriented that way, i.e in Z direction for example to later apply the 
force in that direction).



> Date: Tue, 22 Mar 2011 11:15:54 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] AFM pulling simulations
> 
> 
> 
> X Rules wrote:
> > Hello All,
> > 
> >  I am looking for a very simple (step-by-step) tutorial on AFM pulling 
> > simulations (constant force/ constant velocity) with gromacs.
> > 
> >  Can someone point me to a simple tutorial to perform these simulations 
> > with gromacs?
> > 
> > Thanks,
> > 
> 
> http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling
> 
> -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
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] AFM pulling simulations

[Laura Kingsley]

http://www.gromacs.org/Documentation/Tutorials

On 03/22/2011 11:02 AM, X Rules wrote:

Hello All,

 I am looking for a very simple (step-by-step) tutorial on AFM pulling 
simulations (constant force/ constant velocity) with gromacs.


 Can someone point me to a simple tutorial to perform these 
simulations with gromacs?


Thanks,



--
Laura Kingsley

Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University
Office: RHPH 504A
575 Stadium Mall Dr.
West Lafayette, IN 47907
Office Phone: (765) 496-6643

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[gmx-users] g_dipole: dipole moment autocorrelation function: Bug?

[Nilesh Dhumal]

Hello,

I am trying to calculate the non normalized dipole moment autocorrelation
function for water. I am using flexible spc water model
(define=-DFLEX_SPC). I am using gromacs 4.0.7 version.

I run the simulation for 4 ns.  I run the following command to calculate
 the dipole moment autocorrelation function

 g_dipoles -f water.trr -s water.tpr -nonormalize -corr total -c

I am geting the really high values around +5000 and -100 (dipcorr.xvg).

Is there anything wrong and function is not geting converge to zero?

I didn't get reply.

Does it a bug? Where should I file the bug.

Thanks

Nilesh




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[gmx-users] Re: gmx-users Digest, Vol 83, Issue 153

[Xiaohu Li]

Message: 4
Date: Tue, 22 Mar 2011 22:26:04 +0800
From: " Ye MEI " 
Subject: Re: [gmx-users] New maintenance release: gromacs-4.5.4
To: " Discussion list for GROMACS users "   
Message-ID: <20110326031153...@itcs.ecnu.edu.cn>
Content-Type: text/plain;   charset="utf-8"


Check your error output, you need the -fPIC flag turned on when you are
compiling FFTW which will generate a shared object so that it can be linked
to other library.


Thank you for the new version of gromacs.
But the compilation of gromacs failed on my computer. The commands are as
follows:
make distclean
export CC=icc
export F77=ifort
export CXX=icc
export CFLAGS="-xS -I/apps/fftw3/include"
export FFLAGS="-xS -I/apps/fftw3/include"
export CXXFLAGS="-I/apps/fftw3/include"
export LDFLAGS="-L/apps/fftw3/lib -lfftw3f"
./configure --prefix=/apps/gromacs4.5 --with-fft=fftw3 --with-x
--with-qmmm-gaussian
make

and the error message is
icc  -shared  .libs/calcmu.o .libs/calcvir.o .libs/constr.o .libs/coupling.o
.libs/domdec.o .libs/domdec_box.o .libs/domdec_con.o .libs/domdec_network.o
.libs/domdec_setup.o .libs/domdec_top.o .libs/ebin.o .libs/edsam.o
.libs/ewald.o .libs/force.o .libs/forcerec.o .libs/ghat.o .libs/init.o
.libs/mdatom.o .libs/mdebin.o .libs/minimize.o .libs/mvxvf.o .libs/ns.o
.libs/nsgrid.o .libs/perf_est.o .libs/genborn.o .libs/genborn_sse2_single.o
.libs/genborn_sse2_double.o .libs/genborn_allvsall.o
.libs/genborn_allvsall_sse2_single.o .libs/genborn_allvsall_sse2_double.o
.libs/gmx_qhop_parm.o .libs/gmx_qhop_xml.o .libs/groupcoord.o .libs/pme.o
.libs/pme_pp.o .libs/pppm.o .libs/partdec.o .libs/pull.o .libs/pullutil.o
.libs/rf_util.o .libs/shakef.o .libs/sim_util.o .libs/shellfc.o .libs/stat.o
.libs/tables.o .libs/tgroup.o .libs/tpi.o .libs/update.o .libs/vcm.o
.libs/vsite.o .libs/wall.o .libs/wnblist.o .libs/csettle.o .libs/clincs.o
.libs/qmmm.o .libs/gmx_fft.o .libs/gmx_parallel_3dfft.o
 .libs/fft5d.o .libs/gmx_wallcycle.o .libs/qm_gaussian.o .libs/qm_mopac.o
.libs/qm_gamess.o .libs/gmx_fft_fftw2.o .libs/gmx_fft_fftw3.o
.libs/gmx_fft_fftpack.o .libs/gmx_fft_mkl.o .libs/qm_orca.o
.libs/mdebin_bar.o  -Wl,--rpath
-Wl,/home/ymei/gromacs-4.5.4/src/gmxlib/.libs -Wl,--rpath
-Wl,/apps/gromacs4.5/lib -lxml2 -L/apps/fftw3/lib
/apps/fftw3/lib/libfftw3f.a ../gmxlib/.libs/libgmx.so -lnsl  -pthread
-Wl,-soname -Wl,libmd.so.6 -o .libs/libmd.so.6.0.0
ld: /apps/fftw3/lib/libfftw3f.a(problem.o): relocation R_X86_64_32 against
`a local symbol' can not be used when making a shared object; recompile with
-fPIC
/apps/fftw3/lib/libfftw3f.a: could not read symbols: Bad value

However, it works fine for gromacs 4.5.3. Can anyone help?

Ye MEI

2011-03-22



From： Rossen Apostolov
Date： 2011-03-22  03:24:55
To： Discussion list for GROMACS development; Discussion list for GROMACS
users; gmx-announce
CC：
Subject： [gmx-users] New maintenance release: gromacs-4.5.4

Dear Gromacs community,
A new maintenance release of Gromacs is available for download at
ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz.
Some notable updates in this release:
* Fixed pdb2gmx picking up force field from local instead of library
directory
* Made pdb2gmx vsite generation work again for certain His namings.
* Fixed incorrect virial and pressure averages with certain nst...
values (instantaneous values correct)
* Fixed incorrect cosine viscosity output
* New -multidir alternative for mdrun -multi option
* Several minor fixes in analysis tools
* Several updates to the program documentation
Big thanks to all developers and users!
Happy simulating!
Rossen
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End of gmx-users Digest, Vol 83, Issue 153
**



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=
Xiaohu Li
Post-doctoral Research Associate
Department of Chemistry
Northwestern University
2145 Sheridan Road
Evanston IL 60208
U.S.A
=
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[gmx-users] Parameterization of a molecule containing a radical (oxygen)

[Simone Cirri]

Hi all,
I have a question regarding a new parameterization: actually, I'm wondering
whether or not it is possible to do it.

The molecule is tempol; you cand find its PubChem entry here
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994&loc=ec_rcs
As you can see, the problem of this molecule is its O radical; this, and the
N belonging to the cycle too.
My lab would really benefit from the parameterization (for the AMBER force
field) of tempol, since we commonly use it in our NMR experiments. We don't
know how to treat the oxygen radical and the N bound to it, though.
If this parameterization is impossible to do we will give up, but we would
like to be sure about it.
Thanks in advance for any answer you could provide.

-- 

Simone Cirri
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[gmx-users] g_dipole: dipole moment autocorrelation function: Bug?

[Nilesh Dhumal]

Hello,

I am trying to calculate the non normalized dipole moment autocorrelation
function for water. I am using flexible spc water model
(define=-DFLEX_SPC). I am using gromacs 4.0.7 version.

I run the simulation for 4 ns.  I run the following command to calculate
 the dipole moment autocorrelation function

 g_dipoles -f water.trr -s water.tpr -nonormalize -corr total -c

I am geting the really high values around +5000 and -100 (dipcorr.xvg).

Is there anything wrong and function is not geting converge to zero?

I didn't get reply.

Does it a bug? Where should I file the bug.

