[gmx-users] Fwd: reproducibility of PMF plot with two different starting structures?

[Aswathy]

Hi,

I just want to know about the consistency we could obtain in plotting PMF.

I am using Gromacs 4.0.4 MPI version. Trying to find the PMF of the ligand
transport through the channel. I tried two SMDs (same pull rate, and force
constant) with different starting structures (only ligand poses and
position  are slightly  different). I performed the sampling of these two
pathways, the plots obtained are of  similar overall shapes, but peaks (max
, min) have some variations?

Could you please give your comment on this attempt? Is that expectable?

Thank you,



-- 
Aswathy



-- 
Aswathy
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Re: [gmx-users] enegry minimisation

[Mark Abraham]

- Original Message -
From: sonali dhindwal 
Date: Friday, May 21, 2010 15:38
Subject: Re: [gmx-users] enegry minimisation
To: jalem...@vt.edu, Discussion list for GROMACS users 

---
| > hello Jusitn,
> Thanks for your reply,,
> I am sending you the link,
so that you can see the changes in the protein, I have specifically
shown that part of the protein, where I am seeing changes,
> 
> http://picasaweb.google.co.in/sonali11dhindwal/Protein?feat=directlink
> 
> 
> Yello
beeta sheets are of the protein after EM, and magenta are that of the
refrence structure, you can see how this time,I am surprised myself
that sheets have become longer than the refrence structure.
> I have corrected that   define  =  -DPOSRES also.
> and have taken that posres file generated by pdb2gmx.is this the problem of 
> the visualiser I m using, I am using pymol for it

I wouldn't describe what I can see there as significant change. The criterion 
any visualization program uses for assigning beta-strand vs not-strand is a 
reasonably arbitrary choice, and might differ between programs. It's quite 
plausible that EM could see a residue here and there cross a boundary if they 
were originally close.

Looking at all-atom or heavy-atom RMSD before and after EM (and maybe RMSD also 
over the subset of atoms of direct interest) is a much more reliable indicator 
that nothing has gone wrong. Off the top of my head, for a protein with no 
disordered regions, I'd expect EM on an experimental structure and normal force 
field to move about or less than 0.02nm on heavy-atom RMSD. All the EM is 
really expected to do is (e.g.) make sensible the hydrogen atoms whose 
positions were inferred or generated.

Mark
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Re: [gmx-users] enegry minimisation

[sonali dhindwal]

hello Jusitn,
Thanks for your reply,,
I am sending you the link,
so that you can see the changes in the protein, I have specifically
shown that part of the protein, where I am seeing changes,

http://picasaweb.google.co.in/sonali11dhindwal/Protein?feat=directlink


Yello
beeta sheets are of the protein after EM, and magenta are that of the
refrence structure, you can see how this time,I am surprised myself
that sheets have become longer than the refrence structure.
I have corrected that   define  =  -DPOSRES also.
and have taken that posres file generated by pdb2gmx.is this the problem of the 
visualiser I m using, I am using pymol for it
Thanks

--
Sonali Dhindwal

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[gmx-users] g_bundle issue

[Anirban Ghosh]

Hi ALL,

I tried to calculate the helix tilt of a single helix (TM5) among 7 helices
using g_bundle. In the index file I defined the two groups (top & bottom) as
the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in
the bun_tilt.xvg file I am getting the values as:

---
# This file was created Thu May 20 15:29:50 2010
# by the following command:
# g_bundle -f prot.xtc -s prot.tpr -n TM5_top_bot.ndx -na 1
#
# g_bundle is part of G R O M A C S:
#
# GRowing Old MAkes el Chrono Sweat
#
@title "Axis tilts"
@xaxis  label "Time (ps)"
@yaxis  label "(degrees)"
@TYPE xy
  0  0
  2 0.0197823
  4  0
  6 0.0197823
  8  0
 10  0
 12 0.0197823
 14  0
 16 0.0197823
 18  0
 20 0.0279765
 22  0
 24  0
 26 0.0197823
 28  0
 30  0
 32  0
 34  0
 36  0
 38 0.0197823

And when plotted it gives a blank plot. Why it is coming like this? Am I
doing anything wrong? Any suggestion is welcome.
The contents of the index file is:

[ top ]
1844 1850 1858 1866 1878 1896 1904 1913 1922 1940 1948 1956 1965 1974 1983
1991
[ bottom ]
2000 2008 2014 2024 2032 2041 2050 2067 2079 2092 2101 2109 2118 2124 2132
2138 2146


Regards,

Anirban
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RE: [gmx-users] polymer simulation

[Dallas B. Warren]

If you are referring to something that will generate a coordinate file
(.pdb or .gro) of polymer molecules randomly distributed, then there is
not currently a script with GROMACS that will do that job.  If you have
a single molecule, there are a couple of tools that can randomly spread
those molecules around, though not very well.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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Re: [gmx-users] confusion about segmentation fault during mdrun

[Justin A. Lemkul]

Lan Hua wrote:

Hi Justin,

   I took all your suggestions. But the same thing happened again in the 
NPT step with the "Segmentation fault" for some starting structure.  I 
attached the mdp file I used.  Do you have any idea what else could 
cause this error?


   Thank you very much!



The only advice I can give is here (with special attention to the "Diagnosing an 
Unstable System" section):


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

I know you have explained your reasoning for using version 3.1.4, but do realize 
that there have been numerous bug fixes and feature upgrades in the last 8 
(yikes!) years of Gromacs development that may affect stability.  I have never 
used 3.1.4, so if there's some inherent issue with that version, you can also 
check the list archive for anyone that had similar issues back when 3.1.4 was 
actually a recent release.


-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] confusion about segmentation fault during mdrun

[Lan Hua]

Hi Justin,

   I took all your suggestions. But the same thing happened again in the NPT
step with the "Segmentation fault" for some starting structure.  I attached
the mdp file I used.  Do you have any idea what else could cause this error?

   Thank you very much!

Best,
Lan

On Wed, May 19, 2010 at 6:03 PM, Justin A. Lemkul  wrote:

>
>
> Lan Hua wrote:
>
>> Hi Justin,
>>
>>   I appreciated your quick answers.  So if I understand correctly, using
>> constraints = hbonds with the time step of 2fs, it should be fine, right?
>>
>>
> Maybe.  If your goal is REMD (I'm not clear from your original post) then
> stability may be an issue at higher temperatures, in which case you may need
> to constrain all bonds or decrease your time step, maybe both.  At ambient
> temperatures, what you propose is likely stable.  Look into the relevant
> literature for similar force fields and applications to be sure.
>
> -Justin
>
>  Thanks,
>> Lan
>>
>>
>> On Wed, May 19, 2010 at 3:52 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Lan Hua wrote:
>>
>>Hi Justin,
>>
>>  Thank you so much for your quick reply and good suggestions.
>>The following is my answer.
>>
>>On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   Lan Hua wrote:
>>
>>   Hi All,
>>
>>I understand that the error of segmentation fault
>>may come
>>   from many reasons, but I just couldn't figure out the
>>reason of
>>   this error in my simulations.  I want to run md
>>simulations with
>>   explicit water for 20 structures of one domain (residue
>>77-148)
>>   of calmodulin (PDB 1CFC).  These 20 starting structures
>>are from
>>   one REMD simulation in implicit water.  The following is
>>what I
>>   did to run simulations for these 20 structures.  I used
>>gromacs
>>   version 3.1.4 with ffamber ports.  The force field is
>> amber03
>>   and water model is TIP3P.
>>
>>
>>   Do you have any particular reason for using software that is
>>eight
>>   years old? You will get a massive performance upgrade with
>>4.0.7, as
>>   well as the ability to use multiple processors per replica.  In
>>   versions prior to 4.0, you can only use one processor per
>>REMD replica.
>>
>>The reason that I am using gromacs 3.1.4 is to prepare some
>>input files for simulations at fold...@home in which version
>>3.1.4 is recommended.
>>
>>
>>OK, as long as you've got a reason...
>>
>>
>>
>>
>> 1.  get rid of the steric clash in the starting structure
>>
>>
>>   What do you mean?  Energy minimization?  How did you did do this
>>   prior to step 2 (generating a topology)?
>>
>>I used the "protein preparation wizard" which is implemented in
>>maestro package to do this.   Actually in this wizard, energy
>>minimization is performed on protein.
>>
>> 2.  after doing pdb2gmx, then minimze the protein
>> 3,   use "-bt dodecahedron -d 0.9 -c"  in the command
>>line of
>>   editconf
>> 4,  after doing genbox, first minimize the water with
>>protein
>>   rigid and then minimize the whole system
>>
>>
>>   A lot of these steps are redundant and probably unnecessary.
>> Some tips:
>>
>>
>> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
>>
>>
>>Thanks for the tips. I went to the link, but I am still a little
>>bit confused about which steps are unnecessary.  You mean step 7
>>and step 8?  I did this in case simulations at f...@h would be
>> crashed.
>>
>>
>>I just mean the repeated, separate energy minimizations.  I guess
>>there's no harm in it, but generally I find that minimizing the
>>protein in vacuo, then with and without restraints in solvent, etc.
>>is unnecessary.  I'd suggest just building the system (solvent and
>>all), and minimizing the whole thing (without restraints).  I don't
>>think you stand to gain anything with your procedure.
>>
>>
>>
>>
>> 5,  run md simulation with position restraint for protein
>>   heavy atoms with nose-hoover thermostat for 20ps
>> 6,  run NPT simulations with nose-hoover thermostat and
>>   Parrinello-Rahman thermostat for 500ps
>> 7,  run NVT simulation for another 100ps
>> 8, then energy minimze the whole system again.
>>
>>   Every time, there are always "segmentation fault" in step
>>6 for
>>   some starting structures which could be different in
>>every try.
>> 

[gmx-users] polymer simulation

[Sudip Roy]

Dear all,

I would like to know that is there any gromacs tool which can generate a
polymer melt?
If not, is there any tool you can suggest which can do the job.

Thank you.

Sudip

--
**

Dr. Sudip Roy
Physical Chemistry and Material Science Division
Scientist C
National Chemical Laboratory
Pune 411008
India

Tel.  +91 2590 2735 Office
Email s@ncl.res.in



Disclaimer:

This message and the information contained herein is proprietary and 
confidential and subject to the policy statement of the National Chemical 
Laboratory, Pune, India. You may review the policy at 
http://www.ncl-india.org/common/webmailDisclaimer.htm
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Re: [gmx-users] mdrun segmentation fault

[Justin A. Lemkul]

Sikandar Mashayak wrote:

It happens immediately at step 0., and the log file looks like :




That suggests to me that the system is inherently unstable, which can occur for 
a variety of reasons.


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

A few more comments below.



