Re: [gmx-users] lipid-SPC/SPCE interactions in lipid.itp (Tieleman website)

[Facundo Ciocco Aloia]

thanks Justin,

best regards,

2013/3/5 Justin Lemkul 

>
>
> On 3/5/13 7:48 PM, fciocco wrote:
>
>> Hi,
>>
>> I have a quick question:
>>
>> the ;; lipid-SPC/SPCE interactions section :
>> LOOW1 2.50200e-03  2.06700e-06
>>LOMOW1 2.50200e-03  2.06700e-06
>>LNLOW1 2.98000e-03  3.25900e-06
>> LCOW1 3.59800e-03  6.04400e-06
>>LH1OW1 3.26800e-03  5.71200e-06
>>LH2OW1 4.30700e-03  8.17000e-06
>> LPOW1 4.92600e-03  8.21000e-06
>>LOSOW1 2.60500e-03  2.24100e-06
>>LP2OW1 3.94400e-03  7.80300e-06
>>LP3OW1 4.82100e-03  9.53900e-06
>>LC3OW1 4.97800e-03  9.85000e-06
>>LC2OW1 3.96900e-03  6.93800e-06
>>
>>   in the [ nonbond_params ] section in lipid.itp file downloaded from
>> Tieleman's site should be include in the ffnonbonded.itp file?
>>
>> the KALP-DPPC tutorial says: In the [ nonbond_params ] section, you will
>> find the line ";; parameters for lipid-GROMOS interactions." Delete this
>> line and all of the subsequent lines in this section; but I'm not 100%
>> sure
>> if I have to delete the lipid-SPC/SPCE interactions lines.
>>
>>
> The C6/C12 parameters for the OW atom type are slightly different in 53A6
> than they were in Gromos87 (looks like mostly rounding differences in the
> nonbonded parameter files).  The parameters listed in lipid.itp are based
> on Gromos87, so if you're using 53A6, then do as the tutorial says and
> delete the lines.  The necessary interactions will simply be calculated
> according to normal combination rules.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
>
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Re: [gmx-users] lipid-SPC/SPCE interactions in lipid.itp (Tieleman website)

[Justin Lemkul]

On 3/5/13 7:48 PM, fciocco wrote:

Hi,

I have a quick question:

the ;; lipid-SPC/SPCE interactions section :
LOOW1 2.50200e-03  2.06700e-06
   LOMOW1 2.50200e-03  2.06700e-06
   LNLOW1 2.98000e-03  3.25900e-06
LCOW1 3.59800e-03  6.04400e-06
   LH1OW1 3.26800e-03  5.71200e-06
   LH2OW1 4.30700e-03  8.17000e-06
LPOW1 4.92600e-03  8.21000e-06
   LOSOW1 2.60500e-03  2.24100e-06
   LP2OW1 3.94400e-03  7.80300e-06
   LP3OW1 4.82100e-03  9.53900e-06
   LC3OW1 4.97800e-03  9.85000e-06
   LC2OW1 3.96900e-03  6.93800e-06

  in the [ nonbond_params ] section in lipid.itp file downloaded from
Tieleman's site should be include in the ffnonbonded.itp file?

the KALP-DPPC tutorial says: In the [ nonbond_params ] section, you will
find the line ";; parameters for lipid-GROMOS interactions." Delete this
line and all of the subsequent lines in this section; but I'm not 100% sure
if I have to delete the lipid-SPC/SPCE interactions lines.



The C6/C12 parameters for the OW atom type are slightly different in 53A6 than 
they were in Gromos87 (looks like mostly rounding differences in the nonbonded 
parameter files).  The parameters listed in lipid.itp are based on Gromos87, so 
if you're using 53A6, then do as the tutorial says and delete the lines.  The 
necessary interactions will simply be calculated according to normal combination 
rules.