Thanks

Nilesh





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Re: [gmx-users] AFM pulling simulations

[Justin A. Lemkul]

X Rules wrote:

Hello All,

 I am looking for a very simple (step-by-step) tutorial on AFM pulling 
simulations (constant force/ constant velocity) with gromacs.


 Can someone point me to a simple tutorial to perform these simulations 
with gromacs?


Thanks,



http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling

-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] AFM pulling simulations

[X Rules]

Hello All, 

 I am looking for a very simple (step-by-step) tutorial on AFM pulling 
simulations (constant force/ constant velocity) with gromacs. 

 Can someone point me to a simple tutorial to perform these simulations with 
gromacs?

Thanks,

  -- 
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Re: [gmx-users] New maintenance release: gromacs-4.5.4

[Ye MEI]

Thank you for the new version of gromacs.
But the compilation of gromacs failed on my computer. The commands are as 
follows:
make distclean
export CC=icc
export F77=ifort
export CXX=icc
export CFLAGS="-xS -I/apps/fftw3/include"
export FFLAGS="-xS -I/apps/fftw3/include"
export CXXFLAGS="-I/apps/fftw3/include"
export LDFLAGS="-L/apps/fftw3/lib -lfftw3f"
./configure --prefix=/apps/gromacs4.5 --with-fft=fftw3 --with-x 
--with-qmmm-gaussian
make

and the error message is
icc  -shared  .libs/calcmu.o .libs/calcvir.o .libs/constr.o .libs/coupling.o 
.libs/domdec.o .libs/domdec_box.o .libs/domdec_con.o .libs/domdec_network.o 
.libs/domdec_setup.o .libs/domdec_top.o .libs/ebin.o .libs/edsam.o 
.libs/ewald.o .libs/force.o .libs/forcerec.o .libs/ghat.o .libs/init.o 
.libs/mdatom.o .libs/mdebin.o .libs/minimize.o .libs/mvxvf.o .libs/ns.o 
.libs/nsgrid.o .libs/perf_est.o .libs/genborn.o .libs/genborn_sse2_single.o 
.libs/genborn_sse2_double.o .libs/genborn_allvsall.o 
.libs/genborn_allvsall_sse2_single.o .libs/genborn_allvsall_sse2_double.o 
.libs/gmx_qhop_parm.o .libs/gmx_qhop_xml.o .libs/groupcoord.o .libs/pme.o 
.libs/pme_pp.o .libs/pppm.o .libs/partdec.o .libs/pull.o .libs/pullutil.o 
.libs/rf_util.o .libs/shakef.o .libs/sim_util.o .libs/shellfc.o .libs/stat.o 
.libs/tables.o .libs/tgroup.o .libs/tpi.o .libs/update.o .libs/vcm.o 
.libs/vsite.o .libs/wall.o .libs/wnblist.o .libs/csettle.o .libs/clincs.o 
.libs/qmmm.o .libs/gmx_fft.o .libs/gmx_parallel_3dfft.o .libs/fft5d.o 
.libs/gmx_wallcycle.o .libs/qm_gaussian.o .libs/qm_mopac.o .libs/qm_gamess.o 
.libs/gmx_fft_fftw2.o .libs/gmx_fft_fftw3.o .libs/gmx_fft_fftpack.o 
.libs/gmx_fft_mkl.o .libs/qm_orca.o .libs/mdebin_bar.o  -Wl,--rpath 
-Wl,/home/ymei/gromacs-4.5.4/src/gmxlib/.libs -Wl,--rpath 
-Wl,/apps/gromacs4.5/lib -lxml2 -L/apps/fftw3/lib /apps/fftw3/lib/libfftw3f.a 
../gmxlib/.libs/libgmx.so -lnsl  -pthread -Wl,-soname -Wl,libmd.so.6 -o 
.libs/libmd.so.6.0.0
ld: /apps/fftw3/lib/libfftw3f.a(problem.o): relocation R_X86_64_32 against `a 
local symbol' can not be used when making a shared object; recompile with -fPIC
/apps/fftw3/lib/libfftw3f.a: could not read symbols: Bad value

However, it works fine for gromacs 4.5.3. Can anyone help?

Ye MEI

2011-03-22 



From： Rossen Apostolov 
Date： 2011-03-22  03:24:55 
To： Discussion list for GROMACS development; Discussion list for GROMACS users; 
gmx-announce 
CC： 
Subject： [gmx-users] New maintenance release: gromacs-4.5.4 
 
Dear Gromacs community,
A new maintenance release of Gromacs is available for download at 
ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz.
Some notable updates in this release:
* Fixed pdb2gmx picking up force field from local instead of library 
directory
* Made pdb2gmx vsite generation work again for certain His namings.
* Fixed incorrect virial and pressure averages with certain nst... 
values (instantaneous values correct)
* Fixed incorrect cosine viscosity output
* New -multidir alternative for mdrun -multi option
* Several minor fixes in analysis tools
* Several updates to the program documentation
Big thanks to all developers and users!
Happy simulating!
Rossen
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Re: [gmx-users] changing charged groups in CHARMM RNA

[maria goranovic]

thank you for the reply. That settles that.

On Tue, Mar 22, 2011 at 2:56 PM, Justin A. Lemkul  wrote:

>
>
> maria goranovic wrote:
>
>> This must be specific to charmm's implementation in gromacs? Out of
>> curiosity, why can one not use charge groups ?
>>
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-September/054106.html
>
> -Justin
>
>
>> On Tue, Mar 22, 2011 at 2:45 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>maria goranovic wrote:
>>
>>Dear List
>>
>>I was looking at the charged groups in a charmm nucleotide, and
>>could see several groups containing 4 to 14 atoms with integer
>>charges. However, the default topology does not have these
>>charged groups. each atom is given a charged group in the
>>default topology. Can we foresee any problems in replacing the
>>default charged groups generated by pdb2gmx by custom-made
>>charged groups of integer values ? Along the same lines, will
>>this lead to a significant increase in performance, besides the
>>advantage of transferability ?
>>
>>
>>With the CHARMM force field, you should not use charge groups.  Each
>>atom should be its own "group."
>>
>>-Justin
>>
>>
>>Thanking you in advance
>>
>>Maria
>>
>>
>>
>>-- Maria G.
>>Technical University of Denmark
>>Copenhagen
>>
>>
>>-- 
>>
>>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 www
>>interface or send it to gmx-users-requ...@gromacs.org
>>.
>>
>>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>> --
>> Maria G.
>> Technical University of Denmark
>> Copenhagen
>>
>
> --
> 
>
> 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
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>



-- 
Maria G.
Technical University of Denmark
Copenhagen
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Re: [gmx-users] changing charged groups in CHARMM RNA

[Justin A. Lemkul]

maria goranovic wrote:
This must be specific to charmm's implementation in gromacs? Out of 
curiosity, why can one not use charge groups ?


http://lists.gromacs.org/pipermail/gmx-users/2010-September/054106.html

-Justin



On Tue, Mar 22, 2011 at 2:45 PM, Justin A. Lemkul > wrote:




maria goranovic wrote:

Dear List

I was looking at the charged groups in a charmm nucleotide, and
could see several groups containing 4 to 14 atoms with integer
charges. However, the default topology does not have these
charged groups. each atom is given a charged group in the
default topology. Can we foresee any problems in replacing the
default charged groups generated by pdb2gmx by custom-made
charged groups of integer values ? Along the same lines, will
this lead to a significant increase in performance, besides the
advantage of transferability ?


With the CHARMM force field, you should not use charge groups.  Each
atom should be its own "group."

-Justin


Thanking you in advance

Maria



-- 
Maria G.

Technical University of Denmark
Copenhagen


-- 



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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--
Maria G.
Technical University of Denmark
Copenhagen


--


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] changing charged groups in CHARMM RNA

[maria goranovic]

This must be specific to charmm's implementation in gromacs? Out of
curiosity, why can one not use charge groups ?