Input Parameters:
   integrator   = md
   nsteps   = 2
   init_step= 0
   ns_type  = Grid
   nstlist  = 10
   ndelta   = 2
   nstcomm  = 0
   comm_mode= Linear
   nstlog   = 1000
   nstxout  = 600
   nstvout  = 600
   nstfout  = 600
   nstenergy= 1000
   nstxtcout= 1000
   init_t   = 0
   delta_t  = 0.001
   xtcprec  = 1
   nkx  = 44
   nky  = 42
   nkz  = 120
   pme_order= 4
   ewald_rtol   = 1e-05
   ewald_geometry   = 1
   epsilon_surface  = -1
   optimize_fft = FALSE
   ePBC = xyz
   bPeriodicMols= FALSE
   bContinuation= FALSE
   bShakeSOR= FALSE
   etc  = Nose-Hoover
   epc  = No
   epctype  = Isotropic
   tau_p= 1
   ref_p (3x3):
  ref_p[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   compress (3x3):
  compress[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   refcoord_scaling = No
   posres_com (3):
  posres_com[0]= 0.0e+00
  posres_com[1]= 0.0e+00
  posres_com[2]= 0.0e+00
   posres_comB (3):
  posres_comB[0]= 0.0e+00
  posres_comB[1]= 0.0e+00
  posres_comB[2]= 0.0e+00
   andersen_seed= 815131
   rlist= 1.1
   rtpi = 0.05
   coulombtype  = PME
   rcoulomb_switch  = 0
   rcoulomb = 1.1
   vdwtype  = Cut-off
   rvdw_switch  = 0
   rvdw = 1.1
   epsilon_r= 1
   epsilon_rf   = 1
   tabext   = 1
   implicit_solvent = No
   gb_algorithm = Still
   gb_epsilon_solvent   = 80
   nstgbradii   = 1
   rgbradii = 2
   gb_saltconc  = 0
   gb_obc_alpha = 1
   gb_obc_beta  = 0.8
   gb_obc_gamma = 4.85
   sa_surface_tension   = 2.092
   DispCorr = EnerPres
   free_energy  = no
   init_lambda  = 0
   sc_alpha = 0
   sc_power = 0
   sc_sigma = 0.3
   delta_lambda = 0
   nwall= 0
   wall_type= 9-3
   wall_atomtype[0] = -1
   wall_atomtype[1] = -1
   wall_density[0]  = 0
   wall_density[1]  = 0
   wall_ewald_zfac  = 3
   pull = no
   disre= No
   disre_weighting  = Conservative
   disre_mixed  = FALSE
   dr_fc= 1000
   dr_tau   = 0
   nstdisreout  = 100
   orires_fc= 0
   orires_tau   = 0
   nstorireout  = 100
   dihre-fc = 1000
   em_stepsize  = 0.01
   em_tol   = 100
   niter= 20
   fc_stepsize  = 0
   nstcgsteep   = 1000
   nbfgscorr= 10
   ConstAlg = Lincs
   shake_tol= 0.0001
   lincs_order  = 4
   lincs_warnangle  = 30
   lincs_iter   = 1
   bd_fric  = 0
   ld_seed  = 1993
   cos_accel= 0
   deform (3x3):
  deform[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  deform[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  deform[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   userint1 = 0
   userint2 = 0
   userint3 = 0
   userint4 = 0
   userreal1= 0
   userreal2= 0
   userreal3= 0
   userreal4= 0
grpopts:
   nrdf:   0   12822
   ref_t:   0 300
   tau_t:   0 0.2
anneal:  No  No
ann_npoints:   0   0
   acc:   0   0   0
   nfreeze:   Y   Y   Y   N   
N   N

   energygrp_flags[  0]: 1 0
   energygrp_flags[  1]: 0 0
   efield-x:
  n = 0
   efield-xt:
  n = 0
   efield-y:
  n = 0
   efield-yt:
  n = 0
   efield-z:
  n = 0
   efield-zt:
  n = 0
   bQMMM= FALSE
   QMconstraints= 0
   QMMMscheme   = 0
   scalefactor  = 1
qm_opts:
   ngQM = 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw: 

Re: [gmx-users] mdrun segmentation fault

[Sikandar Mashayak]

It happens immediately at step 0., and the log file looks like :



Input Parameters:
   integrator   = md
   nsteps   = 2
   init_step= 0
   ns_type  = Grid
   nstlist  = 10
   ndelta   = 2
   nstcomm  = 0
   comm_mode= Linear
   nstlog   = 1000
   nstxout  = 600
   nstvout  = 600
   nstfout  = 600
   nstenergy= 1000
   nstxtcout= 1000
   init_t   = 0
   delta_t  = 0.001
   xtcprec  = 1
   nkx  = 44
   nky  = 42
   nkz  = 120
   pme_order= 4
   ewald_rtol   = 1e-05
   ewald_geometry   = 1
   epsilon_surface  = -1
   optimize_fft = FALSE
   ePBC = xyz
   bPeriodicMols= FALSE
   bContinuation= FALSE
   bShakeSOR= FALSE
   etc  = Nose-Hoover
   epc  = No
   epctype  = Isotropic
   tau_p= 1
   ref_p (3x3):
  ref_p[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   compress (3x3):
  compress[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   refcoord_scaling = No
   posres_com (3):
  posres_com[0]= 0.0e+00
  posres_com[1]= 0.0e+00
  posres_com[2]= 0.0e+00
   posres_comB (3):
  posres_comB[0]= 0.0e+00
  posres_comB[1]= 0.0e+00
  posres_comB[2]= 0.0e+00
   andersen_seed= 815131
   rlist= 1.1
   rtpi = 0.05
   coulombtype  = PME
   rcoulomb_switch  = 0
   rcoulomb = 1.1
   vdwtype  = Cut-off
   rvdw_switch  = 0
   rvdw = 1.1
   epsilon_r= 1
   epsilon_rf   = 1
   tabext   = 1
   implicit_solvent = No
   gb_algorithm = Still
   gb_epsilon_solvent   = 80
   nstgbradii   = 1
   rgbradii = 2
   gb_saltconc  = 0
   gb_obc_alpha = 1
   gb_obc_beta  = 0.8
   gb_obc_gamma = 4.85
   sa_surface_tension   = 2.092
   DispCorr = EnerPres
   free_energy  = no
   init_lambda  = 0
   sc_alpha = 0
   sc_power = 0
   sc_sigma = 0.3
   delta_lambda = 0
   nwall= 0
   wall_type= 9-3
   wall_atomtype[0] = -1
   wall_atomtype[1] = -1
   wall_density[0]  = 0
   wall_density[1]  = 0
   wall_ewald_zfac  = 3
   pull = no
   disre= No
   disre_weighting  = Conservative
   disre_mixed  = FALSE
   dr_fc= 1000
   dr_tau   = 0
   nstdisreout  = 100
   orires_fc= 0
   orires_tau   = 0
   nstorireout  = 100
   dihre-fc = 1000
   em_stepsize  = 0.01
   em_tol   = 100
   niter= 20
   fc_stepsize  = 0
   nstcgsteep   = 1000
   nbfgscorr= 10
   ConstAlg = Lincs
   shake_tol= 0.0001
   lincs_order  = 4
   lincs_warnangle  = 30
   lincs_iter   = 1
   bd_fric  = 0
   ld_seed  = 1993
   cos_accel= 0
   deform (3x3):
  deform[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  deform[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  deform[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   userint1 = 0
   userint2 = 0
   userint3 = 0
   userint4 = 0
   userreal1= 0
   userreal2= 0
   userreal3= 0
   userreal4= 0
grpopts:
   nrdf:   0   12822
   ref_t:   0 300
   tau_t:   0 0.2
anneal:  No  No
ann_npoints:   0   0
   acc:   0   0   0
   nfreeze:   Y   Y   Y   N
N   N
   energygrp_flags[  0]: 1 0
   energygrp_flags[  1]: 0 0
   efield-x:
  n = 0
   efield-xt:
  n = 0
   efield-y:
  n = 0
   efield-yt:
  n = 0
   efield-z:
  n = 0
   efield-zt:
  n = 0
   bQMMM= FALSE
   QMconstraints= 0
   QMMMscheme   = 0
   scalefactor  = 1
qm_opts:
   ngQM = 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Will do PME sum in reciprocal space.

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) p

Re: [gmx-users] mdrun segmentation fault

[Justin A. Lemkul]

Sikandar Mashayak wrote:

Hi

I have gromacs input files for md simulation, with these set up files 
(*.mdp,*.top,*.itp *.gro), I can successfully run grompp and mdrun on 
one machine, but when I move it to other machine, I get segmentation 
fault when I do mdrun. Both the machines have exactly same types of 
installation of gromacs 4.0.7 . Also, I can run water tutorials 
successfully on both the machines.


So what could be the source of segmentation fault?



MD is chaotic, so you may not get the same result every time you run a 
simulation.  Since you've not said how quickly the seg fault occurs it is 
exceptionally hard to diagnose.  Generally, seg faults with mdrun occur because 
the system crashes from an instability.  Without substantially more information 
(system contents, .mdp settings, relevant log file output, etc) there is not 
much more to suggest.


-Justin


thanks
sikandar



--


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] mdrun segmentation fault

[Sikandar Mashayak]

Hi

I have gromacs input files for md simulation, with these set up files
(*.mdp,*.top,*.itp *.gro), I can successfully run grompp and mdrun on one
machine, but when I move it to other machine, I get segmentation fault when
I do mdrun. Both the machines have exactly same types of installation of
gromacs 4.0.7 . Also, I can run water tutorials successfully on both the
machines.

So what could be the source of segmentation fault?

thanks
sikandar
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[gmx-users] Re: graphite and pi density

[Vitaly Chaban]

> I want to put charge (as pi density) on each carbon atom at 1 A top and
> below of each carbon atom of graphaite sheet. Basically I want put a atom,
> X, with charge -0.5 and mass 0 at 0.5 A  below and above the carbon atom.
>
> How can I do this?
> Thanks
> Nilesh


Hi Nilesh,

Looks interesting. How did you estimate this charge of -0.5 ?

Dummy atoms in gromacs should be useful to do what you want.

~Vitaly

--
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[gmx-users] RE: g_densmap

[Ricardo Cuya Guizado]

Dear Mark


I used this sequence to obtain the gro file (gro reference in the next 
calculations)
g_densmap_d -f tmp-prueba.gro -n index.ndx -o tmp_prueba1.gro -princ

Select a group for determining
the system size:

 

Group 0 ( 
System) has  6370 elements

 

Group 1 (   
HEME) has47 elements

 

Group 2 (
SOL) has  6321 elements

 

Group 3 (
NA+) has 2 elements

 

Group 4 (  NA) has 1 elements

 

Group 5 (  NC) has 1 elements

 

Group 6 (
CHB) has 1 elements

 

Group 7 (
CHD) has 1 elements

 

Group 8 (
CHB-CHD) has 2 elements

 

Group 9
(   Carb_ring) has 4 elements

 

Group10 (
CHC) has 1 elements

 

Group11 (
CHA) has 1 elements

 

Group12 ( 
nitrog) has 3 elements

 

Group13 (   
ow_teste) has 1 elements

 

Group14 (
HW1_HW2) has  4214 elements

 

Group15 (  OW) has  2107 elements

 

Group16 (  Fe) has 1 elements

 

 

Select a group: 0

 

Selected 0: 'System'

 

system size :  5.486 
5.648  6.394 (nm)

 

center 
:  3.463  3.499 
1.671 (nm)

 

box vectors :  4.471 
4.471  4.563 (nm)

 

box angles 
:  60.66  60.66 
90.00 (degrees)

 

box volume 
:  65.78   (nm^3)

 

 

 

Select group for the
determining the orientation

 

Group 0 ( 
System) has  6370 elements

 

Group 1 (   
HEME) has47 elements

 

Group 2 (
SOL) has  6321 elements

 

Group 3 (
NA+) has 2 elements

 