-Justin

--


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


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[gmx-users] lipid-SPC/SPCE interactions in lipid.itp (Tieleman website)

[fciocco]

Hi, 

I have a quick question: 

the ;; lipid-SPC/SPCE interactions section : 
   LOOW1 2.50200e-03  2.06700e-06
  LOMOW1 2.50200e-03  2.06700e-06
  LNLOW1 2.98000e-03  3.25900e-06
   LCOW1 3.59800e-03  6.04400e-06
  LH1OW1 3.26800e-03  5.71200e-06
  LH2OW1 4.30700e-03  8.17000e-06
   LPOW1 4.92600e-03  8.21000e-06
  LOSOW1 2.60500e-03  2.24100e-06
  LP2OW1 3.94400e-03  7.80300e-06
  LP3OW1 4.82100e-03  9.53900e-06
  LC3OW1 4.97800e-03  9.85000e-06
  LC2OW1 3.96900e-03  6.93800e-06

 in the [ nonbond_params ] section in lipid.itp file downloaded from
Tieleman's site should be include in the ffnonbonded.itp file?

the KALP-DPPC tutorial says: In the [ nonbond_params ] section, you will
find the line ";; parameters for lipid-GROMOS interactions." Delete this
line and all of the subsequent lines in this section; but I'm not 100% sure 
if I have to delete the lipid-SPC/SPCE interactions lines.

thank in advance, 
Facundo  



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Re: [gmx-users] Re: BAR histogram results

[Justin Lemkul]

On 3/5/13 10:56 AM, Sonia Aguilera wrote:

Thank you Justin,

I will add some lamda points between 0.1 to 0.5 and 0.5 to 0.9. I have a
quick question related to recalculation. If I add, for example, a new lamda
value of 0.3, I will set the following setting in the mdp file:

init_lambda  = 0.3
delta_lambda = 0
foreign_lambda   = 0.1 0.5

Does it mean that I have to repeat my simulations for 0.1 and 0.5 so that
they can have foreign lambda 0.3?



That would make sense to me, yes.

-Justin

--


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


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[gmx-users] how to get pdb2gmx to use an arbitrarily located forcefield.ff directory?

[Christopher Neale]

Thank you, Francesco, for the assistance. However, I still can not get it to 
work (see below). Can you please specify exactly what you have done and perhaps 
show a listing of the directory structure?

My command was: pdb2gmx -f protein.pdb -ff charmm36

I tried this in a number of ways, all eventually failed:

neither GMXLIB or GMXDATA set:
Error: "Could not find force field 'charmm36' in current directory, install 
tree or GMXDATA path."

# define GMXDATA
export GMXLIB=""
export GMXDATA=~/gromacs/CHARMM36/share 
Error: "Could not find force field 'charmm36' in current directory, install 
tree or GMXDATA path."

# define GMXLIB:
export GMXLIB=~/gromacs/CHARMM36/share/gromacs/top
export GMXDATA=""
the charmm36 ff is found, but after selecting a water model, I get:
Error: "Library file residuetypes.dat not found in current dir nor in your 
GMXLIB path."

# define both:
export GMXDATA=~/gromacs/CHARMM36/share  
export GMXLIB=~/gromacs/CHARMM36/share/gromacs/top 
the charmm36 ff is found, but after selecting a water model, I get:
Error: "Library file residuetypes.dat not found in current dir nor in your 
GMXLIB path."

# set GMXLIB to the regular installation:
export GMXDATA=~/gromacs/CHARMM36/share  
export GMXLIB=/usr/local/gromacs-4.5.5/share/gromacs/top/
Error: "Could not find force field 'charmm36' in current directory, install 
tree or GMXDATA path."

# the reverse of the idea above:
export GMXDATA=/usr/local/gromacs-4.5.5/share
export GMXLIB=~/gromacs/CHARMM36/share/gromacs/top
Error: "Library file residuetypes.dat not found in current dir nor in your 
GMXLIB path."

Here is a listing of the artificial directory structure that I created to try 
to get this to work:

[nealec@pegasus check]$ ls ~/gromacs/CHARMM36/
share
[nealec@pegasus check]$ ls ~/gromacs/CHARMM36/share/
gromacs
[nealec@pegasus check]$ ls ~/gromacs/CHARMM36/share/gromacs/
top
[nealec@pegasus check]$ ls ~/gromacs/CHARMM36/share/gromacs/top/
charmm36.ff
[nealec@pegasus check]$ ls ~/gromacs/CHARMM36/share/gromacs/top/charmm36.ff/
aminoacids.arnaminoacids.n.tdb  aminoacids.vsd  dna.arndna.n.tdb 
ffnabonded.itp forcefield.doc  ions.itppopc.itp   rna.hdbrna.rtp   
tip3p.itp   watermodels.dat
aminoacids.c.tdb  aminoacids.r2batomtypes.atp   dna.c.tdb  dna.rtp   
ffnanonbonded.itp  forcefield.itp  lipids.hdb  rna.arnrna.n.tdb  spce.itp  
tip4p.itp
aminoacids.hdbaminoacids.rtpcmap.itpdna.hdbffbonded.itp  
ffnonbonded.itpgb.itp  lipids.rtp  rna.c.tdb  rna.r2bspc.itp   
tips3p.itp

Thank you,
Chris.