On Tue, Mar 22, 2011 at 2:45 PM, Justin A. Lemkul  wrote:

>
>
> maria goranovic wrote:
>
>> Dear List
>>
>> I was looking at the charged groups in a charmm nucleotide, and could see
>> several groups containing 4 to 14 atoms with integer charges. However, the
>> default topology does not have these charged groups. each atom is given a
>> charged group in the default topology. Can we foresee any problems in
>> replacing the default charged groups generated by pdb2gmx by custom-made
>> charged groups of integer values ? Along the same lines, will this lead to a
>> significant increase in performance, besides the advantage of
>> transferability ?
>>
>
> With the CHARMM force field, you should not use charge groups.  Each atom
> should be its own "group."
>
> -Justin
>
>
>  Thanking you in advance
>>
>> Maria
>>
>>
>>
>> --
>> Maria G.
>> Technical University of Denmark
>> Copenhagen
>>
>>
> --
> 
>
> 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 www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Maria G.
Technical University of Denmark
Copenhagen
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Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx

[maria goranovic]

the gro file was the input. I am attaching a pdb as well

CRYST1100.0100.0100.0  90.00  90.00  90.00 P 1   1
ATOM  1  P   G   A   4   5.488  -0.842   0.708  1.00  0.00
P
ATOM  2  OP1 G   A   4   6.418   0.258   1.047  1.00  0.00
O
ATOM  3  OP2 G   A   4   5.367  -1.998   1.624  1.00  0.00
O
ATOM  4  O5' G   A   4   4.010  -0.213   0.513  1.00  0.00
O
ATOM  5  C5' G   A   4   3.816   1.098   0.014  1.00  0.00
C
ATOM  6  C4' G   A   4   2.324   1.432  -0.121  1.00  0.00
C
ATOM  7  O4' G   A   4   1.623   0.448  -0.862  1.00  0.00
O
ATOM  8  C3' G   A   4   1.584   1.482   1.211  1.00  0.00
C
ATOM  9  O3' G   A   4   1.869   2.669   1.934  1.00  0.00
O
ATOM 10  C2' G   A   4   0.136   1.413   0.721  1.00  0.00
C
ATOM 11  O2' G   A   4  -0.363   2.696   0.397  1.00  0.00
O
ATOM 12  C1' G   A   4   0.241   0.597  -0.574  1.00  0.00
C
ATOM 13  N9  G   A   4  -0.450  -0.705  -0.438  1.00  0.00
N
ATOM 14  C8  G   A   4   0.075  -1.954  -0.237  1.00  0.00
C
ATOM 15  N7  G   A   4  -0.808  -2.911  -0.197  1.00  0.00
N
ATOM 16  C5  G   A   4  -2.017  -2.251  -0.377  1.00  0.00
C
ATOM 17  C6  G   A   4  -3.346  -2.767  -0.450  1.00  0.00
C
ATOM 18  O6  G   A   4  -3.705  -3.941  -0.398  1.00  0.00
O
ATOM 19  N1  G   A   4  -4.299  -1.762  -0.593  1.00  0.00
N
ATOM 20  C2  G   A   4  -4.002  -0.413  -0.682  1.00  0.00
C
ATOM 21  N2  G   A   4  -5.023   0.438  -0.804  1.00  0.00
N
ATOM 22  N3  G   A   4  -2.751   0.071  -0.652  1.00  0.00
N
ATOM 23  C4  G   A   4  -1.809  -0.897  -0.499  1.00  0.00
C
ATOM 24  H5' G   A   4   4.293   1.204  -0.960  1.00  0.00
H
ATOM 25 H5'' G   A   4   4.269   1.819   0.696  1.00  0.00
H
ATOM 26  H4' G   A   4   2.217   2.395  -0.623  1.00  0.00
H
ATOM 27  H3' G   A   4   1.819   0.589   1.792  1.00  0.00
H
ATOM 28  H2' G   A   4  -0.503   0.940   1.465  1.00  0.00
H
ATOM 29 HO2' G   A   4  -1.301   2.614   0.210  1.00  0.00
H
ATOM 30  H1' G   A   4  -0.225   1.145  -1.393  1.00  0.00
H
ATOM 31  H8  G   A   4   1.129  -2.132  -0.139  1.00  0.00
H
ATOM 32  H1  G   A   4  -5.265  -2.065  -0.635  1.00  0.00
H
ATOM 33  H21 G   A   4  -5.974   0.099  -0.815  1.00  0.00
H
ATOM 34  H22 G   A   4  -4.841   1.428  -0.876  1.00  0.00
H
END


On Tue, Mar 22, 2011 at 2:43 PM, Daniel Adriano Silva M
wrote:

> Hi,
>
> Is this your input? (a GRO file?). Can you paste the PDB corresponding to
> the RNA nucleotide that you are interested on? I think the file may be small
> enough to paste it here so someone can try to reproduce what is happening to
> you.
>
> Daniel
>
>
> 2011/3/22 maria goranovic 
>
>> Sorry for the incomplete reply.
>> version 4.5.3,
>> command: pdb2gmx -f guan.pdb -ignh
>> I tried using -ter, but that did not help.
>>
>>
>> input coordinate file, pulled out from an RNA molecule.
>>
>> Gromacs Runs On Most of All Computer Systems
>>34
>> 1GP1   5.549   4.916   5.071
>> 1G  OP12   5.642   5.026   5.105
>> 1G  OP23   5.537   4.800   5.162
>> 1G  O5'4   5.401   4.979   5.051
>> 1G  C5'5   5.382   5.110   5.001
>> 1G  C4'6   5.232   5.143   4.988
>> 1G  O4'7   5.162   5.045   4.914
>> 1G  C3'8   5.158   5.148   5.121
>> 1G  O3'9   5.187   5.267   5.193
>> 1G  C2'   10   5.014   5.141   5.072
>> 1G  O2'   11   4.964   5.270   5.040
>> 1G  C1'   12   5.024   5.060   4.943
>> 1G   N9   13   4.955   4.930   4.956
>> 1G   C8   14   5.008   4.805   4.976
>> 1G   N7   15   4.919   4.709   4.980
>> 1G   C5   16   4.798   4.775   4.962
>> 1G   C6   17   4.665   4.723   4.955
>> 1G   O6   18   4.630   4.606   4.960
>> 1G   N1   19   4.570   4.824   4.941
>>  1G   C2   20   4.600   4.959   4.932
>> 1G   N2   21   4.498   5.044   4.920
>> 1G   N3   22   4.725   5.007   4.935
>> 1G   C4   23   4.819   4.910   4.950
>> 1G  H5'   24   5.429   5.120   4.904
>> 1G H5''   25   5.427   5.182   5.070
>> 1G  H4'   26   5.222   5.240   4.938
>> 1G  H3'   27   5.182   5.059   5.179
>> 1G  H2'   28   4.950   5.094   5.146
>> 1G HO2'   29   4.870   5.261   5.021
>> 1G  H1'   30   4.978   5.115   4.861
>> 1G   H8   31   5.113   4.787   4.986
>> 1G   H1   32   4.474   4.794   4.936
>> 1G  H21   33   4.403   5.010   4.918
>> 1G  H22   34   4.516   5.143   4.912
>>   10.0  10.0  10.0
>>
>>
>> On Tue, Mar 22, 2011 at 2:09 PM, Mark Abraham wrote:
>>
>>>  On 22/03/2011 8:15 PM, maria goranovic wrote:
>>>
>>> is this a bug of some kind then? someone ? anyone?
>>>
>>>
>>> It's still hard to say. I asked you for you

Re: [gmx-users] changing charged groups in CHARMM RNA

[Justin A. Lemkul]

maria goranovic wrote:

Dear List

I was looking at the charged groups in a charmm nucleotide, and could 
see several groups containing 4 to 14 atoms with integer charges. 
However, the default topology does not have these charged groups. each 
atom is given a charged group in the default topology. Can we foresee 
any problems in replacing the default charged groups generated by 
pdb2gmx by custom-made charged groups of integer values ? Along the same 
lines, will this lead to a significant increase in performance, besides 
the advantage of transferability ? 



With the CHARMM force field, you should not use charge groups.  Each atom should 
be its own "group."