Group 4 (  NA) has 1 elements

 

Group 5 (  NC) has 1 elements

 

Group 6 (
CHB) has 1 elements

 

Group 7 (
CHD) has 1 elements

 

Group 8 (
CHB-CHD) has 2 elements

 

Group 9 (  
Carb_ring) has 4 elements

 

Group10 (
CHC) has 1 elements

 

Group11 (
CHA) has 1 elements

 

Group12 ( 
nitrog) has 3 elements

 

Group13 (   
ow_teste) has 1 elements

 

Group14 (
HW1_HW2) has  4214 elements

 

Group15 (  OW) has  2107 elements

 

Group16 (  Fe) has 1 elements

 




Select a group: 8

 

Selected 8: 'CHB-CHD'

 

new system size :  5.486 
5.648  6.394

 

shift  
: -0.110 -0.145 -0.026 (nm)

 

new center  : 
3.353  3.353  1.645 (nm)

 

new box vectors :  4.471 
4.471  4.563 (nm)

 

new box angles  : 
60.66  60.66  90.00 (degrees)

 

new box volume  : 
65.78   (nm^3)

 

 

 

Select a group for output:

 

Group 0 ( 
System) has  6370 elements

 

Group 1 (   
HEME) has47 elements

 

Group 2 (
SOL) has  6321 elements

 

Group 3 (
NA+) has 2 elements

 

Group 4 (  NA) has 1 elements

 

Group 5 (  NC) has 1 elements

 

Group 6 (
CHB) has 1 elements

 

Group 7 (
CHD) has 1 elements

 

Group 8 (
CHB-CHD) has 2 elements

 

Group 9 (  
Carb_ring) has 4 elements

 

Group10 (
CHC) has 1 elements

 

Group11 (
CHA) has 1 elements

 

Group12 ( 
nitrog) has 3 elements

 

Group13 (   
ow_teste) has 1 elements

 

Group14 (
HW1_HW2) has  4214 elements

 

Group15 (  OW) has  2107 elements

 

Group16 (  Fe) has 1 elements

 

Select a group: 0

 

Selected 0: 'System'

 

where CHB-CHD (molecular axis) must to coincide with the axis (X or Y).

My molecule is well centered and the box axis coincide with the molecular axis 
(chosen according to my interest)

The results are similar to make it in two steps
(1) g_densmap_d -f tmp-prueba.gro -n index.ndx -o tmp_prueba1.gro -princ(2) 
g_densmap_d -f tmp-prueba1.gro -n index.ndx -o tmp_prueba2.gro -c

The molecule was centered in every step simulation.

trjconv_mpi_d -s heme_centered.tpr -f dm10nsheme.xtc -o dm10nsheme_cent.xtc 
-center -boxcenter rect -pbc mol


The box was rotate to XY plane concide with the XY molecular plane in every 
step simulation

trjconv_mpi_d -s tmp_prueba2.gro -f dm10nsheme_cent.xtc -o 
dm10nsppix_cent_norotTrans.xtc -fit rot+trans



To obtain the XY density map

g_densmap_mpi_d -f  m10nsppix_cent_norotTrans.xtc -s tmp_prueba2.gro -n 
index.ndx -o tmpdensmaphemeXY.xpm
when I applied the g_densmap tool, there is not difference with my previous 
result. In the density map, my molecule appear in the corner, and white diffuse 
regions (maybe by the box rotations) appear.



I think the problem will be the way that I eliminate the rotations and 
translations.
But I don't have a clear idea of what I've done wrong

Regards

Ricardo
..
Please use a descriptive
subject line to help everybody.

 

I suspect 

[gmx-users] graphite and pi density

[Nilesh Dhumal]

Hello,

I want to put charge (as pi density) on each carbon atom at 1 A top and
below of each carbon atom of graphaite sheet. Basically I want put a atom,
X, with charge -0.5 and mass 0 at 0.5 A  below and above the carbon atom.

How can I do this?

Thanks

Nilesh










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[gmx-users] PCA

[pawan raghav]

I have a little concept problem regarding principal component analysis. So
my question is about ED sampling are as follows:

1. I have read from the manual that g_covar calculates and diagonalize the
(mass-weighted) covariance matrix. So what is the meaning of mass-weighted
in covariance matrix?

2. g_covar output the eigenval.xvg and and eigenvec.trr, but when I opened
the eigenval.xvg file it will shows nothing, i don't know what was wrong
with it?

3. what is the difference between covariance matrix and normal mode analysis
because both were used to generate the eigenval.xvg and eigenvec.trr file?

4. g_anaeig analyze the eigenvectors, so it is possible to fitted all the
structures generated at the time of simulations of single structure without
using the other structure?

I mean to say that it is possible to use single structure as initial to
simulate and ED sampling?

5. what is the need of eigenvec2.trr input file in g_anaeig to generate the
single number of covariance matrix as shown in manual? I have used to input
only one eigenvec.trr and eigenval.xvg, then it is right to do this?

6. I have used eigenval.xvg as input file in g_anaeig which do not shows
nothing when used to open in xmgrace. Then how this file used for generating
eigcomp.xvg, proj.xvg, eigrmsf.xvg, 2dproj.xvg, 3dproj.pdb (which I have
successfully generated).

7. One last question is related to g_analyze that it reads ascii file and
analyze data sets, but in actual it used some graph.xvg file as input. I am
confused about this graph.xvg file which file should I used for input to
calculate the cosine content of the principal components.

-- 
Pawan
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Re: [gmx-users] enegry minimisation

[Justin A. Lemkul]

sonali dhindwal wrote:

Thanks for your reply Justin,
this is rms for protein backbone, it is showing as 0.02
but when i check it in pymol by aligning two molecules rms is 0.256, and 
there is change in the structre of the protein.




Sounds like that's the same result (potentially).  Gromacs uses nm for RMSD, 
maybe PyMOL uses Angstrom?


Can you render an image and post it?  I can't really grasp what's happening 
without seeing it.  EM should not be making large changes to your structure, and 
a backbone RMSD of 0.02 nm does not sound like enough to cause serious 
distortion.  Instructions for sharing the image (should you choose to provide 
it) can be found here (bullet point #4):


http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette

-Justin


Regards
--
Sonali Dhindwal


--- On *Thu, 20/5/10, Justin A. Lemkul //* wrote:


From: Justin A. Lemkul 
Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users" 
Date: Thursday, 20 May, 2010, 6:46 PM



sonali dhindwal wrote:
 > Hello Gaurav,
 > when i did g_rms with structre before energy minimisation as
refrence and strucutre after energy minimisation, it came to be
around 0.02.
 >

Is that backbone RMSD or does it consider all protein atoms?  In
either case, a value of 0.02 indicates a very small amount of change
in the protein structure, which makes it very hard to believe that
any large-scale alteration of the secondary structure is happening.

-Justin

 > --
 > Sonali Dhindwal
 >
 >
 > --- On *Thu, 20/5/10, Gaurav Goel />/* wrote:
 >
 >
 > From: Gaurav Goel >
 > Subject: Re: [gmx-users] enegry minimisation
 > To: jalem...@vt.edu ,
"Discussion list for GROMACS users"
 > >
 > Date: Thursday, 20 May, 2010, 5:36 PM
 >
 > Can you try using g_rms to compare the difference between the
 > structures before and after EM.
 >
 > -Gaurav
 >
 > On Thu, May 20, 2010 at 7:53 AM, Justin A. Lemkul

 > >> wrote:
 >  >
 >  >
 >  > sonali dhindwal wrote:
 >  >>
 >  >> Hello Gaurav,
 >  >> Thanks for your reply,
 >  >> I did position restrained enegry minimisation, and used
 > following .mdp
 >  >> file for the same
 >  >>
 >  >> title = protein
 >  >> cpp = /usr/bin/cpp ; the c pre-processor
 >  >> define = -DPOSRE
 >  >> constraints = none
 >  >> integrator = steep
 >  >> dt = 0.002 ; ps !
 >  >> nsteps = 1000
 >  >> nstlist = 10
 >  >> ns_type = grid
 >  >> rlist = 0.9
 >  >> coulombtype = PME
 >  >> rcoulomb = 0.9
 >  >> rvdw = 0.9
 >  >> fourierspacing = 0.12
 >  >> fourier_nx = 0
 >  >> fourier_ny = 0
 >  >> fourier_nz = 0
 >  >> pme_order = 4
 >  >> ewald_rtol = 1e-5
 >  >> optimize_fft = yes
 >  >> ;
 >  >> ; Energy minimizing stuff
 >  >> ;
 >  >> emtol = 1000.0
 >  >> emstep = 0.01
 >  >> pbc = xyz
 >  >>
 >  >> I included define = -DPOSRE, for restraining the atom
postion,
 >  >> I used posre.itp which was genertaed by pdb2gmx.
 >  >>
 >  >> Have I done it correctly, because after this also many of the
 > beeta sheets
 >  >> have become short, forming loops.
 >  >
 >  > Well, you haven't properly defined position restraints.
The default
 >  > (produced by pdb2gmx) requires "define = -DPOSRES" not
"-DPOSRE."
 > If you
 >  > have for some reason modified the topology, then maybe your
 > approach is
 >  > correct, but otherwise your position restraints are not being
 > applied.
 >  >
 >  > I also find it very curious that such substantial changes are
 > taking place
 >  > during a simple energy minimization. Are you sure the
effects you are
 >  > seeing are not simply due to the visualization software
you are using
 >  > guessing the incorrect secondary structure type? I have
had that
 > experience
 >  > numerous times, especially in the case of beta-strands. DSSP
 > tells me that,
 >  > geometrically, I have beta-strands, but the visualization
 > software renders
 >  > coil structures.
 >  >
 >  > In any case, large structural deviations during EM suggest
something
 >  > fundamentally wrong with the model. Usually the changes in
EM are
 > small,
 >  > since it is performed at 0 K. Only huge forces would cause any
 > sort of
 >  > structural change.
 >  >
 >  >> I also want to ask what is the meaning of fx fy and fz :
 >  >>
 >  

Re: [gmx-users] enegry minimisation

[Justin A. Lemkul]

sonali dhindwal wrote:

Hello Gaurav,
when i did g_rms with structre before energy minimisation as refrence 
and strucutre after energy minimisation, it came to be around 0.02.




Is that backbone RMSD or does it consider all protein atoms?  In either case, a 
value of 0.02 indicates a very small amount of change in the protein structure, 
which makes it very hard to believe that any large-scale alteration of the 
secondary structure is happening.


-Justin


--
Sonali Dhindwal


--- On *Thu, 20/5/10, Gaurav Goel //* wrote:


From: Gaurav Goel 
Subject: Re: [gmx-users] enegry minimisation
To: jalem...@vt.edu, "Discussion list for GROMACS users"

Date: Thursday, 20 May, 2010, 5:36 PM

Can you try using g_rms to compare the difference between the
structures before and after EM.