-- original message --

Hi Chris,
I don't know if thngs changed in gromacs 4.6.x, but I succesfully did what
you are triying to do setting the two variable GMXLIB and GMXDATA at the
same time.

Francesco


2013/3/5 Christopher Neale <[hidden email]>

> Hello,
>
> I have downloaded the charmm36.ff directory and would like to use it with
> pdb2gmx. Everything works fine if I put it in the current directory or the
> share/gromacs/top directory of the binary that I am using. However, I'd
> like to be able to put the charmm36.ff directory in an arbitrary place.
>
> I tried setting GMXLIB, no luck. I also tried setting GMXDATA and also,
> separately, creating a directory structure share/gromacs/top/charm36ff and
> then setting GMXDATA to share/ (which seems absurdly convoluted, but is
> implied that it should work by the description of GMXDATA here
> http://www.gromacs.org/Documentation/Terminology/Environment_Variablesand the 
> text at the output of pdb2gmx:
>
> Fatal error:
> Could not find force field 'charmm36' in current directory, install tree
> or GMXDATA path.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> I can get around this by making a link in the current directory and then
> using sed to change the directory structure in the resulting .top file,
> after which I can remove the link in the .top file.
>
> Thank you for any advice,
> Chris. 

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Re: [gmx-users] how to get pdb2gmx to use an arbitrarily located forcefield.ff directory?

[francesco oteri]

Hi Chris,
I don't know if thngs changed in gromacs 4.6.x, but I succesfully did what
you are triying to do setting the two variable GMXLIB and GMXDATA at the
same time.

Francesco


2013/3/5 Christopher Neale 

> Hello,
>
> I have downloaded the charmm36.ff directory and would like to use it with
> pdb2gmx. Everything works fine if I put it in the current directory or the
> share/gromacs/top directory of the binary that I am using. However, I'd
> like to be able to put the charmm36.ff directory in an arbitrary place.
>
> I tried setting GMXLIB, no luck. I also tried setting GMXDATA and also,
> separately, creating a directory structure share/gromacs/top/charm36ff and
> then setting GMXDATA to share/ (which seems absurdly convoluted, but is
> implied that it should work by the description of GMXDATA here
> http://www.gromacs.org/Documentation/Terminology/Environment_Variablesand the 
> text at the output of pdb2gmx:
>
> Fatal error:
> Could not find force field 'charmm36' in current directory, install tree
> or GMXDATA path.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> I can get around this by making a link in the current directory and then
> using sed to change the directory structure in the resulting .top file,
> after which I can remove the link in the .top file.
>
> Thank you for any advice,
> Chris.
>
> --
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-- 
Cordiali saluti, Dr.Oteri Francesco
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[gmx-users] only 4 zero eigvals for NMA

[Hyuntae Na]

Dear, I am studying several protein fluctuation proteins using NMA (Normal Mode 
Analysis). In the mean time, I found out in many cases that NMA hessian matrix 
has about 3-4 zero eigenvalues even though having 6 zero eigenvalues are 
expected. I tried to reduce the tolerance level lesser than 10^-6 for the 
l-bfgs minimization, but still it have only 4 zero eigenvalues. Following is 
the 9 smallest eigenvalues (you can see that it has only 4 close-to-zero 
eigenvalues):-1.8476593e-06-1.2164109e-06-1.4830436e-071.3104790e-061.1364704e+001.7418209e+002.2836573e+003.7218206e+004.4875873e+00
 Theoretically, NMA should have 6 zero eigenvalues which represents the freedom 
of the rotation and translation. I wonder why this happens. Is there anyone who 
can help me for this problem? In order to specify the case, I leave a link to 
download a zip file that contains files for one NMA tests having the problem: 
script, mdp, pdb, gro, topol, etc. The zip file also includes the 
eigenvalue/vector 
files.https://skydrive.live.com/redir?resid=37B4631A59B510F!34933 Thank you 
very much. -- Hyuntae--
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[gmx-users] how to get pdb2gmx to use an arbitrarily located forcefield.ff directory?