-Justin


Thanking you in advance

Maria



--
Maria G.
Technical University of Denmark
Copenhagen



--


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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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx

[Justin A. Lemkul]

maria goranovic wrote:
Sorry for the incomplete reply. 
version 4.5.3, 
command: pdb2gmx -f guan.pdb -ignh

I tried using -ter, but that did not help.




It appears that pdb2gmx is not equipped to handle the case of an isolated 
nucleotide.  Keep in mind that pdb2gmx is intended for use with repeat building 
blocks of monomers, not isolated molecules.  The default behavior is to assign a 
5' end with no phosphate (i.e. RG rather than pRG).  Attempting to choose "None" 
for a terminus leaves an incomplete phosphate group (i.e. PO3 instead of PO4) 
and thus a fatal error about a "dangling bond."  I'm guessing this has been your 
experience?


There are two potential solutions:

1. Write an .rtp entry of a complete, custom RG nucleotide with the desired PO4 
5' end.


2. Write a new entry in rna.n.tdb that adds another phosphate oxygen and adjusts 
charges appropriately by replacing the existing O and P atoms, at least.


-Justin

input coordinate file, pulled out from an RNA molecule. 


Gromacs Runs On Most of All Computer Systems
   34
1GP1   5.549   4.916   5.071
1G  OP12   5.642   5.026   5.105
1G  OP23   5.537   4.800   5.162
1G  O5'4   5.401   4.979   5.051
1G  C5'5   5.382   5.110   5.001
1G  C4'6   5.232   5.143   4.988
1G  O4'7   5.162   5.045   4.914
1G  C3'8   5.158   5.148   5.121
1G  O3'9   5.187   5.267   5.193
1G  C2'   10   5.014   5.141   5.072
1G  O2'   11   4.964   5.270   5.040
1G  C1'   12   5.024   5.060   4.943
1G   N9   13   4.955   4.930   4.956
1G   C8   14   5.008   4.805   4.976
1G   N7   15   4.919   4.709   4.980
1G   C5   16   4.798   4.775   4.962
1G   C6   17   4.665   4.723   4.955
1G   O6   18   4.630   4.606   4.960
1G   N1   19   4.570   4.824   4.941
1G   C2   20   4.600   4.959   4.932
1G   N2   21   4.498   5.044   4.920
1G   N3   22   4.725   5.007   4.935
1G   C4   23   4.819   4.910   4.950
1G  H5'   24   5.429   5.120   4.904
1G H5''   25   5.427   5.182   5.070
1G  H4'   26   5.222   5.240   4.938
1G  H3'   27   5.182   5.059   5.179
1G  H2'   28   4.950   5.094   5.146
1G HO2'   29   4.870   5.261   5.021
1G  H1'   30   4.978   5.115   4.861
1G   H8   31   5.113   4.787   4.986
1G   H1   32   4.474   4.794   4.936
1G  H21   33   4.403   5.010   4.918
1G  H22   34   4.516   5.143   4.912
  10.0  10.0  10.0


On Tue, Mar 22, 2011 at 2:09 PM, Mark Abraham > wrote:


On 22/03/2011 8:15 PM, maria goranovic wrote:

is this a bug of some kind then? someone ? anyone?


It's still hard to say. I asked you for your GROMACS version and
input coordinate file, and you didn't give us either (in full).
While you're there, what pdb2gmx command did you use?

Mark



just bumping,

maria

On Mon, Mar 21, 2011 at 10:17 AM, maria goranovic
mailto:mariagorano...@gmail.com>> wrote:

Here are the contents of my input coordinate file. 

CRYST10.0000.0000.000  90.00  90.00  90.00 P 1
  1

ATOM  1  P   G   A   4   5.488  -0.842   0.708  1.00
 0.00   P
ATOM  2  OP1 G   A   4   6.418   0.258   1.047  1.00
 0.00   O
ATOM  3  OP2 G   A   4   5.367  -1.998   1.624  1.00
 0.00   O
ATOM  4  O5' G   A   4   4.010  -0.213   0.513  1.00
 0.00   O
ATOM  5  C5' G   A   4   3.816   1.098   0.014  1.00
 0.00   C
ATOM  6  C4' G   A   4   2.324   1.432  -0.121  1.00
 0.00   C
ATOM  7  O4' G   A   4   1.623   0.448  -0.862  1.00
 0.00   O
ATOM  8  C3' G   A   4   1.584   1.482   1.211  1.00
 0.00   C

ATOM 33  H21 G   A   4  -5.974   0.099  -0.815  1.00
 0.00   H
ATOM 34  H22 G   A   4  -4.841   1.428  -0.876  1.00
 0.00   H



Of course it would be best if pdb2gmx worked as it is if I
just have a single nucleotide, and not a chain?


Here, I am wondering if the above problem is occurring because
pdb2gmx is not being able to deal with an isolated nucleotide
(while it might be able to deal with an polymer)

Maria


On Sat, Mar 19, 2011 at 5:44 AM, Mark Abraham
mailto:mark.abra...@anu.edu.au>> wrote:



On 19/03/11, *maria goranovic * mailto:mariagorano...@gmail.com>> wrote:

Dear All

I am trying to generate a topology for guanosine
monophosphate: i.e. an RNA base with a phosphate at the
5' Carbon. I tried to read in a pdb 

Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx

[Daniel Adriano Silva M]

Hi,

Is this your input? (a GRO file?). Can you paste the PDB corresponding to
the RNA nucleotide that you are interested on? I think the file may be small
enough to paste it here so someone can try to reproduce what is happening to
you.

Daniel

2011/3/22 maria goranovic 

> Sorry for the incomplete reply.
> version 4.5.3,
> command: pdb2gmx -f guan.pdb -ignh
> I tried using -ter, but that did not help.
>
>
> input coordinate file, pulled out from an RNA molecule.
>
> Gromacs Runs On Most of All Computer Systems
>34
> 1GP1   5.549   4.916   5.071
> 1G  OP12   5.642   5.026   5.105
> 1G  OP23   5.537   4.800   5.162
> 1G  O5'4   5.401   4.979   5.051
> 1G  C5'5   5.382   5.110   5.001
> 1G  C4'6   5.232   5.143   4.988
> 1G  O4'7   5.162   5.045   4.914
> 1G  C3'8   5.158   5.148   5.121
> 1G  O3'9   5.187   5.267   5.193
> 1G  C2'   10   5.014   5.141   5.072
> 1G  O2'   11   4.964   5.270   5.040
> 1G  C1'   12   5.024   5.060   4.943
> 1G   N9   13   4.955   4.930   4.956
> 1G   C8   14   5.008   4.805   4.976
> 1G   N7   15   4.919   4.709   4.980
> 1G   C5   16   4.798   4.775   4.962
> 1G   C6   17   4.665   4.723   4.955
> 1G   O6   18   4.630   4.606   4.960
> 1G   N1   19   4.570   4.824   4.941
> 1G   C2   20   4.600   4.959   4.932
> 1G   N2   21   4.498   5.044   4.920
> 1G   N3   22   4.725   5.007   4.935
> 1G   C4   23   4.819   4.910   4.950
> 1G  H5'   24   5.429   5.120   4.904
> 1G H5''   25   5.427   5.182   5.070
> 1G  H4'   26   5.222   5.240   4.938
> 1G  H3'   27   5.182   5.059   5.179
> 1G  H2'   28   4.950   5.094   5.146
> 1G HO2'   29   4.870   5.261   5.021
> 1G  H1'   30   4.978   5.115   4.861
> 1G   H8   31   5.113   4.787   4.986
> 1G   H1   32   4.474   4.794   4.936
> 1G  H21   33   4.403   5.010   4.918
> 1G  H22   34   4.516   5.143   4.912
>   10.0  10.0  10.0
>
>
> On Tue, Mar 22, 2011 at 2:09 PM, Mark Abraham wrote:
>
>>  On 22/03/2011 8:15 PM, maria goranovic wrote:
>>
>> is this a bug of some kind then? someone ? anyone?
>>
>>
>> It's still hard to say. I asked you for your GROMACS version and input
>> coordinate file, and you didn't give us either (in full). While you're
>> there, what pdb2gmx command did you use?
>>
>> Mark
>>
>>
>>  just bumping,
>>
>>  maria
>>
>> On Mon, Mar 21, 2011 at 10:17 AM, maria goranovic <
>> mariagorano...@gmail.com> wrote:
>>
>>> Here are the contents of my input coordinate file.
>>>
>>>  CRYST10.0000.0000.000  90.00  90.00  90.00 P 1   1
>>> ATOM  1  P   G   A   4   5.488  -0.842   0.708  1.00  0.00
>>> P
>>> ATOM  2  OP1 G   A   4   6.418   0.258   1.047  1.00  0.00
>>> O
>>> ATOM  3  OP2 G   A   4   5.367  -1.998   1.624  1.00  0.00
>>> O
>>> ATOM  4  O5' G   A   4   4.010  -0.213   0.513  1.00  0.00
>>> O
>>> ATOM  5  C5' G   A   4   3.816   1.098   0.014  1.00  0.00
>>> C
>>> ATOM  6  C4' G   A   4   2.324   1.432  -0.121  1.00  0.00
>>> C
>>> ATOM  7  O4' G   A   4   1.623   0.448  -0.862  1.00  0.00
>>> O
>>> ATOM  8  C3' G   A   4   1.584   1.482   1.211  1.00  0.00
>>> C
>>> 
>>> ATOM 33  H21 G   A   4  -5.974   0.099  -0.815  1.00  0.00
>>> H
>>> ATOM 34  H22 G   A   4  -4.841   1.428  -0.876  1.00  0.00
>>> H
>>>
>>>
>>>Of course it would be best if pdb2gmx worked as it is if I just have
>>> a single nucleotide, and not a chain?
>>>
>>>
>>>  Here, I am wondering if the above problem is occurring because pdb2gmx
>>> is not being able to deal with an isolated nucleotide (while it might be
>>> able to deal with an polymer)
>>>
>>>  Maria
>>>
>>>
>>>  On Sat, Mar 19, 2011 at 5:44 AM, Mark Abraham 
>>> wrote:
>>>