-Gaurav

On Thu, May 20, 2010 at 7:53 AM, Justin A. Lemkul > wrote:
 >
 >
 > sonali dhindwal wrote:
 >>
 >> Hello Gaurav,
 >> Thanks for your reply,
 >> I did position restrained enegry minimisation, and used
following .mdp
 >> file for the same
 >>
 >> title = protein
 >> cpp = /usr/bin/cpp ; the c pre-processor
 >> define = -DPOSRE
 >> constraints = none
 >> integrator = steep
 >> dt = 0.002 ; ps !
 >> nsteps = 1000
 >> nstlist = 10
 >> ns_type = grid
 >> rlist = 0.9
 >> coulombtype = PME
 >> rcoulomb = 0.9
 >> rvdw = 0.9
 >> fourierspacing = 0.12
 >> fourier_nx = 0
 >> fourier_ny = 0
 >> fourier_nz = 0
 >> pme_order = 4
 >> ewald_rtol = 1e-5
 >> optimize_fft = yes
 >> ;
 >> ; Energy minimizing stuff
 >> ;
 >> emtol = 1000.0
 >> emstep = 0.01
 >> pbc = xyz
 >>
 >> I included define = -DPOSRE, for restraining the atom postion,
 >> I used posre.itp which was genertaed by pdb2gmx.
 >>
 >> Have I done it correctly, because after this also many of the
beeta sheets
 >> have become short, forming loops.
 >
 > Well, you haven't properly defined position restraints. The default
 > (produced by pdb2gmx) requires "define = -DPOSRES" not "-DPOSRE."
If you
 > have for some reason modified the topology, then maybe your
approach is
 > correct, but otherwise your position restraints are not being
applied.
 >
 > I also find it very curious that such substantial changes are
taking place
 > during a simple energy minimization. Are you sure the effects you are
 > seeing are not simply due to the visualization software you are using
 > guessing the incorrect secondary structure type? I have had that
experience
 > numerous times, especially in the case of beta-strands. DSSP
tells me that,
 > geometrically, I have beta-strands, but the visualization
software renders
 > coil structures.
 >
 > In any case, large structural deviations during EM suggest something
 > fundamentally wrong with the model. Usually the changes in EM are
small,
 > since it is performed at 0 K. Only huge forces would cause any
sort of
 > structural change.
 >
 >> I also want to ask what is the meaning of fx fy and fz :
 >>
 >
 > Force constants (kJ mol^-1 nm^-2) in the x, y, and z directions.
 >
 >> ; atom type fx fy fz
 >> 1 1 1000 1000 1000
 >> 5 1 1000 1000 1000
 >> 6 1 1000 1000 1000
 >> 7 1 1000 1000 1000
 >> 8 1 1000 1000 1000
 >> 9 1 1000 1000 1000
 >> 11 1 1000 1000 1000
 >> 12 1 1000 1000 1000
 >> 15 1 1000 1000 1000
 >> 18 1 1000 1000 1000
 >> 19 1 1000 1000 1000
 >> 20 1 1000 1000 1000
 >> 21 1 1000 1000 1000
 >> 22 1 1000 1000 1000
 >> 23 1 1000 1000 1000
 >>
 >> which is there in posre.itp file, and if these should have value
of 1000
 >> 1000 1000 each ?
 >>
 >
 > These default values are typically quite sufficient to restrain the
 > structure.
 >
 > -Justin
 >
 >> Thanks in advance.
 >> --
 >> Sonali Dhindwal
 >>
 >>
 >> --- On *Wed, 19/5/10, Gaurav Goel />/* wrote:
 >>
 >>
 >> From: Gaurav Goel >
 >> Subject: Re: [gmx-users] enegry minimisation
 >> To: "sonali dhindwal" >
 >> Date: Wednesday, 19 May, 2010, 8:39 PM
 >>
 >> For position restraints you need to do the following:
 >>
 >> 1. define a name.itp file which looks like:
 >>
 >> ; In this topology include file, you will find position restraint
 >> ; entries for all the heavy atoms in your original pdb file.
 >> ; This means that all the protons which were added by pdb2gmx are
 >> ; not restrained.
 >>
 >> [ position_restraints ]
 >> ; atom type fx fy fz
 >> 1 1 1000 1000 1000
 >> 5 1 1000 1000 1000
 >> 6 1 1000 1000 1000
 >> ...
 >> ...
 >> _
 >> 1,5,6 etc. are the atom indices you want to restrain. section 4.3.1
 >> in manual.

Re: [gmx-users] enegry minimisation

[sonali dhindwal]

Hello Gaurav,
when i did g_rms with structre before energy minimisation as refrence and 
strucutre after energy minimisation, it came to be around 0.02.

--
Sonali Dhindwal

--- On Thu, 20/5/10, Gaurav Goel  wrote:

From: Gaurav Goel 
Subject: Re: [gmx-users] enegry minimisation
To: jalem...@vt.edu, "Discussion list for GROMACS users" 
Date: Thursday, 20 May, 2010, 5:36 PM

Can you try using g_rms to compare the difference between the
structures before and after EM.

-Gaurav

On Thu, May 20, 2010 at 7:53 AM, Justin A. Lemkul  wrote:
>
>
> sonali dhindwal wrote:
>>
>> Hello Gaurav,
>> Thanks for your reply,
>> I did position restrained enegry minimisation, and used following .mdp
>> file for the same
>>
>> title=  protein
>> cpp  =  /usr/bin/cpp ; the c pre-processor
>> define   =  -DPOSRE
>> constraints  =  none
>> integrator   =  steep
>> dt   =  0.002; ps !
>> nsteps   =  1000
>> nstlist  =  10
>> ns_type  =  grid
>> rlist=  0.9
>> coulombtype  =  PME
>> rcoulomb =  0.9
>> rvdw =  0.9
>> fourierspacing   =  0.12
>> fourier_nx   =  0
>> fourier_ny   =  0
>> fourier_nz   =  0
>> pme_order=  4
>> ewald_rtol   =  1e-5
>> optimize_fft =  yes
>> ;
>> ;  Energy minimizing stuff
>> ;
>> emtol=  1000.0
>> emstep   =  0.01
>> pbc=  xyz
>>
>> I included define =  -DPOSRE, for restraining the atom postion,
>> I used posre.itp  which was genertaed by pdb2gmx.
>>
>> Have I done it correctly, because after this also many of the beeta sheets
>> have become short, forming loops.
>
> Well, you haven't properly defined position restraints.  The default
> (produced by pdb2gmx) requires "define = -DPOSRES" not "-DPOSRE."  If you
> have for some reason modified the topology, then maybe your approach is
> correct, but otherwise your position restraints are not being applied.
>
> I also find it very curious that such substantial changes are taking place
> during a simple energy minimization.  Are you sure the effects you are
> seeing are not simply due to the visualization software you are using
> guessing the incorrect secondary structure type?  I have had that experience
> numerous times, especially in the case of beta-strands.  DSSP tells me that,
> geometrically, I have beta-strands, but the visualization software renders
> coil structures.
>
> In any case, large structural deviations during EM suggest something
> fundamentally wrong with the model.  Usually the changes in EM are small,
> since it is performed at 0 K.  Only huge forces would cause any sort of
> structural change.
>
>> I also want to ask what is the meaning of fx fy and fz :
>>
>
> Force constants (kJ mol^-1 nm^-2) in the x, y, and z directions.
>
>> ; atom  type  fx  fy  fz
>> 1 1  1000  1000  1000
>> 5 1  1000  1000  1000
>> 6 1  1000  1000  1000
>> 7 1  1000  1000  1000
>> 8 1  1000  1000  1000
>> 9 1  1000  1000  1000
>>11 1  1000  1000  1000
>>12 1  1000  1000  1000
>>15 1  1000  1000  1000
>>18 1  1000  1000  1000
>>19 1  1000  1000  1000
>>20 1  1000  1000  1000
>>21 1  1000  1000  1000
>>22 1  1000  1000  1000
>>23 1  1000  1000  1000
>>
>> which is there in posre.itp file, and if these should have value of 1000
>> 1000 1000 each ?
>>
>
> These default values are typically quite sufficient to restrain the
> structure.
>
> -Justin
>
>> Thanks in advance.
>> --
>> Sonali Dhindwal
>>
>>
>> --- On *Wed, 19/5/10, Gaurav Goel //* wrote:
>>
>>
>>From: Gaurav Goel 
>>Subject: Re: [gmx-users] enegry minimisation
>>To: "sonali dhindwal" 
>>Date: Wednesday, 19 May, 2010, 8:39 PM
>>
>>For position restraints you need to do the following:
>>
>>1. define a name.itp file which looks like:
>>
>>; In this topology include file, you will find position restraint
>>; entries for all the heavy atoms in your original pdb file.
>>; This means that all the protons which were added by pdb2gmx are
>>; not restrained.
>>
>>[ position_restraints ]
>>; atom type fx fy fz
>>1 1 1000 1000 1000
>>5 1 1000 1000 1000
>>6 1 1000 1000 1000
>>...
>>...
>>_
>>1,5,6 etc. are the atom indices you want to restrain. section 4.3.1
>>in manual.
>>
>>2. Add "define = -Dname" to your mdp file
>>
>>3. Add following lines to your topology file
>>; Include Position restraint file
>>#ifdef name
>>#include "name.itp"
>>#endif
>>
>>4. compile and run.
>>
>>I'm sure you will find mroe information on position-restrain
>>simulation on gmx-users archive.
>>
>>-Gaurav
>>
>>On Wed, May 19, 2010 at 10:26 AM, sonali dhindwal
>>>> wrote:
>>
>>Hello Gaurav,
>>Can you please help me in suggesting where should I look for
>>providing parameter

Re: [gmx-users] Re: OPLS-AA/L force field

[Oliver Grant]

*If you are familiar to ambertools (tleap mainly), so you can create your
molecule there, save the amber parameters and use acpype to convert from
amber to gromacs format.

*Thanks Alan, I use tleap and then amb2gmx.pl. It works great, the only
problem is the NAc groups aren't restrained properly so have to manually
edit them in. I'll have to do some reading about acpype...


On 20 May 2010 13:28, Alan  wrote:

> Dear Oliver,
>
>
> On Thu, May 20, 2010 at 13:21,  wrote:
>
>> I'm using GLYCAM06, so it involves a bit more effort to generate a .top
>> and
>> .gro file than just using pdb2gmx but I thought I'd leave it out as I just
>> wanted to explain the method I use to include it. Apologies for the
>> confusion!
>>
>
> If you are familiar to ambertools (tleap mainly), so you can create your
> molecule there, save the amber parameters and use acpype to convert from
> amber to gromacs format.
>
> Alan
>
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <<
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>
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[gmx-users] Re: OPLS-AA/L force field

[Alan]

Dear Oliver,

On Thu, May 20, 2010 at 13:21,  wrote:

> I'm using GLYCAM06, so it involves a bit more effort to generate a .top and
> .gro file than just using pdb2gmx but I thought I'd leave it out as I just
> wanted to explain the method I use to include it. Apologies for the
> confusion!
>

If you are familiar to ambertools (tleap mainly), so you can create your
molecule there, save the amber parameters and use acpype to convert from
amber to gromacs format.

Alan

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] Re: acetonitrile from amber to gromacs

[Alan]

Nice, glad you did progress. See below.

On Thu, May 20, 2010 at 12:38,  wrote:

> thanks for your helpful hints. i updated acpype, created a pdb file with
> a single molecule and ran
>
> acpype -i ch3cn_210_single.pdb
>
> which generated an .itp and other interesting files. that's
> nice. (remember, i want to use gromacs with amber99sb force field and i
> downloaded 3 files from the amber site: ch3cn_210.pdb,
> frcmod.ch3cn,prep.ch3cn.have you ever seen their content?)
>
> 1) the charges do not match the ones listed in the prep.ch3cn file.
> shall i just change them by hand accordingly?
>

It doesn't match because it's using am1bcc, which was parametrised to
reproduce the RESP charges, but obviously (sqm is semi-empirical method, not
like gaussian)  it won't be accurate.