[Christopher Neale]

Hello,

I have downloaded the charmm36.ff directory and would like to use it with 
pdb2gmx. Everything works fine if I put it in the current directory or the 
share/gromacs/top directory of the binary that I am using. However, I'd like to 
be able to put the charmm36.ff directory in an arbitrary place.

I tried setting GMXLIB, no luck. I also tried setting GMXDATA and also, 
separately, creating a directory structure share/gromacs/top/charm36ff and then 
setting GMXDATA to share/ (which seems absurdly convoluted, but is implied that 
it should work by the description of GMXDATA here 
http://www.gromacs.org/Documentation/Terminology/Environment_Variables and the 
text at the output of pdb2gmx:

Fatal error:
Could not find force field 'charmm36' in current directory, install tree or 
GMXDATA path.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I can get around this by making a link in the current directory and then using 
sed to change the directory structure in the resulting .top file, after which I 
can remove the link in the .top file.

Thank you for any advice,
Chris.

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Re: [gmx-users] GROMACS 4.6.1 released

[Szilárd Páll]

On Tue, Mar 5, 2013 at 8:14 PM, Mark Abraham wrote:

> *Hi GROMACS users,
>
> GROMACS 4.6.1 is officially released. It contains numerous bug fixes, some
> simulation performance enhancements and some documentation updates. We
> encourage all users to upgrade their installations from 4.6.
>
> You can find the code, manual, release notes, installation instructions and
> test
> suite at the links below.
>
> ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.1.tar.gz
> ftp://ftp.gromacs.org/pub/manual/manual-4.6.1.pdf
> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.1.x


Link incorrect. Here's the correct one:
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x


>
> http://www.gromacs.org/Documentation/Installation_Instructions
> http://gromacs.googlecode.com/files/regressiontests-4.6.1.tar.gz
>
> Happy simulating!
>
> The GROMACS development team*
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[gmx-users] GROMACS 4.6.1 released

[Mark Abraham]

*Hi GROMACS users,

GROMACS 4.6.1 is officially released. It contains numerous bug fixes, some
simulation performance enhancements and some documentation updates. We
encourage all users to upgrade their installations from 4.6.

You can find the code, manual, release notes, installation instructions and
test
suite at the links below.

ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.1.tar.gz
ftp://ftp.gromacs.org/pub/manual/manual-4.6.1.pdf
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.1.x
http://www.gromacs.org/Documentation/Installation_Instructions
http://gromacs.googlecode.com/files/regressiontests-4.6.1.tar.gz

Happy simulating!

The GROMACS development team*
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[gmx-users] Re: BAR histogram results

[Sonia Aguilera]

Thank you Justin,

I will add some lamda points between 0.1 to 0.5 and 0.5 to 0.9. I have a
quick question related to recalculation. If I add, for example, a new lamda
value of 0.3, I will set the following setting in the mdp file:

init_lambda  = 0.3
delta_lambda = 0
foreign_lambda   = 0.1 0.5

Does it mean that I have to repeat my simulations for 0.1 and 0.5 so that
they can have foreign lambda 0.3? 

Thank you, 

Sonia Aguilera



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Re: [gmx-users] Error when extending simulation

[sebastian]

On 03/05/2013 03:50 PM, Mark Abraham wrote:

... and your GROMACS version!
   


4.6 running on nodes with NVIDIA Keppler K10 and Intel E5 CPU


Mark

On Tue, Mar 5, 2013 at 3:11 PM, Justin Lemkul  wrote:

   


On 3/5/13 4:41 AM, sebastian wrote:

 

On 03/04/2013 09:47 AM, sebastian wrote:

   

Hi Gromacs user,

when I try to extend on of my simulations with

mdrun -deffnm pdz_cis_NVT_disre_equi_3  -cpi
pdz_cis_NVT_disre_equi_3.cpt -append

I get the  following error

Fatal error:
Count mismatch for state entry disre_rm3tav, code count is 0, file count
is 13

and have no idea whats wrong.


 

I tried the same thing for a second simulation and get the same error. It
seems
that this error is connected with restraints. Extending the same
simulation
without any restraints everything is working perfectly fine.