 On 19/03/11, *maria goranovic *  wrote:

 Dear All

  I am trying to generate a topology for guanosine monophosphate: i.e.
 an RNA base with a phosphate at the 5' Carbon. I tried to read in a pdb 
 file
 containing all atoms, and used pdb2gmx with CHARMM. However, the output
 coordinate file has no phosphate group on it. Why does the phosphate
 disappear, and why does pdb2gmx not even give me a warning?


  That does sound suspicious, but it's hard to say what went wrong. What
 GROMACS version was it, and what were the contents of your input coordinate
 file?


  Assuming that a molecule like GMP does not have a topology, I am
 guessing I might have to make a new residue within CHARMM. that should not
 be too much work because there is no new angle/dihedral/bond/atom type to 
 be
 be added. Can someone please help me with a simple workflow so I do not 
>

[gmx-users] changing charged groups in CHARMM RNA

[maria goranovic]

Dear List

I was looking at the charged groups in a charmm nucleotide, and could see
several groups containing 4 to 14 atoms with integer charges. However, the
default topology does not have these charged groups. each atom is given a
charged group in the default topology. Can we foresee any problems in
replacing the default charged groups generated by pdb2gmx by custom-made
charged groups of integer values ? Along the same lines, will this lead to a
significant increase in performance, besides the advantage of
transferability ?

Thanking you in advance

Maria



-- 
Maria G.
Technical University of Denmark
Copenhagen
-- 
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.
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Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx

[maria goranovic]

Sorry for the incomplete reply.
version 4.5.3,
command: pdb2gmx -f guan.pdb -ignh
I tried using -ter, but that did not help.


input coordinate file, pulled out from an RNA molecule.

Gromacs Runs On Most of All Computer Systems
   34
1GP1   5.549   4.916   5.071
1G  OP12   5.642   5.026   5.105
1G  OP23   5.537   4.800   5.162
1G  O5'4   5.401   4.979   5.051
1G  C5'5   5.382   5.110   5.001
1G  C4'6   5.232   5.143   4.988
1G  O4'7   5.162   5.045   4.914
1G  C3'8   5.158   5.148   5.121
1G  O3'9   5.187   5.267   5.193
1G  C2'   10   5.014   5.141   5.072
1G  O2'   11   4.964   5.270   5.040
1G  C1'   12   5.024   5.060   4.943
1G   N9   13   4.955   4.930   4.956
1G   C8   14   5.008   4.805   4.976
1G   N7   15   4.919   4.709   4.980
1G   C5   16   4.798   4.775   4.962
1G   C6   17   4.665   4.723   4.955
1G   O6   18   4.630   4.606   4.960
1G   N1   19   4.570   4.824   4.941
1G   C2   20   4.600   4.959   4.932
1G   N2   21   4.498   5.044   4.920
1G   N3   22   4.725   5.007   4.935
1G   C4   23   4.819   4.910   4.950
1G  H5'   24   5.429   5.120   4.904
1G H5''   25   5.427   5.182   5.070
1G  H4'   26   5.222   5.240   4.938
1G  H3'   27   5.182   5.059   5.179
1G  H2'   28   4.950   5.094   5.146
1G HO2'   29   4.870   5.261   5.021
1G  H1'   30   4.978   5.115   4.861
1G   H8   31   5.113   4.787   4.986
1G   H1   32   4.474   4.794   4.936
1G  H21   33   4.403   5.010   4.918
1G  H22   34   4.516   5.143   4.912
  10.0  10.0  10.0


On Tue, Mar 22, 2011 at 2:09 PM, Mark Abraham wrote:

>  On 22/03/2011 8:15 PM, maria goranovic wrote:
>
> is this a bug of some kind then? someone ? anyone?
>
>
> It's still hard to say. I asked you for your GROMACS version and input
> coordinate file, and you didn't give us either (in full). While you're
> there, what pdb2gmx command did you use?
>
> Mark
>
>
>  just bumping,
>
>  maria
>
> On Mon, Mar 21, 2011 at 10:17 AM, maria goranovic <
> mariagorano...@gmail.com> wrote:
>
>> Here are the contents of my input coordinate file.
>>
>>  CRYST10.0000.0000.000  90.00  90.00  90.00 P 1   1
>> ATOM  1  P   G   A   4   5.488  -0.842   0.708  1.00  0.00
>>   P
>> ATOM  2  OP1 G   A   4   6.418   0.258   1.047  1.00  0.00
>>   O
>> ATOM  3  OP2 G   A   4   5.367  -1.998   1.624  1.00  0.00
>>   O
>> ATOM  4  O5' G   A   4   4.010  -0.213   0.513  1.00  0.00
>>   O
>> ATOM  5  C5' G   A   4   3.816   1.098   0.014  1.00  0.00
>>   C
>> ATOM  6  C4' G   A   4   2.324   1.432  -0.121  1.00  0.00
>>   C
>> ATOM  7  O4' G   A   4   1.623   0.448  -0.862  1.00  0.00
>>   O
>> ATOM  8  C3' G   A   4   1.584   1.482   1.211  1.00  0.00
>>   C
>> 
>> ATOM 33  H21 G   A   4  -5.974   0.099  -0.815  1.00  0.00
>>   H
>> ATOM 34  H22 G   A   4  -4.841   1.428  -0.876  1.00  0.00
>>   H
>>
>>
>>Of course it would be best if pdb2gmx worked as it is if I just have a
>> single nucleotide, and not a chain?
>>
>>
>>  Here, I am wondering if the above problem is occurring because pdb2gmx
>> is not being able to deal with an isolated nucleotide (while it might be
>> able to deal with an polymer)
>>
>>  Maria
>>
>>
>>  On Sat, Mar 19, 2011 at 5:44 AM, Mark Abraham 
>> wrote:
>>
>>>
>>>
>>> On 19/03/11, *maria goranovic *  wrote:
>>>
>>> Dear All
>>>
>>>  I am trying to generate a topology for guanosine monophosphate: i.e. an
>>> RNA base with a phosphate at the 5' Carbon. I tried to read in a pdb file
>>> containing all atoms, and used pdb2gmx with CHARMM. However, the output
>>> coordinate file has no phosphate group on it. Why does the phosphate
>>> disappear, and why does pdb2gmx not even give me a warning?
>>>
>>>
>>>  That does sound suspicious, but it's hard to say what went wrong. What
>>> GROMACS version was it, and what were the contents of your input coordinate
>>> file?
>>>
>>>
>>>  Assuming that a molecule like GMP does not have a topology, I am
>>> guessing I might have to make a new residue within CHARMM. that should not
>>> be too much work because there is no new angle/dihedral/bond/atom type to be
>>> be added. Can someone please help me with a simple workflow so I do not miss
>>> something important?
>>>
>>>
>>>  The procedure is outlined here:
>>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_FieldYour
>>>  case should be a reasonably straightforward exercise in assigning
>>> sensible atom types from the pre-existing options.
>>>
>>>
>>>
>>>
>>> Mark
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromac

Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx

[Mark Abraham]

On 22/03/2011 8:15 PM, maria goranovic wrote:

is this a bug of some kind then? someone ? anyone?