However, you're right, if you have the RESP charges in prep.ch3cn just copy
them by hand accordingly.

Or even better, if you want to learn more about the whole stuff, double
check if the parameters you got from the Manchester site are OK, why not
trying q4md-forcefieldtools.org/RED/? Once you got the charges (they should
be very close if not the same from  prep.ch3cn), you can use acpype just to
generate the topology by providing a c3n.MOL2 file with the charges
calculated by RED and then using "acpype -di c3n.mol2 -c user".


> 2) dummy atoms as listed in the prep.ch3cn are not present in the new
> .itp file.
>

I guess you don't know how a prep file works, so see
http://ambermd.org/doc/prep.html.


>  3) the force constants seem totally different. shall i again just adjust
> them to the original file obtained from the amber site?
>

If using acpype with default mode, so you'd get GAFF parameters. You may
want to try:

acpype -di c3n.mol2 -c user -a amber

However, it still may diff. If you read Jaime's paper and you agree with
what he did, so you can "copy&paste" his parameters as well.


>  is there another way of using acpype, with a proper args list, that i
> should use in this situation?
>

Read the Wikis in the acpype site and 'acpype -h'. I am always keen for
suggestions.

Another possible way, would be using tleap from AmberTools, generate just
one molecule, save parameters and use acpype to convert from amber to
gromacs, something like

acpype -p c3n.prmtop -x c3n.inpcrd

If doing so, you'd get the exactly Jaime's topology but in gromacs format
(gro and top file, not itp, so you may need to adjust things in the top file
in order to create a itp, but should be a simple task).

> BTW, how did you get this message "cannot find template for residue
> > C3N in our library"?
> i got that message *within* the following output when running:
> >acpype -i ch3cn_210.pdb
> [...]
> Warning: cannot find template for residue C3N in our library.
> You will not be able to save prmtop for this molecule.
> Warning: cannot find template for residue C3N in our library.
> You will not be able to save prmtop for this molecule.
> [gtkleap]$ #check C3N
> [gtkleap]$ saveamberparm C3N ch3cn_210_AC.prmtop ch3cn_210_AC.inpcrd
> Error: dparm pchg does not exist!
>
>
> ++end_quote+
> ERROR: Sleap failed
> ==> Removing temporary files...
> ACPYPE FAILED: [Errno 2] No such file or directory: 'ch3cn_210_AC.inpcrd'
> Total time of execution: 7s
>

Ah, ok, I should've know this... It's a fall back routine to try to use
'sleap', but sleap is broken in AmberTools 1.3 and 1.4, unfortunately.

Thanks for trying acpype.

Cheers,

Alan

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Re: OPLS-AA/L force field

[Oliver Grant]

*I guess that depends on what you mean by "works fine."  *

I mean the method of using pdb2gmx to generate a top and gro and then
appending the gro files and including the .itp files in the .top file, works
if you want to use two force fields. Originally I thought that was the
question.

*I guess it all depends on what you mean (below) by "non amber force field"*

I'm using GLYCAM06, so it involves a bit more effort to generate a .top and
.gro file than just using pdb2gmx but I thought I'd leave it out as I just
wanted to explain the method I use to include it. Apologies for the
confusion!

Oliver



-Justin

On 20 May 2010 13:00, Justin A. Lemkul  wrote:

>
>
> Oliver Grant wrote:
>
>> The force fields have to be compatible but this way works fine.
>>
>>
> I guess that depends on what you mean by "works fine."  If you mean that
> you can produce a stable simulation, then yes, it may "work," but I would
> question the underlying premise of combining different force fields.  If,
> for example, you're using an AMBER force field for, say, a protein, and OPLS
> for a small molecule, then what you're doing is wrong.  The combination
> rules required by both force fields are different, as are the underlying
> derivation schemes and quite possibly some more details I'm not thinking
> about at the moment.
>
> I guess it all depends on what you mean (below) by "non amber force field"
> and how different it is from the actual requirements of the AMBER force
> field you're using.  If this "non amber force field" was designed to be
> compatible with your chosen force field, and there was some suitable
> derivation scheme involved, then things will probably work.  If you're
> mixing and matching parameter sets, be prepared for very tough questions
> from any reviewers who see your work.
>
> -Justin
>
>  On 19 May 2010 12:50, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Oliver Grant wrote:
>>
>>Can you not run pdb2gmx for each of your molecules that you want
>>separate force fields for? Then cat the gro files, renumber and
>>include the molecule types as .itp files in the .top file as
>>below. If I'm doing anything wrong please let me know! :)
>>
>>
>>Combining different force fields into a single system completely
>>invalidates it, so yes, I'd say you're doing something wrong :)
>>
>>-Justin
>>
>>
>> ;
>>;This is your topology file
>>
>>;"What If None Of Your Dreams Come True ?" (E. Costello)
>>;
>>; Include forcefield parameters
>>#include "ffamber99sb.itp"
>>
>>[ atomtypes ]
>>
>>  
>> from
>>the top file of the non amber force field
>>;name  bond_typemasscharge   ptype  sigma
>>   epsilon
>>CYCY  0.  0.  A   3.39967e-01  4.57730e-01
>>O  O  0.  0.  A   2.95992e-01  8.78640e-01
>>HOHO  0.  0.  A   0.0e+00  0.0e+00
>>H1H1  0.  0.  A   2.47135e-01  6.56888e-02
>>O2O2  0.  0.  A   2.95992e-01  8.78640e-01
>>N  N  0.  0.  A   3.25000e-01  7.11280e-01
>>H2H2  0.  0.  A   2.29317e-01  6.56888e-02
>>OYOY  0.  0.  A   3.1e-01  7.11280e-01
>>HCHC  0.  0.  A   2.64953e-01  6.56888e-02
>>H  H  0.  0.  A   1.06908e-01  6.56888e-02
>>C  C  0.  0.  A   3.39967e-01  3.59824e-01
>>OSOS  0.  0.  A   3.1e-01  7.11280e-01
>>CGCG  0.  0.  A   3.39967e-01  4.57730e-01
>>OHOH  0.  0.  A   3.06647e-01  8.80314e-01
>>
>>#include
>>
>>  
>> "protein.itp"from
>>the top file of the amber force field, contains everything
>>usually specified here under [molecule types].
>>
>>; Include Position restraint file
>>#ifdef POSRES
>>#include "posre.itp"
>>#endif
>>
>>#ifdef POSRES_CA
>>#include "CA_posre.itp"
>>#endif
>>
>>#include
>>
>>  
>> "trisacc.itp"from
>>the top file of the non amber force field, contains charges etc.
>>
>>; Include Position restraint file
>>#ifdef POSRES_trisacc
>>#include "trisacc_posre.itp"
>>#endif
>>
>>; Include water topology
>>#include "ffamber_tip3p.itp"
>>
>>#ifdef POSRES_WATER
>>; Position restraint for each water oxygen
>>[ position_restraints ]
>>;  i funct   fcxfcyfcz
>

Re: [gmx-users] enegry minimisation

[Gaurav Goel]

Can you try using g_rms to compare the difference between the
structures before and after EM.

-Gaurav

On Thu, May 20, 2010 at 7:53 AM, Justin A. Lemkul  wrote:
>
>
> sonali dhindwal wrote:
>>
>> Hello Gaurav,
>> Thanks for your reply,
>> I did position restrained enegry minimisation, and used following .mdp
>> file for the same
>>
>> title            =  protein
>> cpp              =  /usr/bin/cpp ; the c pre-processor
>> define           =  -DPOSRE
>> constraints      =  none
>> integrator       =  steep
>> dt               =  0.002    ; ps !
>> nsteps           =  1000
>> nstlist          =  10
>> ns_type          =  grid
>> rlist            =  0.9
>> coulombtype      =  PME
>> rcoulomb         =  0.9
>> rvdw             =  0.9
>> fourierspacing   =  0.12
>> fourier_nx       =  0
>> fourier_ny       =  0
>> fourier_nz       =  0
>> pme_order        =  4
>> ewald_rtol       =  1e-5
>> optimize_fft     =  yes
>> ;
>> ;      Energy minimizing stuff
>> ;
>> emtol            =  1000.0
>> emstep           =  0.01
>> pbc            =  xyz
>>
>> I included define =  -DPOSRE, for restraining the atom postion,
>> I used posre.itp  which was genertaed by pdb2gmx.
>>
>> Have I done it correctly, because after this also many of the beeta sheets
>> have become short, forming loops.
>
> Well, you haven't properly defined position restraints.  The default
> (produced by pdb2gmx) requires "define = -DPOSRES" not "-DPOSRE."  If you
> have for some reason modified the topology, then maybe your approach is
> correct, but otherwise your position restraints are not being applied.
>
> I also find it very curious that such substantial changes are taking place
> during a simple energy minimization.  Are you sure the effects you are
> seeing are not simply due to the visualization software you are using
> guessing the incorrect secondary structure type?  I have had that experience
> numerous times, especially in the case of beta-strands.  DSSP tells me that,
> geometrically, I have beta-strands, but the visualization software renders
> coil structures.
>
> In any case, large structural deviations during EM suggest something
> fundamentally wrong with the model.  Usually the changes in EM are small,
> since it is performed at 0 K.  Only huge forces would cause any sort of
> structural change.
>
>> I also want to ask what is the meaning of fx fy and fz :
>>
>
> Force constants (kJ mol^-1 nm^-2) in the x, y, and z directions.
>
>> ; atom  type      fx      fy      fz
>>     1     1  1000  1000  1000
>>     5     1  1000  1000  1000
>>     6     1  1000  1000  1000
>>     7     1  1000  1000  1000
>>     8     1  1000  1000  1000
>>     9     1  1000  1000  1000
>>    11     1  1000  1000  1000
>>    12     1  1000  1000  1000
>>    15     1  1000  1000  1000
>>    18     1  1000  1000  1000
>>    19     1  1000  1000  1000
>>    20     1  1000  1000  1000
>>    21     1  1000  1000  1000
>>    22     1  1000  1000  1000
>>    23     1  1000  1000  1000
>>
>> which is there in posre.itp file, and if these should have value of 1000
>> 1000 1000 each ?
>>
>
> These default values are typically quite sufficient to restrain the
> structure.
>
> -Justin
>
>> Thanks in advance.
>> --
>> Sonali Dhindwal
>>
>>
>> --- On *Wed, 19/5/10, Gaurav Goel //* wrote:
>>
>>
>>    From: Gaurav Goel 
>>    Subject: Re: [gmx-users] enegry minimisation
>>    To: "sonali dhindwal" 
>>    Date: Wednesday, 19 May, 2010, 8:39 PM
>>
>>    For position restraints you need to do the following:
>>
>>    1. define a name.itp file which looks like:
>>
>>    ; In this topology include file, you will find position restraint
>>    ; entries for all the heavy atoms in your original pdb file.
>>    ; This means that all the protons which were added by pdb2gmx are
>>    ; not restrained.
>>
>>    [ position_restraints ]
>>    ; atom type fx fy fz
>>    1 1 1000 1000 1000
>>    5 1 1000 1000 1000
>>    6 1 1000 1000 1000
>>    ...
>>    ...
>>    _
>>    1,5,6 etc. are the atom indices you want to restrain. section 4.3.1
>>    in manual.
>>
>>    2. Add "define = -Dname" to your mdp file
>>
>>    3. Add following lines to your topology file
>>    ; Include Position restraint file
>>    #ifdef name
>>    #include "name.itp"
>>    #endif
>>
>>    4. compile and run.
>>
>>    I'm sure you will find mroe information on position-restrain
>>    simulation on gmx-users archive.
>>
>>    -Gaurav
>>
>>    On Wed, May 19, 2010 at 10:26 AM, sonali dhindwal
>>    >    > wrote:
>>
>>        Hello Gaurav,
>>        Can you please help me in suggesting where should I look for
>>        providing parameters to constrain the protein backbone and then
>>        do EM and then how to run a short MD simulation by constraining
>>        the protein backbone.
>>        Sorry to bother you, but as I am new to Gromacs, your help will
>>        be highly appreciable.
>>        Thanks in advance
>>
>>        --
>>        Sonali Dhindwal
>>
>>
>>        --- On *Wed, 19/5/10, Gaurav Goel

Re: [gmx-users] Re: OPLS-AA/L force field

[Justin A. Lemkul]

Oliver Grant wrote:

The force fields have to be compatible but this way works fine.