  Any suggestion is very much appreciated
   


 

I would suggest filing a bug report on redmine.gromacs.org.  Please
include all files necessary to reproduce the problem.

-Justin

--
==**==

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

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Re: [gmx-users] Error when extending simulation

[Mark Abraham]

... and your GROMACS version!

Mark

On Tue, Mar 5, 2013 at 3:11 PM, Justin Lemkul  wrote:

>
>
> On 3/5/13 4:41 AM, sebastian wrote:
>
>> On 03/04/2013 09:47 AM, sebastian wrote:
>>
>>> Hi Gromacs user,
>>>
>>> when I try to extend on of my simulations with
>>>
>>> mdrun -deffnm pdz_cis_NVT_disre_equi_3  -cpi
>>> pdz_cis_NVT_disre_equi_3.cpt -append
>>>
>>> I get the  following error
>>>
>>> Fatal error:
>>> Count mismatch for state entry disre_rm3tav, code count is 0, file count
>>> is 13
>>>
>>> and have no idea whats wrong.
>>>
>>>
>> I tried the same thing for a second simulation and get the same error. It
>> seems
>> that this error is connected with restraints. Extending the same
>> simulation
>> without any restraints everything is working perfectly fine.
>>
>>  Any suggestion is very much appreciated
>>>
>>>
> I would suggest filing a bug report on redmine.gromacs.org.  Please
> include all files necessary to reproduce the problem.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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Re: [gmx-users] Error when extending simulation

[Justin Lemkul]

On 3/5/13 4:41 AM, sebastian wrote:

On 03/04/2013 09:47 AM, sebastian wrote:

Hi Gromacs user,

when I try to extend on of my simulations with

mdrun -deffnm pdz_cis_NVT_disre_equi_3  -cpi pdz_cis_NVT_disre_equi_3.cpt 
-append

I get the  following error

Fatal error:
Count mismatch for state entry disre_rm3tav, code count is 0, file count is 13

and have no idea whats wrong.



I tried the same thing for a second simulation and get the same error. It seems
that this error is connected with restraints. Extending the same simulation
without any restraints everything is working perfectly fine.


Any suggestion is very much appreciated



I would suggest filing a bug report on redmine.gromacs.org.  Please include all 
files necessary to reproduce the problem.


-Justin

--


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


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Re: [gmx-users] Errors in compiling gromacs 4.5.6

[Mark Abraham]

See
http://www.gromacs.org/Documentation/Installation_Instructions_4.5#Details_for_building_the_FFTW_prerequisite

Mark

On Tue, Mar 5, 2013 at 9:44 AM, Ekta Jain  wrote:

> Dear gmx Users,
> I am very new to Linux and probably this is a very general thing i may be
> seeking help for.
>
> I am facing problems in compiling GROMACS after installing the
> prerequisites (fftw-3.3.3)
>
> I get the following error towards the end of "make"
>
> # make
>
> recompile with -fPIC
> /usr/local/lib/libfftw3f.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make[3]: *** [libmd.la] Error 1
> make[3]: Leaving directory `/root/Desktop/gromacs-4.5.6/src/mdlib'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/root/Desktop/gromacs-4.5.6/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/root/Desktop/gromacs-4.5.6/src'
> make: *** [all-recursive] Error 1
>
> I have gone through all instructions given on the the GROMACS installation
> page (
> http://www.gromacs.org/Documentation/Installation_Instructions_4.5#Compilation
> )
> incase this was to happen but nothing given there fixes it.
>
> There was no problem in FFTW-3.3.3 compiling and installation.
>
> Appreciate any help.
>
> Best Regards,
>
> Ekta Jain
> Research Analyst
> Biotechnology and Bio-resources Division
> The Energy and Resources Institute, India Habitat Centre
> Lodhi Road, New Delhi - 110033
> #09958818853
> ekta.j...@teri.res.in
>
> 
>
> Disclaimer:
>
> The information contained in this e-mail is intended for the person or entity
> to which it is addressed, and it may contain confidential and/or privileged
> material. Any review or other use of this mail or taking any action based on 
> it
> by persons or entities other than the intended recipient is strictly 
> prohibited.
> If you receive this e-mail by mistake, please contact the sender, and delete 
> all
> copies of this mail.This e-mail has been scanned and verified by McAfee SaaS
> Email Security, formerly MX Logic.
>
>
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Re: [gmx-users] Re: gInstallation Problems with Gromacs4.6