It's still hard to say. I asked you for your GROMACS version and input 
coordinate file, and you didn't give us either (in full). While you're 
there, what pdb2gmx command did you use?


Mark


just bumping,

maria

On Mon, Mar 21, 2011 at 10:17 AM, maria goranovic 
mailto:mariagorano...@gmail.com>> wrote:


Here are the contents of my input coordinate file.

CRYST10.0000.0000.000  90.00  90.00  90.00 P 1   1
ATOM  1  P   G   A   4   5.488  -0.842   0.708  1.00  0.00
  P
ATOM  2  OP1 G   A   4   6.418   0.258   1.047  1.00  0.00
  O
ATOM  3  OP2 G   A   4   5.367  -1.998   1.624  1.00  0.00
  O
ATOM  4  O5' G   A   4   4.010  -0.213   0.513  1.00  0.00
  O
ATOM  5  C5' G   A   4   3.816   1.098   0.014  1.00  0.00
  C
ATOM  6  C4' G   A   4   2.324   1.432  -0.121  1.00  0.00
  C
ATOM  7  O4' G   A   4   1.623   0.448  -0.862  1.00  0.00
  O
ATOM  8  C3' G   A   4   1.584   1.482   1.211  1.00  0.00
  C

ATOM 33  H21 G   A   4  -5.974   0.099  -0.815  1.00  0.00
  H
ATOM 34  H22 G   A   4  -4.841   1.428  -0.876  1.00  0.00
  H



Of course it would be best if pdb2gmx worked as it is if I just
have a single nucleotide, and not a chain?


Here, I am wondering if the above problem is occurring because
pdb2gmx is not being able to deal with an isolated nucleotide
(while it might be able to deal with an polymer)

Maria


On Sat, Mar 19, 2011 at 5:44 AM, Mark Abraham
mailto:mark.abra...@anu.edu.au>> wrote:



On 19/03/11, *maria goranovic * mailto:mariagorano...@gmail.com>> wrote:

Dear All

I am trying to generate a topology for guanosine
monophosphate: i.e. an RNA base with a phosphate at the 5'
Carbon. I tried to read in a pdb file containing all atoms,
and used pdb2gmx with CHARMM. However, the output coordinate
file has no phosphate group on it. Why does the phosphate
disappear, and why does pdb2gmx not even give me a warning?


That does sound suspicious, but it's hard to say what went
wrong. What GROMACS version was it, and what were the contents
of your input coordinate file?



Assuming that a molecule like GMP does not have a topology, I
am guessing I might have to make a new residue within CHARMM.
that should not be too much work because there is no new
angle/dihedral/bond/atom type to be be added. Can someone
please help me with a simple workflow so I do not miss
something important?


The procedure is outlined here:

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
Your case should be a reasonably straightforward exercise in
assigning sensible atom types from the pre-existing options.






Mark
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-- 
Maria G.

Technical University of Denmark
Copenhagen




--
Maria G.
Technical University of Denmark
Copenhagen


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Re: [gmx-users] Annealing of shell polarizable water model

[Justin A. Lemkul]

Ivan Gladich wrote:

Dear David
Dear all
I did the serial run with the same topology and grompp: even if the 
simulation time is still short (due by the serial run), the temperature 
profiles are the same (see attached file).


As further check, I removed the annealing and the temperature rises to 
160 K after ~0.5ps without problem.
So I do not think that it is a problem of the shell polarizability with 
the running in parallel.

Could be a problem of the shell polarizability with annealing?



You could test that relatively easily with a simple box of water.  The result 
would be useful.


Other than that, maybe the thermostat itself is causing the problem?  I always 
do annealing with a weak coupling method, not Nose-Hoover.  I've had stability 
problems with unequilibrated systems with N-H.  In principle, it shouldn't 
matter, but setting tcoupl to Berendsen and/or V-rescale would be another very 
useful diagnostic.


-Justin


Thanks again
Ivan


On 03/22/2011 10:45 AM, Ivan Gladich wrote:

Yes, I am running in parallel...
Now I will try to run in serial to see if the problem persist
Thanks
Ivan

On 03/22/2011 10:00 AM, David van der Spoel wrote:

On 2011-03-22 10.37, Ivan Gladich wrote:

Dear all,
I would like to heat, very slowly, a ice box of 1796 SWM4-NDP water.
This kind of water has 4 sites plus a shell and I am using a small time
step (0.1 fms) to heat my ice box from 0 K top 160K in 1 ns.
To do that I used a linear annealing from 0 to 160 K.
Are you running in parallel? Unfortunately polarizable MD is broken 
on more than 1 core. There is a redmine issue for this, and it will 
be fixed soon.


The simulation runs without problem but I cannot reach the desire
temperature.
In other words, if I look my md.log file I can see the ref_t that 
linear

increase from 0 to 160 K in 1 ns but the system temperature seems to do
not follow the thermostate temperature.
If I plot the temperature obtained from g_energy, the temperature of 
the

system remains constant at ~36 K.
I attach also my temperature profile up to 600ps. Due to the small time
step the simulation takes a bit of time but it is clear that the
temperature remain constant


I have tried to find in the mail list some similar problem without
success...
Here below I report my grompp. Maybe I missed something.
Thank in advance for any suggestions.
Ivan
#3
; VARIOUS PREPROCESSING OPTIONS
title = Ice SWM4-NDP
cpp = /usr/bin/cpp
include =
define =

; RUN CONTROL PARAMETERS
integrator = md
dt = 0.0001
nsteps = 1400

; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps =

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 0
nstvout = 0
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1
; Output frequency for energies to log file and energy file
nstlog = 5000
nstenergy = 1000
; Output frequency and precision for xtc file
nstxtcout = 1
xtc-precision = 1000

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 5
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 1.1
;domain-decomposition =

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.1
; Method for doing Van der Waals
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 1.1

; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres

; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
optimize_fft = no

;OPTIONS FOR ANNELING
annealing = single
annealing_npoints = 2
annealing_time = 0 1000
annealing_temp = 0 160

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = Nose-hoover
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 160.00
; Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 2.0
compressibility = 4.5E-5
ref_p = 0.0
; Random seed for Andersen thermostat
andersen_seed = 815131

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 0
gen_seed = 1993

;CONSTRAINTS
constraints = hbonds
constraint_algorithm = LINCS















--


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

=

Re: [gmx-users] Annealing of shell polarizable water model

[Ivan Gladich]

Dear David
Dear all
I did the serial run with the same topology and grompp: even if the 
simulation time is still short (due by the serial run), the temperature 
profiles are the same (see attached file).


As further check, I removed the annealing and the temperature rises to 
160 K after ~0.5ps without problem.
So I do not think that it is a problem of the shell polarizability with 
the running in parallel.

Could be a problem of the shell polarizability with annealing?

Thanks again
Ivan


On 03/22/2011 10:45 AM, Ivan Gladich wrote:

Yes, I am running in parallel...
Now I will try to run in serial to see if the problem persist
Thanks
Ivan

On 03/22/2011 10:00 AM, David van der Spoel wrote:

On 2011-03-22 10.37, Ivan Gladich wrote:

Dear all,
I would like to heat, very slowly, a ice box of 1796 SWM4-NDP water.
This kind of water has 4 sites plus a shell and I am using a small time
step (0.1 fms) to heat my ice box from 0 K top 160K in 1 ns.
To do that I used a linear annealing from 0 to 160 K.
Are you running in parallel? Unfortunately polarizable MD is broken 
on more than 1 core. There is a redmine issue for this, and it will 
be fixed soon.