I guess that depends on what you mean by "works fine."  If you mean that you can 
produce a stable simulation, then yes, it may "work," but I would question the 
underlying premise of combining different force fields.  If, for example, you're 
using an AMBER force field for, say, a protein, and OPLS for a small molecule, 
then what you're doing is wrong.  The combination rules required by both force 
fields are different, as are the underlying derivation schemes and quite 
possibly some more details I'm not thinking about at the moment.


I guess it all depends on what you mean (below) by "non amber force field" and 
how different it is from the actual requirements of the AMBER force field you're 
using.  If this "non amber force field" was designed to be compatible with your 
chosen force field, and there was some suitable derivation scheme involved, then 
things will probably work.  If you're mixing and matching parameter sets, be 
prepared for very tough questions from any reviewers who see your work.


-Justin

On 19 May 2010 12:50, Justin A. Lemkul > wrote:




Oliver Grant wrote:

Can you not run pdb2gmx for each of your molecules that you want
separate force fields for? Then cat the gro files, renumber and
include the molecule types as .itp files in the .top file as
below. If I'm doing anything wrong please let me know! :)


Combining different force fields into a single system completely
invalidates it, so yes, I'd say you're doing something wrong :)

-Justin


 ;
;This is your topology file

;"What If None Of Your Dreams Come True ?" (E. Costello)
;
; Include forcefield parameters
#include "ffamber99sb.itp"

[ atomtypes ]

from
the top file of the non amber force field
;name  bond_typemasscharge   ptype  sigma
 epsilon

CYCY  0.  0.  A   3.39967e-01  4.57730e-01
O  O  0.  0.  A   2.95992e-01  8.78640e-01
HOHO  0.  0.  A   0.0e+00  0.0e+00
H1H1  0.  0.  A   2.47135e-01  6.56888e-02
O2O2  0.  0.  A   2.95992e-01  8.78640e-01
N  N  0.  0.  A   3.25000e-01  7.11280e-01
H2H2  0.  0.  A   2.29317e-01  6.56888e-02
OYOY  0.  0.  A   3.1e-01  7.11280e-01
HCHC  0.  0.  A   2.64953e-01  6.56888e-02
H  H  0.  0.  A   1.06908e-01  6.56888e-02
C  C  0.  0.  A   3.39967e-01  3.59824e-01
OSOS  0.  0.  A   3.1e-01  7.11280e-01
CGCG  0.  0.  A   3.39967e-01  4.57730e-01
OHOH  0.  0.  A   3.06647e-01  8.80314e-01

#include

"protein.itp"from
the top file of the amber force field, contains everything
usually specified here under [molecule types].

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

#ifdef POSRES_CA
#include "CA_posre.itp"
#endif

#include

"trisacc.itp"from
the top file of the non amber force field, contains charges etc.

; Include Position restraint file
#ifdef POSRES_trisacc
#include "trisacc_posre.itp"
#endif

; Include water topology
#include "ffamber_tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
  11   1000   1000   1000
#endif

; Include generic topology for ions
#include "Na_amber99sb.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_A   1
trisacc1
SOL 10697
Na  4



2010/5/19 you zou mailto:zou@live.com>
>>


   Hi Justin,

   Thank you for your help, But when I run x2top command there
is one
   error that is:
   "
   Can not find forcefield for atom C1-1 with 2 bonds
   Can not find forcefield for atom C4-4 with 2 bonds
   ...
   Program x2top, VERSION 4.0.5
   Source cod

Re: [gmx-users] enegry minimisation

[Justin A. Lemkul]

sonali dhindwal wrote:

Hello Gaurav,
Thanks for your reply,
I did position restrained enegry minimisation, and used following .mdp 
file for the same


title=  protein
cpp  =  /usr/bin/cpp ; the c pre-processor
define   =  -DPOSRE
constraints  =  none
integrator   =  steep
dt   =  0.002; ps !
nsteps   =  1000
nstlist  =  10
ns_type  =  grid
rlist=  0.9
coulombtype  =  PME
rcoulomb =  0.9
rvdw =  0.9
fourierspacing   =  0.12
fourier_nx   =  0
fourier_ny   =  0
fourier_nz   =  0
pme_order=  4
ewald_rtol   =  1e-5
optimize_fft =  yes
;
;  Energy minimizing stuff
;
emtol=  1000.0
emstep   =  0.01
pbc=  xyz

I included define =  -DPOSRE, for restraining the atom postion,
I used posre.itp  which was genertaed by pdb2gmx.

Have I done it correctly, because after this also many of the beeta 
sheets have become short, forming loops.


Well, you haven't properly defined position restraints.  The default (produced 
by pdb2gmx) requires "define = -DPOSRES" not "-DPOSRE."  If you have for some 
reason modified the topology, then maybe your approach is correct, but otherwise 
your position restraints are not being applied.


I also find it very curious that such substantial changes are taking place 
during a simple energy minimization.  Are you sure the effects you are seeing 
are not simply due to the visualization software you are using guessing the 
incorrect secondary structure type?  I have had that experience numerous times, 
especially in the case of beta-strands.  DSSP tells me that, geometrically, I 
have beta-strands, but the visualization software renders coil structures.


In any case, large structural deviations during EM suggest something 
fundamentally wrong with the model.  Usually the changes in EM are small, since 
it is performed at 0 K.  Only huge forces would cause any sort of structural change.



I also want to ask what is the meaning of fx fy and fz :



Force constants (kJ mol^-1 nm^-2) in the x, y, and z directions.


; atom  type  fx  fy  fz
 1 1  1000  1000  1000
 5 1  1000  1000  1000
 6 1  1000  1000  1000
 7 1  1000  1000  1000
 8 1  1000  1000  1000
 9 1  1000  1000  1000
11 1  1000  1000  1000
12 1  1000  1000  1000
15 1  1000  1000  1000
18 1  1000  1000  1000
19 1  1000  1000  1000
20 1  1000  1000  1000
21 1  1000  1000  1000
22 1  1000  1000  1000
23 1  1000  1000  1000

which is there in posre.itp file, and if these should have value of 1000 
1000 1000 each ?




These default values are typically quite sufficient to restrain the structure.

-Justin


Thanks in advance.
--
Sonali Dhindwal


--- On *Wed, 19/5/10, Gaurav Goel //* wrote:


From: Gaurav Goel 
Subject: Re: [gmx-users] enegry minimisation
To: "sonali dhindwal" 
Date: Wednesday, 19 May, 2010, 8:39 PM

For position restraints you need to do the following:

1. define a name.itp file which looks like:

; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained.

[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
5 1 1000 1000 1000
6 1 1000 1000 1000
...
...
_
1,5,6 etc. are the atom indices you want to restrain. section 4.3.1
in manual.

2. Add "define = -Dname" to your mdp file

3. Add following lines to your topology file
; Include Position restraint file
#ifdef name
#include "name.itp"
#endif

4. compile and run.

I'm sure you will find mroe information on position-restrain
simulation on gmx-users archive.

-Gaurav

On Wed, May 19, 2010 at 10:26 AM, sonali dhindwal
> wrote:

Hello Gaurav,
Can you please help me in suggesting where should I look for
providing parameters to constrain the protein backbone and then
do EM and then how to run a short MD simulation by constraining
the protein backbone.
Sorry to bother you, but as I am new to Gromacs, your help will
be highly appreciable.
Thanks in advance

--
Sonali Dhindwal


--- On *Wed, 19/5/10, Gaurav Goel />/* wrote:


From: Gaurav Goel >

Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users"
>
Date: Wednesday, 19 May, 2010, 6:44 PM


After adding water you can do energy minimization (EM) in
two steps:

1. Constrain the protein backbone and do EM.
2. Now do EM on the full system.
3. Run a short MD simulation by constraining the prot

Re: [gmx-users] Re: OPLS-AA/L force field

[Oliver Grant]

The force fields have to be compatible but this way works fine.

On 19 May 2010 12:50, Justin A. Lemkul  wrote:

>
>
> Oliver Grant wrote:
>
>> Can you not run pdb2gmx for each of your molecules that you want separate
>> force fields for? Then cat the gro files, renumber and include the molecule
>> types as .itp files in the .top file as below. If I'm doing anything wrong
>> please let me know! :)
>>
>
> Combining different force fields into a single system completely
> invalidates it, so yes, I'd say you're doing something wrong :)
>
> -Justin
>
>
>>  ;
>> ;This is your topology file
>>
>> ;"What If None Of Your Dreams Come True ?" (E. Costello)
>> ;
>> ; Include forcefield parameters
>> #include "ffamber99sb.itp"
>>
>> [ atomtypes ]
>> from
>> the top file of the non amber force field
>> ;name  bond_typemasscharge   ptype  sigma  epsilon
>> CYCY  0.  0.  A   3.39967e-01  4.57730e-01
>> O  O  0.  0.  A   2.95992e-01  8.78640e-01
>> HOHO  0.  0.  A   0.0e+00  0.0e+00
>> H1H1  0.  0.  A   2.47135e-01  6.56888e-02
>> O2O2  0.  0.  A   2.95992e-01  8.78640e-01
>> N  N  0.  0.  A   3.25000e-01  7.11280e-01
>> H2H2  0.  0.  A   2.29317e-01  6.56888e-02
>> OYOY  0.  0.  A   3.1e-01  7.11280e-01
>> HCHC  0.  0.  A   2.64953e-01  6.56888e-02
>> H  H  0.  0.  A   1.06908e-01  6.56888e-02
>> C  C  0.  0.  A   3.39967e-01  3.59824e-01
>> OSOS  0.  0.  A   3.1e-01  7.11280e-01
>> CGCG  0.  0.  A   3.39967e-01  4.57730e-01
>> OHOH  0.  0.  A   3.06647e-01  8.80314e-01
>>
>> #include
>> "protein.itp"from
>> the top file of the amber force field, contains everything usually specified
>> here under [molecule types].
>>
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre.itp"
>> #endif
>>
>> #ifdef POSRES_CA
>> #include "CA_posre.itp"
>> #endif
>>
>> #include
>> "trisacc.itp"from
>> the top file of the non amber force field, contains charges etc.
>>
>> ; Include Position restraint file
>> #ifdef POSRES_trisacc
>> #include "trisacc_posre.itp"
>> #endif
>>
>> ; Include water topology
>> #include "ffamber_tip3p.itp"
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct   fcxfcyfcz
>>   11   1000   1000   1000
>> #endif
>>
>> ; Include generic topology for ions
>> #include "Na_amber99sb.itp"
>>
>> [ system ]
>> ; Name
>> Protein in water
>>
>> [ molecules ]
>> ; Compound#mols
>> Protein_A   1
>> trisacc1
>> SOL 10697
>> Na  4
>>
>>
>>
>> 2010/5/19 you zou mailto:zou@live.com>>
>>
>>
>>Hi Justin,
>>
>>Thank you for your help, But when I run x2top command there is one
>>error that is:
>>"
>>Can not find forcefield for atom C1-1 with 2 bonds
>>Can not find forcefield for atom C4-4 with 2 bonds
>>...
>>Program x2top, VERSION 4.0.5
>>Source code file: x2top.c, line: 207
>>
>>Fatal error:
>>Could only find a forcefield type for 6 out of 24 atoms"
>>
>>I don't know how can I adjust this error.
>>I have one more question again, this command give me a top file, if
>>I want gro file of this pdb (drug that has removed from drug-enzyme
>>complex) how can I do that?
>>
>>you zou wrote:
>>> Dear Users,
>>> > I have one question about Drug-Enzyme Complex,Similar to
>> tutorial If I
>>
>>>
>>  want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug
>>   > but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg
>>   > Beta version" server too, or not?
>>
>>No. You can't use two different force fields in one simulation system.
>>
>>
>>
>>> If I can't use this server, how can I make .gro file and .itp file
>> for > drug that remove from initial .pdb file?
>>>
>>There are several programs in the User Contributions from the website,
>> x2top
>>
>>(which is distributed with Gromacs), or you can build the topology by
>> hand. No matter what you choose, you need a thorough understanding of
>> the mechanics of your chosen force field, methods of validation, and of
>> course Chapter 5 in the
>>
>>Gromacs manual.
>>
>>
>>Thanks
>>
>>
>>
>>  
>>Hotmail: Free, trusted and rich email service. Get it now.
>>

[gmx-users] g_bundle issue

[Anirban Ghosh]

Hi ALL,

I tried to calculate the helix tilt of a single helix (TM5) among 7 helices
using g_bundle. In the index file I defined the two groups (top & bottom) as
the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in
the bun_tilt.xvg file I am getting the values as:

---
# This file was created Thu May 20 15:29:50 2010
# by the following command:
# g_bundle -f prot.xtc -s prot.tpr -n TM5_top_bot.ndx -na 1
#
# g_bundle is part of G R O M A C S:
#
# GRowing Old MAkes el Chrono Sweat
#
@title "Axis tilts"
@xaxis  label "Time (ps)"
@yaxis  label "(degrees)"
@TYPE xy
  0  0
  2 0.0197823
  4  0
  6 0.0197823
  8  0
 10  0
 12 0.0197823
 14  0
 16 0.0197823
 18  0
 20 0.0279765
 22  0
 24  0
 26 0.0197823
 28  0
 30  0
 32  0
 34  0
 36  0
 38 0.0197823

And when plotted it gives a blank plot. Why it is coming like this? Am I
doing anything wrong? Any suggestion is welcome.
The contents of the index file is:

[ top ]
1844 1850 1858 1866 1878 1896 1904 1913 1922 1940 1948 1956 1965 1974 1983
1991
[ bottom ]
2000 2008 2014 2024 2032 2041 2050 2067 2079 2092 2101 2109 2118 2124 2132
2138 2146


Regards,

Anirban
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Re: [gmx-users] enegry minimisation

[sonali dhindwal]

Hello Gaurav,
Thanks for your reply,
I did position restrained enegry minimisation, and used following .mdp file for 
the same

title    =  protein
cpp  =  /usr/bin/cpp ; the c pre-processor
define   =  -DPOSRE
constraints  =  none
integrator   =  steep
dt   =  0.002    ; ps !
nsteps   =  1000
nstlist  =  10
ns_type  =  grid
rlist    =  0.9
coulombtype  =  PME
rcoulomb =  0.9
rvdw =  0.9
fourierspacing   =  0.12
fourier_nx   =  0
fourier_ny   =  0
fourier_nz   =  0
pme_order    =  4
ewald_rtol   =  1e-5
optimize_fft =  yes
;
;  Energy minimizing stuff
;
emtol    =  1000.0
emstep   =  0.01
pbc            =  xyz

I included define =  -DPOSRE, for restraining the atom postion,
I used posre.itp  which was genertaed by pdb2gmx.

Have I done it correctly, because after this also many of the beeta sheets have 
become short, forming loops.
I also want to ask what is the meaning of fx fy and fz :

; atom  type  fx  fy  fz
 1 1  1000  1000  1000
 5 1  1000  1000  1000
 6 1  1000  1000  1000
 7 1  1000  1000  1000
 8 1  1000  1000  1000
 9 1  1000  1000  1000
    11 1  1000  1000  1000
    12 1  1000  1000  1000
    15 1  1000  1000  1000
    18 1  1000  1000  1000
    19 1  1000  1000  1000
    20 1  1000  1000  1000
    21 1  1000  1000  1000
    22 1  1000  1000  1000
    23 1  1000  1000  1000

which is there in posre.itp file, and if these should have value of 1000 1000 
1000 each ?

Thanks in advance.
--
Sonali Dhindwal

--- On Wed, 19/5/10, Gaurav Goel  wrote:

From: Gaurav Goel 
Subject: Re: [gmx-users] enegry minimisation
To: "sonali dhindwal" 
Date: Wednesday, 19 May, 2010, 8:39 PM

For position restraints you need to do the following:

1. define a name.itp file which looks like:

; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.

; This means that all the protons which were added by pdb2gmx are
; not restrained.

[ position_restraints ]
; atom  type  fx  fy  fz
 1 1  1000  1000  1000
 5 1  1000  1000  1000

 6 1  1000  1000  1000
...
...
_
1,5,6 etc. are the atom indices you want to restrain. section 4.3.1 in manual.

2. Add  "define  =  -Dname" to your mdp file


3. Add following lines to your topology file
; Include Position restraint file
#ifdef name
#include "name.itp"
#endif

4. compile and run.

I'm sure you will find mroe information on position-restrain simulation on 
gmx-users archive.


-Gaurav

On Wed, May 19, 2010 at 10:26 AM, sonali dhindwal 
 wrote:


Hello Gaurav,
Can you please help me in suggesting where should I look for providing 
parameters to constrain the protein backbone and then do EM and then how to run 
a short MD simulation by constraining the protein backbone.

Sorry to bother you, but as I am new to Gromacs, your help will be highly 
appreciable.
Thanks in advance

--
Sonali Dhindwal

--- On Wed, 19/5/10, Gaurav Goel  wrote:


From: Gaurav Goel 

Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users" 
Date: Wednesday, 19 May, 2010, 6:44 PM


After adding water you can do energy minimization
 (EM) in two steps:

1. Constrain the protein backbone and do EM.
2. Now do EM on the full system.
3. Run a short MD simulation by constraining the protein backbone.

The above three steps will help hydrate the protein molecule with minimal 
distortion of protein structure.

4. Now run a MD on full system.

for details looks here:
http://www.google.com/url?sa=t&source=web&ct=res&cd=2&ved=0CBcQFjAB&url=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdf&ei=jOPzS8a3Lab2MdX1_aAO&usg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymg&sig2=bY3NqXHmruR7eSLVyAuCHQ



-Gaurav

On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal  
wrote:




Sorry, but I couldnt get your question,
I have used this .mdp file for energy minimisation after addition of water and 
using GROMOS96 43a1 force field :
title= drg_trp


cpp  = /lib/cpp ; location of cpp on SGI
define   = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4]
constraints  = none
integrator   = steep
dt   = 0.002; ps !


nsteps   =
 2000
nstlist  = 10
ns_type  = grid
rlist= 0.9
coulombtype  = PME ; Use particle-mesh ewald
rcoulomb = 0.9
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
;
;   Energy minimizing stuff
;
emtol   =
 1000.0
emstep  = 0.01

I hope it will help you to guide me further
Thanks
--
Sonali Dhindwal

--- On Wed, 19/5/10, Erik Marklund  wrote:



From: Erik Marklund

Re: [gmx-users] adding constraints

[Justin A. Lemkul]

subarna thakur wrote:

Hi all,
I want to add constraints for bond length of a ligand.Where do I place 
the constraints statement in the .rtp file or in the .top file? 
 


Are you looking to constrain only one single bond length?  If so, just add a 
[constraints] section to your topology.  The .rtp file won't do you any good, 
unless you're looking to build a complete .rtp entry and re-process with 
pdb2gmx, but I don't know if [constraints] is a valid entry in an .rtp file.


If you're looking to constrain all bond lengths, leave the topology alone and 
add "constraints = all-bonds" in your .mdp file.


-Justin


Subarna Thakur



--


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] Charge assignment

[Justin A. Lemkul]

Michael McGovern wrote:

Hi everyone.

  I'm working on getting parameters for a protein system that has some 
linker residues in it.  These linkers are nothing too strange, they just 
have some amine groups.  I can get bonded parameters from the prodrg 
server.  I know the charge groups are unreliable.  I'm using the 53A6 
parameter set, and I read how the charges there were derived.  They 
specifically did the iteration of parameters manually to give the same 
charges for the same functional groups.  Does this mean I can take 
charges from the same functional groups in the rtp files for amino acids 
and use those charges in my linkers?  If it is necessary to validate, 
should that be done on the linkers as molecules in their acidic, 
unlinked form?  
Thanks everyone.





Generally, the functional groups in the GROMOS parameter sets are very 
transferrable, as their derivation scheme would suggest.  I suppose about the 
only validation you could do would be to prove that the properties of your 
linker molecules (whatever they may be) are reproduced by the application of 
these parameters when not joined to your protein.  Reproduction of 
condensed-phase behavior and thermodynamic properties was the goal of the GROMOS 
derivation.


-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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Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] breaking down total energy

[Justin A. Lemkul]

Moeed wrote:

Hello Justin,

Thanks for your comments. Actually, since I am interested in only 
interaction energies *between* molecules I thought by excluding energies 
between atoms on a single chain what I get from nonbonded interactions 
would not include 1-4 interactions.




OK, I see what you're doing, your approach was just wrong.  The simplest thing 
to do is the following.  First, run a normal MD simulation, no fancy exclusions 
or anything, until you have produced a stable hexane system that reproduces 
whatever observable quantities you have decided upon.  Know what you're looking 
for first!


Then, modify the topology to add the exclusions you want.  It is a whole lot 
easier to simply increase the number given in nrexcl within the [moleculetype] 
definition to take care of all possible interactions than anything else. 
There's nothing wrong with doing it manually (somewhere *after* the atoms have 
been defined, but before the end of the [moleculetype] definition), it's just 
more work.


There is no need for special energygrps or energygrp_excl for your purpose, 
since those exclusions are applied to intermolecular interactions, not 
intramolecular interactions, and they are not dependent upon [exclusions] 
defined in the topology.