[Mark Abraham]

On Tue, Mar 5, 2013 at 5:00 AM, Abhishek Acharya wrote:

> Hello Mark
> Sorry for the misunderstanding. Actually i did not provide any extra flags
> to cmake. I generally edit the CMakeCache.txt file to provide the proper
> paths. I somehow felt that was easier to do. I didn't think that could
> lead to errors. I have installed gromacs 4.6 on multiple systems using the
> same procedure, same mpi and fftw versions,  using shared libraries, but
> only on HPC  i got the mentioned error. So you can imagine my surprise on
> getting such an error.  And i was more surprised when it got configured
> successfully on disabling the shared library flag. If there is problem
> with cmake then i expect it, to give the same error irrespective of
> whether i enable shared libraries or not. Just my thoughts.
>

In theory, there should be no difference. In practice, shared libraries can
cause trouble on various HPC platforms.

The supported way to configure MPI+FFTW is to use an MPI wrapper compiler
(e.g. the command I suggested four days ago) and to follow the installation
instructions. There should be no need to edit the cache for this kind of
normal installation. Because we can have no idea what you've done to the
cache, we can't help you solve any problems, I'm afraid.

Mark
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Re: [gmx-users] g_hbond and contact

[Kavyashree M]

Thank you Sir.

On Tue, Mar 5, 2013 at 4:33 PM, Erik Marklund  wrote:

>
> On Mar 5, 2013, at 10:34 AM, Kavyashree M wrote:
>
>  Sir,
>>
>> I used gromacs 4.6. I got the point - index file will tell how many
>> contacts an
>> atom has made during the trajectory. Whether it has made a contact with an
>> atom only in once or all the time, in the whole trajectory, it will be
>> mentioned.
>> Am I right?
>>
>
> Yes.
>
>
>
>> So from the problem I had, can I say that no. of contact/atom had
>> increased
>> in S2 while the no. of contact/time decreased?
>>
>
> That depends. If 'contact' means unique interactions and 'atom' means e.g.
> all atoms in in your system, then yes.
>
>
>> Its a bit confusing though!
>>
>> Thank you
>> kavya
>>
>> On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund 
>> wrote:
>>
>>  To clarify: the -hbn output is not very indicative of how many contacts
>>> there were since some of them could be present in one frame but absent in
>>> 99. The -num option, however, provides the number of contacts over
>>> time, and its time average probably tells you much more in this case.
>>>
>>> What version of g_hbond are you using? I remember there were several
>>> bugfixes over the last 6 months or so. With the latest version(s) I
>>> believe
>>> that the -merge flag has no effect on contact analysis, which is correct.
>>>
>>> Erik
>>>
>>>
>>>  --
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>
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Re: [gmx-users] g_hbond and contact

[Erik Marklund]

On Mar 5, 2013, at 10:34 AM, Kavyashree M wrote:


Sir,

I used gromacs 4.6. I got the point - index file will tell how many
contacts an
atom has made during the trajectory. Whether it has made a contact  
with an

atom only in once or all the time, in the whole trajectory, it will be
mentioned.
Am I right?


Yes.



So from the problem I had, can I say that no. of contact/atom had  
increased

in S2 while the no. of contact/time decreased?


That depends. If 'contact' means unique interactions and 'atom' means  
e.g. all atoms in in your system, then yes.




Its a bit confusing though!

Thank you
kavya

On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund   
wrote:


To clarify: the -hbn output is not very indicative of how many  
contacts
there were since some of them could be present in one frame but  
absent in
99. The -num option, however, provides the number of contacts  
over

time, and its time average probably tells you much more in this case.

What version of g_hbond are you using? I remember there were several
bugfixes over the last 6 months or so. With the latest version(s) I  
believe
that the -merge flag has no effect on contact analysis, which is  
correct.


Erik



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[gmx-users] costu, fragment force field

[nemethl]

I'm attempting to build a costume fragment library of beta amino acids
with GAFF parametrization. I have converted the AMBER assigned parameters
with acpype, built my .rtp .atp and .itp files. Everything works fine,
until grompp, there i get a lot of "No default Ryckaert-Bell. types"
errors. The problem is, that the dihedrals in question are mentioned in
the ffbonded.itp file, but the atomtypes are not in good order. How do i
figure out the RB parameters for these bonds, in the precise order? Is
there a way to convert the parameters to the desired order?