The simulation runs without problem but I cannot reach the desire
temperature.
In other words, if I look my md.log file I can see the ref_t that 
linear

increase from 0 to 160 K in 1 ns but the system temperature seems to do
not follow the thermostate temperature.
If I plot the temperature obtained from g_energy, the temperature of 
the

system remains constant at ~36 K.
I attach also my temperature profile up to 600ps. Due to the small time
step the simulation takes a bit of time but it is clear that the
temperature remain constant


I have tried to find in the mail list some similar problem without
success...
Here below I report my grompp. Maybe I missed something.
Thank in advance for any suggestions.
Ivan
#3
; VARIOUS PREPROCESSING OPTIONS
title = Ice SWM4-NDP
cpp = /usr/bin/cpp
include =
define =

; RUN CONTROL PARAMETERS
integrator = md
dt = 0.0001
nsteps = 1400

; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps =

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 0
nstvout = 0
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1
; Output frequency for energies to log file and energy file
nstlog = 5000
nstenergy = 1000
; Output frequency and precision for xtc file
nstxtcout = 1
xtc-precision = 1000

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 5
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 1.1
;domain-decomposition =

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.1
; Method for doing Van der Waals
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 1.1

; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres

; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
optimize_fft = no

;OPTIONS FOR ANNELING
annealing = single
annealing_npoints = 2
annealing_time = 0 1000
annealing_temp = 0 160

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = Nose-hoover
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 160.00
; Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 2.0
compressibility = 4.5E-5
ref_p = 0.0
; Random seed for Andersen thermostat
andersen_seed = 815131

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 0
gen_seed = 1993

;CONSTRAINTS
constraints = hbonds
constraint_algorithm = LINCS










--
--
Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic

Tel: +420775504164
e-mail: ivan.glad...@uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
-

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Re: [gmx-users] mdrun the pr.trr

[Erik Marklund]

zen...@graduate.org skrev 2011-03-22 10.22:


when i type this order :szrun 2 2 mdrun_mpi -nice 0 -v -s pr.tpr -o 
pr.trr -c b4md.pdb -g pr.log -e pr.edr &
the process can not run,and there is a problem that t = 0.000 
 ps: Water molecule starting at atom 90777 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates. 

i have made the dt =0.001and nsteps=1 in the em.mdp ,but the order 
(szrun 2 2 mdrun_mpi -nice 0 -v -s pr.tpr -o pr.trr -c b4md.pdb -g 
pr.log -e pr.edr & ) still can not run .how to slove this problem ?
Changing timestep won't help. Your simulation crashes at t=0.0, which 
means your system isn't properly equillibrated, or there are errors in 
the topology.


--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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[gmx-users] New version 4.5.4 of the Gromacs manual

[Rossen Apostolov]

Dear all,

The updated version 4.5.4 of the Gromacs manual is available at 
ftp://ftp.gromacs.org/pub/manual/manual-4.5.4.pdf.


Happy simulating!
Rossen
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[gmx-users] mdrun the pr.trr

[zengyq]

when i type this order :szrun 2 2 mdrun_mpi -nice 0 -v -s pr.tpr -o pr.trr -c 
b4md.pdb -g pr.log -e pr.edr & 
the process can not run,and there is a problem that t = 0.000  ps: Water 
molecule starting at atom 90777 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous 
and current coordinates. 
i have made the dt =0.001and nsteps=1 in the em.mdp ,but the order (szrun 2 
2 mdrun_mpi -nice 0 -v -s pr.tpr -o pr.trr -c b4md.pdb -g pr.log -e pr.edr & ) 
still can not run .how to slove this problem ?
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Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx

[maria goranovic]

is this a bug of some kind then? someone ? anyone?

just bumping,

maria

On Mon, Mar 21, 2011 at 10:17 AM, maria goranovic
wrote:

> Here are the contents of my input coordinate file.
>
> CRYST10.0000.0000.000  90.00  90.00  90.00 P 1   1
> ATOM  1  P   G   A   4   5.488  -0.842   0.708  1.00  0.00
>   P
> ATOM  2  OP1 G   A   4   6.418   0.258   1.047  1.00  0.00
>   O
> ATOM  3  OP2 G   A   4   5.367  -1.998   1.624  1.00  0.00
>   O
> ATOM  4  O5' G   A   4   4.010  -0.213   0.513  1.00  0.00
>   O
> ATOM  5  C5' G   A   4   3.816   1.098   0.014  1.00  0.00
>   C
> ATOM  6  C4' G   A   4   2.324   1.432  -0.121  1.00  0.00
>   C
> ATOM  7  O4' G   A   4   1.623   0.448  -0.862  1.00  0.00
>   O
> ATOM  8  C3' G   A   4   1.584   1.482   1.211  1.00  0.00
>   C
> 
> ATOM 33  H21 G   A   4  -5.974   0.099  -0.815  1.00  0.00
>   H
> ATOM 34  H22 G   A   4  -4.841   1.428  -0.876  1.00  0.00
>   H
>
>
> Of course it would be best if pdb2gmx worked as it is if I just have a
> single nucleotide, and not a chain?
>
>
> Here, I am wondering if the above problem is occurring because pdb2gmx is
> not being able to deal with an isolated nucleotide (while it might be able
> to deal with an polymer)
>
> Maria
>
>
> On Sat, Mar 19, 2011 at 5:44 AM, Mark Abraham wrote:
>
>>
>>
>> On 19/03/11, *maria goranovic *  wrote:
>>
>> Dear All
>>
>> I am trying to generate a topology for guanosine monophosphate: i.e. an
>> RNA base with a phosphate at the 5' Carbon. I tried to read in a pdb file
>> containing all atoms, and used pdb2gmx with CHARMM. However, the output
>> coordinate file has no phosphate group on it. Why does the phosphate
>> disappear, and why does pdb2gmx not even give me a warning?
>>
>>
>> That does sound suspicious, but it's hard to say what went wrong. What
>> GROMACS version was it, and what were the contents of your input coordinate
>> file?
>>
>>
>> Assuming that a molecule like GMP does not have a topology, I am guessing
>> I might have to make a new residue within CHARMM. that should not be too
>> much work because there is no new angle/dihedral/bond/atom type to be be
>> added. Can someone please help me with a simple workflow so I do not miss
>> something important?
>>
>>
>> The procedure is outlined here:
>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_FieldYour
>>  case should be a reasonably straightforward exercise in assigning
>> sensible atom types from the pre-existing options.
>>
>>
>>
>>
>> Mark
>> --
>> 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
>>
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>



-- 
Maria G.
Technical University of Denmark
Copenhagen
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Re: [gmx-users] Annealing of shell polarizable water model

[Ivan Gladich]

Yes, I am running in parallel...
Now I will try to run in serial to see if the problem persist
Thanks
Ivan

On 03/22/2011 10:00 AM, David van der Spoel wrote:

On 2011-03-22 10.37, Ivan Gladich wrote:

Dear all,
I would like to heat, very slowly, a ice box of 1796 SWM4-NDP water.
This kind of water has 4 sites plus a shell and I am using a small time
step (0.1 fms) to heat my ice box from 0 K top 160K in 1 ns.
To do that I used a linear annealing from 0 to 160 K.
Are you running in parallel? Unfortunately polarizable MD is broken on 
more than 1 core. There is a redmine issue for this, and it will be 
fixed soon.