Thank you in advance!

Lukacs Nemeth

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Re: [gmx-users] Error when extending simulation

[sebastian]

On 03/04/2013 09:47 AM, sebastian wrote:

Hi Gromacs user,

when I try to extend on of my simulations with

mdrun -deffnm pdz_cis_NVT_disre_equi_3  -cpi 
pdz_cis_NVT_disre_equi_3.cpt -append


I get the  following error

Fatal error:
Count mismatch for state entry disre_rm3tav, code count is 0, file 
count is 13


and have no idea whats wrong.



I tried the same thing for a second simulation and get the same error. 
It seems that this error is connected with restraints. Extending the 
same simulation without any restraints everything is working perfectly 
fine.



Any suggestion is very much appreciated

Yours

Sebastian


Sebastian again

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Re: [gmx-users] g_hbond and contact

[Kavyashree M]

Sir,

I used gromacs 4.6. I got the point - index file will tell how many
contacts an
atom has made during the trajectory. Whether it has made a contact with an
atom only in once or all the time, in the whole trajectory, it will be
mentioned.
Am I right?

So from the problem I had, can I say that no. of contact/atom had increased
in S2 while the no. of contact/time decreased?

Its a bit confusing though!

Thank you
kavya

On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund  wrote:

> To clarify: the -hbn output is not very indicative of how many contacts
> there were since some of them could be present in one frame but absent in
> 99. The -num option, however, provides the number of contacts over
> time, and its time average probably tells you much more in this case.
>
> What version of g_hbond are you using? I remember there were several
> bugfixes over the last 6 months or so. With the latest version(s) I believe
> that the -merge flag has no effect on contact analysis, which is correct.
>
> Erik
>
>
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[gmx-users] Errors in compiling gromacs 4.5.6

[Ekta Jain]

 Dear gmx Users,I am very new to Linux and probably this is a very general thing i may be seeking help for. I am facing problems in compiling GROMACS after installing the prerequisites (fftw-3.3.3)I get the following error towards the end of "make"# makerecompile with -fPIC/usr/local/lib/libfftw3f.a: could not read symbols: Bad valuecollect2: ld returned 1 exit statusmake[3]: *** [libmd.la] Error 1make[3]: Leaving directory `/root/Desktop/gromacs-4.5.6/src/mdlib'make[2]: *** [all-recursive] Error 1make[2]: Leaving directory `/root/Desktop/gromacs-4.5.6/src'make[1]: *** [all] Error 2make[1]: Leaving directory `/root/Desktop/gromacs-4.5.6/src'make: *** [all-recursive] Error 1I have gone through all instructions given on the the GROMACS installation page (http://www.gromacs.org/Documentation/Installation_Instructions_4.5#Compilation)incase this was to happen but nothing given there fixes it. There was no problem in FFTW-3.3.3 compiling and installation.Appreciate any help.Best Regards,Ekta JainResearch AnalystBiotechnology and Bio-resources DivisionThe Energy and Resources Institute, India Habitat CentreLodhi Road, New Delhi - 110033#09958818853ekta.j...@teri.res.in





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Re: [gmx-users] g_hbond and contact

[Erik Marklund]

To clarify: the -hbn output is not very indicative of how many  
contacts there were since some of them could be present in one frame  
but absent in 99. The -num option, however, provides the number of  
contacts over time, and its time average probably tells you much more  
in this case.


What version of g_hbond are you using? I remember there were several  
bugfixes over the last 6 months or so. With the latest version(s) I  
believe that the -merge flag has no effect on contact analysis, which  
is correct.


Erik

On Mar 5, 2013, at 5:20 AM, Kavyashree M wrote:

I am sorry There is no "7ws" Its a typographic error. What I wanted  
to ask

was -
I am comparing two simulations S1 and S2 for contacts at a given cut  
off

I used g_mdmat and g_hbond to calculate it.
g_hbond outputs: of "-num" and "-hbn" was considered.
   1. -hbn output was analysed to calculate how many  
contacts each

   atom has from both  S1 and S2.
   2. -num output graph was compared from both S1 and S2.
g_mdmat output: of "-no" was considered.
   3. -no output was analysed from both S1 and S2 using the
   third column or the second Y value which gives total
contacts
   of each atom.

It was observed that "1" and "3" matched exactly giving the same  
number of

contacts each atom has (in the whole simulations). indicating that the
number
of contacts each atom has was more in S2 than S1.

But the graph from "2" indicated that the number of contacts (along  
the

trajectory)
in S1 was higher than S2.

My doubt is:
The number of contact per atom follows S2 > S1
while number of contacts per time follows S1 > S2.
I am unclear as to what I  have to conclude from this observations.

-> I used the same cutoff throughout.
-> There has not been any swapping of the trajectory while  
analysing.


Thank you
Kavya


On Tue, Mar 5, 2013 at 1:09 AM, Justin Lemkul  wrote:




On 3/4/13 1:10 PM, Kavyashree M wrote:

On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul   
wrote:



When measuring contacts, you don't measure one group, you measure  
the
number of contacts that occur between groups A and B, which  
considers all

atoms in those two groups.



I gave a group of hydrophobic atoms in both cases
The command I gave -
g_hbond_46  -fx.xtc-s   x.tpr-contact   -n   x.ndx   - 
r   0.4

-hbm   o.xpm   -hbn   o.ndx   -num   o.xvg
my index file contained a group of hydrophobic atoms. which I  
supplied in

the x.ndx.



 You don't define contacts in an index group, you define atoms  
that may

or
may not make contacts with others.


The one I mentioned here is the output index file from the  
g_hbond (4.6

version) - o.ndx.




 [ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_***
*CZ2_CZ3_CH2

]

   5  7ws
   5 10
   5 14
   5 18
   5 22
   5 24
   5 27
   5 30
   5 35
   5292
   5296
   530


There's something very wrong with this index file.  How did you

generate
it? The presence of a repeated atom number (5) and a nonsensical  
one

(7ws)
leads me to believe that you've done something incorrect.  Did  
this come
from g_hbond? It looks like the output of -hbn, which is only  
useful for

decoding hbmap.xpm, nothing else.


I did not generate this. The tool (g_hbond) generated this index  
file.

It
is the -hbn output.



OK, then I still don't know what "7ws" is, but the only purpose for  
this

file is to provide a key to the existence matrix in hbmap.xpm.  Your
previous description indicated that you were using it for some other
analysis, which would not be appropriate.

The other thing worth mentioning here is something that was posted  
to the
list just a few hours ago, that the output of g_hbond -contact may  
not
agree with other methods of calculating contacts, especially in the  
case of

-merge vs. -nomerge.

-Justin



 From this second section Total contacts was extracted for each  
atom and





compared with

that from a second simulation.
These contacts was matching with the contacts of the 3rd column  
from

g_mdmat output -
@ legend string 0 "Total/mean"
@ legend string 1 "Total"
@ legend string 2 "Mean"
@ legend string 3 "# atoms"
@ legend string 4 "Mean/# atoms"
#resratio  tot  mean  natm  mean/atm
   1 1.001   1110.991110.991
   2 1.244   10 8.0411 8.041
   3 1.166   1311.147111.147
   4 1.036   1110.615110.615


While the time dependent contacts in the xvg file shows that the  
first

simulation has more
contacts than the second one..


That shouldn't be unexpected.  Two independent simulations have no
guarantee of doing the same thing, that's why sampling is so  
important.




Thank you
kavya



--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 

Re: [gmx-users] Time-Dependent Electric Field

[Erik Marklund]

From the manual it seems that oscillating electric fields are not yet  
implemented, which surprised me. I've seen colleagues use such in  
gromacs, but that may have been in-house modifications. Should be  
fairly simple to implement though.


Erik

On Mar 4, 2013, at 11:30 PM, raquick wrote:


Gromacs users,

I am trying to run a simulation with a time dependent electric field  
with
frequency of around 16 GHz in the Z direction. What numbers should I  
put in
the .mdp file following E-zt: for a field with this frequency? I  
have looked
at the source code but cannot determine what units the frequency  
should be

in.

Currently, for electric Field I have the following:

E-z = 1  .5   1
E-zt= 1 (some number) 0

I want to know what the "some number" should look like.

Any help is appreciated.

Regards,

Ross Quick



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