The simulation runs without problem but I cannot reach the desire
temperature.
In other words, if I look my md.log file I can see the ref_t that linear
increase from 0 to 160 K in 1 ns but the system temperature seems to do
not follow the thermostate temperature.
If I plot the temperature obtained from g_energy, the temperature of the
system remains constant at ~36 K.
I attach also my temperature profile up to 600ps. Due to the small time
step the simulation takes a bit of time but it is clear that the
temperature remain constant


I have tried to find in the mail list some similar problem without
success...
Here below I report my grompp. Maybe I missed something.
Thank in advance for any suggestions.
Ivan
#3
; VARIOUS PREPROCESSING OPTIONS
title = Ice SWM4-NDP
cpp = /usr/bin/cpp
include =
define =

; RUN CONTROL PARAMETERS
integrator = md
dt = 0.0001
nsteps = 1400

; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps =

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 0
nstvout = 0
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1
; Output frequency for energies to log file and energy file
nstlog = 5000
nstenergy = 1000
; Output frequency and precision for xtc file
nstxtcout = 1
xtc-precision = 1000

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 5
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 1.1
;domain-decomposition =

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.1
; Method for doing Van der Waals
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 1.1

; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres

; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
optimize_fft = no

;OPTIONS FOR ANNELING
annealing = single
annealing_npoints = 2
annealing_time = 0 1000
annealing_temp = 0 160

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = Nose-hoover
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 160.00
; Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 2.0
compressibility = 4.5E-5
ref_p = 0.0
; Random seed for Andersen thermostat
andersen_seed = 815131

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 0
gen_seed = 1993

;CONSTRAINTS
constraints = hbonds
constraint_algorithm = LINCS







--
--
Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic

Tel: +420775504164
e-mail: ivan.glad...@uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
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Re: [gmx-users] Annealing of shell polarizable water model

[David van der Spoel]

On 2011-03-22 10.37, Ivan Gladich wrote:

Dear all,
I would like to heat, very slowly, a ice box of 1796 SWM4-NDP water.
This kind of water has 4 sites plus a shell and I am using a small time
step (0.1 fms) to heat my ice box from 0 K top 160K in 1 ns.
To do that I used a linear annealing from 0 to 160 K.
Are you running in parallel? Unfortunately polarizable MD is broken on 
more than 1 core. There is a redmine issue for this, and it will be 
fixed soon.


The simulation runs without problem but I cannot reach the desire
temperature.
In other words, if I look my md.log file I can see the ref_t that linear
increase from 0 to 160 K in 1 ns but the system temperature seems to do
not follow the thermostate temperature.
If I plot the temperature obtained from g_energy, the temperature of the
system remains constant at ~36 K.
I attach also my temperature profile up to 600ps. Due to the small time
step the simulation takes a bit of time but it is clear that the
temperature remain constant


I have tried to find in the mail list some similar problem without
success...
Here below I report my grompp. Maybe I missed something.
Thank in advance for any suggestions.
Ivan
#3
; VARIOUS PREPROCESSING OPTIONS
title = Ice SWM4-NDP
cpp = /usr/bin/cpp
include =
define =

; RUN CONTROL PARAMETERS
integrator = md
dt = 0.0001
nsteps = 1400

; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps =

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 0
nstvout = 0
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1
; Output frequency for energies to log file and energy file
nstlog = 5000
nstenergy = 1000
; Output frequency and precision for xtc file
nstxtcout = 1
xtc-precision = 1000

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 5
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 1.1
;domain-decomposition =

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.1
; Method for doing Van der Waals
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 1.1

; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres

; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
optimize_fft = no

;OPTIONS FOR ANNELING
annealing = single
annealing_npoints = 2
annealing_time = 0 1000
annealing_temp = 0 160

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = Nose-hoover
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 160.00
; Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 2.0
compressibility = 4.5E-5
ref_p = 0.0
; Random seed for Andersen thermostat
andersen_seed = 815131

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 0
gen_seed = 1993

;CONSTRAINTS
constraints = hbonds
constraint_algorithm = LINCS




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] Annealing of shell polarizable water model

[Ivan Gladich]

Dear all,
 I would like to heat, very slowly, a ice box of 1796 SWM4-NDP 
water.
This kind of water has 4 sites plus a shell and I am using a small time 
step (0.1 fms) to heat my ice box from 0 K top 160K in 1 ns.

To do that  I used a linear annealing from 0 to 160 K.

The simulation runs without problem but I cannot reach the desire 
temperature.
In other words, if I look my md.log file I can see the ref_t that linear 
increase from 0 to 160 K in 1 ns but the system temperature seems to do 
not follow the thermostate temperature.
If I plot the temperature obtained from g_energy, the temperature of the 
system remains constant at ~36 K.
I attach also my temperature profile up to 600ps. Due to the small time 
step the simulation takes a bit of time but it is clear that the 
temperature remain constant



I have tried to find in the mail list some similar problem without 
success...

Here below I report my grompp. Maybe I missed something.
Thank in advance for any suggestions.
Ivan
#3
; VARIOUS PREPROCESSING OPTIONS
title= Ice SWM4-NDP
cpp  = /usr/bin/cpp
include  =
define   =

; RUN CONTROL PARAMETERS
integrator   =  md
dt   = 0.0001
nsteps   = 1400

; mode for center of mass motion removal
comm-mode= Linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps=

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 0
nstvout  = 0
nstfout  = 0
; Checkpointing helps you continue after crashes
nstcheckpoint= 1
; Output frequency for energies to log file and energy file
nstlog   = 5000
nstenergy= 1000
; Output frequency and precision for xtc file
nstxtcout= 1
xtc-precision= 1000

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 5
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc  = xyz
; nblist cut-off
rlist= 1.1
;domain-decomposition =

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.1
; Method for doing Van der Waals
vdw-type = Cut-off
rvdw-switch  = 0
rvdw = 1.1

; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres

; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
optimize_fft = no

;OPTIONS FOR ANNELING
annealing = single
annealing_npoints = 2
annealing_time = 0 1000
annealing_temp = 0 160

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl   = Nose-hoover
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t= 160.00
; Pressure coupling
Pcoupl   = Parrinello-Rahman
Pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p=  2.0
compressibility =  4.5E-5
ref_p =  0.0
; Random seed for Andersen thermostat
andersen_seed= 815131

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel  = yes
gen_temp = 0
gen_seed = 1993

;CONSTRAINTS
constraints  = hbonds
constraint_algorithm = LINCS

--
--
Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic

Tel: +420775504164
e-mail: ivan.glad...@uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
-

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Re: [gmx-users] checking gen_seed

[Kwee Hong]

Alright, thx Mark.




From: Mark Abraham 
To: Discussion list for GROMACS users 
Sent: Tuesday, March 22, 2011 15:44:51
Subject: Re: [gmx-users] checking gen_seed

On 22/03/2011 6:28 PM, Kwee Hong wrote: 
Hi all,
>
>
>I've accidentally deleted my mdp and .tpr  file.. :(
>Is there a way I could check the gen_seed of my simulation   from the 
>.tpr or the output of my simulation as I need the   info to simulate 
>the 
>same system at another temerature?
I don't think gen_seed is saved in the .tpr, but you can see with gmxdump.

At a different temperature it generates different velocities anyway, so I 
don't think there is value in controlling this variable.

More importantly, if you're simulating long enough to approach convergence, 
the value of gen_seed doesn't matter because the simulation has converged. 
If you're not simulating that long, then it also doesn't matter, in that 
your results won't be worth much even if you used the same gen_seed at the 
same temperature...

Mark


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Re: [gmx-users] checking gen_seed

[Mark Abraham]

On 22/03/2011 6:28 PM, Kwee Hong wrote:

Hi all,

I've accidentally deleted my mdp and .tpr  file.. :(
Is there a way I could check the gen_seed of my simulation from the 
.tpr or the output of my simulation as I need the info to simulate the 
same system at another temerature?


I don't think gen_seed is saved in the .tpr, but you can see with gmxdump.

At a different temperature it generates different velocities anyway, so 
I don't think there is value in controlling this variable.


More importantly, if you're simulating long enough to approach 
convergence, the value of gen_seed doesn't matter because the simulation 
has converged. If you're not simulating that long, then it also doesn't 
matter, in that your results won't be worth much even if you used the 
same gen_seed at the same temperature...


Mark
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[gmx-users] checking gen_seed

[Kwee Hong]

Hi all,

I've accidentally deleted my mdp and .tpr  file.. :(
Is there a way I could check the gen_seed of my simulation from the .tpr or the 
output of my simulation as I need the info to simulate the same system at 
another temerature?


Thanks.

Joyce

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