Once you have a suitably modified topology, use mdrun -rerun on the original 
trajectory.


-Justin


*
This is from previous posts:

Question: Can I not take for
instance LJ energy values which are coming from a specific NO. of molecuels
in simulation box and calculate interaction energies for pairs or "mol"
number of molecules?

Your answer:

Not easily.  You will still have intramolecular terms that are not 
covered by
the 1-4 interactions.  *For example, if the two ends of your molecule 
interact
with one another, this interaction will contribute to your nonbonded 
energies.*

*
That is why I thought I have to exclude interaction in a single chain 
between atoms, so that for instance atoms 1 and 20 do not see each other.


I manual I found only about how extra exlusion within a molecue cab 
added in [exclusions].. I dont think this helps me.


How can I define all possible intramolecular exclusions in order to save 
only intermolecular energy contributions?



top file:

Include forcefield parameters

#include "ffoplsaa.itp"

[ moleculetype ]
; Namenrexcl
Hexane  3

[ exclusions ]
??

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
chargeB  massB
 1   opls_157  1HEX C1  1  -0.18 12.011   ; qtot 
-0.18
 2   opls_140  1HEXH11  1   0.06  1.008   ; qtot 
-0.12
 3   opls_140  1HEXH12  1   0.06  1.008   ; qtot 
-0.06
 4   opls_140  1HEXH13  1   0.06  1.008   ; qtot 0
 5   opls_158  1HEX C2  2  -0.12 12.011   ; qtot 
-0.12
 6   opls_140  1HEXH21  2   0.06  1.008   ; qtot 
-0.06
 7   opls_140  1HEXH22  2   0.06  1.008   ; qtot 0
 8   opls_158  1HEX C3  3  -0.12 12.011   ; qtot 
-0.12
 9   opls_140  1HEXH31  3   0.06  1.008   ; qtot 
-0.06
10   opls_140  1HEXH32  3   0.06  1.008   ; qtot 0
11   opls_158  1HEX C4  4  -0.12 12.011   ; qtot 
-0.12
12   opls_140  1HEXH41  4   0.06  1.008   ; qtot 
-0.06
13   opls_140  1HEXH42  4   0.06  1.008   ; qtot 0
14   opls_158  1HEX C5  5  -0.12 12.011   ; qtot 
-0.12
15   opls_140  1HEXH51  5   0.06  1.008   ; qtot 
-0.06
16   opls_140  1HEXH52  5   0.06  1.008   ; qtot 0
17   opls_157  1HEX C6  6  -0.18 12.011   ; qtot 
-0.18
18   opls_140  1HEXH61  6   0.06  1.008   ; qtot 
-0.12
19   opls_140  1HEXH62  6   0.06  1.008   ; qtot 
-0.06
20   opls_140  1HEXH63  6   0.06  1.008   ; qtot 0

[ bonds ]
;  aiaj functc0c1c2c3
1 2 1 
1 3 1 
1 4 1 
1 5 1 
5 6 1 
5 7 1 
5 8 1 
8 9 1 
810 1 
811 1 
   1112 1 
   1113 1 
   1114 1 
   1415 1 
   1416 1 
   1417 1 
   1718 1 
   1719 1 
   1720 1 


[ pairs ]
;  aiaj functc0c1c2c3
1 9 1 
110 1 
111 1 
2 6 1 
2 7 1 
2 8 1 
3 6 1 
3 7 1 
3 8 1 

[gmx-users] g_helixorient issue

[Anirban Ghosh]

Hi ALL,

I am trying to find out the tilt of a helix during a simulation. I am using
g_helixorient with the -otilt option. However I am getting the following
output, which when plotted using xmgrace, gives a straight along y=0.
---
#
# g_helixorient is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@title "Cumulative local helix tilt"
@xaxis  label "Time(ps)"
@yaxis  label "Tilt (degrees)"
@TYPE xy
  2 03.595408201224.23953723907
5.74576044083 5.64022207262.993204355243.96751046181
6.915472984316.317507743845.708302021031.80687570572
7.904520511635.554297924044.3107757568413.4955091476
10.86933803566.696783542631.318642735488.81209087372
15.092011451716.443498611513.575768470812.6605091095
9.89414119725.959523200992.222523212434.23878717422
11.912554740915.239257812510.13733291632.50473761559
2.987089633940
  4 0   0.1932501047851.85375285149
4.660104274755.734657764433.596650362013.71966171265
5.862170696265.205702304844.286367416385.67181348801
11.8561506271 10.8149480825.253306865693.01665711403
3.188149690636.1265802383410.878685951213.1984567642
15.8662624359 17.9544162759.977549552923.82837629318
7.255657672884.875072002413.158228397375.81644439697
6.565203189857.591495513925.399117946622.35803961754
4.941868305210
  6.0047684 02.78084087372 2.5538725853
3.536648511898.4336194992114.915288925213.8589410782
6.6992340087911.7872600555 17.235452652 10.804684639
12.89069366468.979190826425.7719144821210.7680120468
9.713017463688.8874626159711.251163482710.2795152664
8.691395759587.554894447333.242376565931.74266982079
2.973826408394.069952487953.690156698232.21045541763
2.921667337424.463324546814.281089782713.39760541916
4.103402614590
  8 0 5.4110045433 5.6742272377
8.93139266968  11.787487038.761271476755.92636489868
2.527382135396.2623438835110.01829242712.88692927361
8.243747711184.966527462018.7450408935517.1016178131
14.6491327286 8.43484878549.4807758331311.1341199875
11.373338699314.302871704112.88017845157.42469358444
3.84174942974.058297157291.937186241152.07590007782
6.721652030949.818412780769.60572147369 6.2793135643
4.37946939468
---

How to visualize this file properly? Why is the .xvg file written in this
manner? Any suggestion is welcome.

Regards,

Anirban
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Re: [gmx-users] Re: Re: energy decreasing in NVE simulation

[Tsjerk Wassenaar]

Hi Yun-an Yan,

In addition to the other things, COMM removal is also a source of
energy drift. It is better to center your solute afterwards.

Cheers,

Tsjerk

On Thu, May 20, 2010 at 1:05 PM, Yan Yun-an  wrote:
> Dear Erik,
>
> Thank you so much for your prompt reply. I appreciate it.
>
> Yun-an Yan
>
> Erik Marklund writes:
>
>>For more exotic NVE-systems I had to do some or several of the following
>
>>things to get stable Etot:
>
>>* have an even shorter timestep than one would expect from the applied
>>constraints and such.
>
> I will try a timestep with 0.5 fs.
>
>>* use double precision.
>
> The double precision is already in use.
>
>>* apply the constraints with lower tolerance/more iterations etc.
>
> I thought shake_tol = 1.e-8 is small enough. May I try an even smaller
> value?
>
> Or the lincs algorithm with lincs_order=8 and lincs_iter=2 is recommended
>
> instead of shake?
>
>>Then there's a few things I notice in your setup:
>>* I see that you do not use constrints at all. I would give it a shot.
>
> I will try.
>
>>* Why do you have two separate comm-grps?
>
> Since it is a solute-solvent fashion MD, I am trying to keeping the solute
>
> part close the center of the simulation box. But it does not work in this
> way.
>
> Do you have any idea about that?
>
>>Erik Marklund
>>
>>--
>>---
>>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
>>erikm at xray.bmc.uu.sehttp://folding.bmc.uu.se/
>
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
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[gmx-users] Re: Re: energy decreasing in NVE simulation

[Yan Yun-an]

Dear Erik,

Thank you so much for your prompt reply. I appreciate it.

Yun-an Yan

Erik Marklund writes:

>For more exotic NVE-systems I had to do some or several of the  
following


>things to get stable Etot:

>* have an even shorter timestep than one would expect from the applied
>constraints and such.

I will try a timestep with 0.5 fs.
>* use double precision.
The double precision is already in use.
>* apply the constraints with lower tolerance/more iterations etc.
I thought shake_tol = 1.e-8 is small enough. May I try an even  
smaller value?
Or the lincs algorithm with lincs_order=8 and lincs_iter=2 is  
recommended

instead of shake?
>Then there's a few things I notice in your setup:
>* I see that you do not use constrints at all. I would give it a shot.
I will try.

>* Why do you have two separate comm-grps?
Since it is a solute-solvent fashion MD, I am trying to keeping the  
solute
part close the center of the simulation box. But it does not work in  
this way.

Do you have any idea about that?

>Erik Marklund
>
>--
>---
>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
>erikm at xray.bmc.uu.sehttp://folding.bmc.uu.se/
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Re: [gmx-users] Re: acetonitrile from amber to gromacs

[vedat durmaz]

Alan schrieb:
> Dear Vedat,
>
> On Wed, May 19, 2010 at 20:36,  > wrote:
>
> @rui
> acpypi -i ch3cn_210.pdb
> says: "cannot find template for residue C3N in our library". and
> indeed,
> there's no residue C3N in my ffamber99sb.rtp file
>
> (and i don't know, how to use it in order to generate my topology
> or even
> an rtp file?!)
>
>
> Have a bit of patience and try to read a bit more about ACPYPE.
>
> 1) Read the info there, I am sure you'll find it useful;
> 2) You'll learn that you need to have just one molecule in a pdb and
> not the whole box if you want the topologi of C3N.
> 3) It took me 2s to get the topology with acpype but months to write
> the code, so if you'd take some few minutes to read and use an updated
> version (it's not acpypi anymore BTW)...
>
thanks for your helpful hints. i updated acpype, created a pdb file with
a single molecule and ran

acpype -i ch3cn_210_single.pdb

which generated an .itp and other interesting files. that's
nice. (remember, i want to use gromacs with amber99sb force field and i
downloaded 3 files from the amber site: ch3cn_210.pdb,
frcmod.ch3cn,prep.ch3cn.have you ever seen their content?)

1) the charges do not match the ones listed in the prep.ch3cn file.
shall i just change them by hand accordingly?
2) dummy atoms as listed in the prep.ch3cn are not present in the new
.itp file.
3) the force constants seem totally different. shall i again just adjust
them to the original file obtained from the amber site?

is there another way of using acpype, with a proper args list, that i
should use in this situation?

i know, that's many questions, but is has to be done!

> BTW, how did you get this message "cannot find template for residue
> C3N in our library"?
i got that message *within* the following output when running:
>acpype -i ch3cn_210.pdb
[...]
Warning: cannot find template for residue C3N in our library.
 You will not be able to save prmtop for this molecule.
Warning: cannot find template for residue C3N in our library.
 You will not be able to save prmtop for this molecule.
[gtkleap]$ #check C3N
[gtkleap]$ saveamberparm C3N ch3cn_210_AC.prmtop ch3cn_210_AC.inpcrd
Error: dparm pchg does not exist!

++end_quote+
ERROR: Sleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'ch3cn_210_AC.inpcrd'
Total time of execution: 7s


>
> acpype.googlecode.com 
>
> Regards,
> Alan
>
> -- 
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <<
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Re: [gmx-users] Essential Dynamics

[Luca Mollica]

On 05/20/2010 10:40 AM, Carla Jamous wrote:

Hi everyone,

Please I need a piece of information not related to gromacs.
I'm searching for a document or article that may explain Essential 
Dynamics to beginners.


Thanks
Carla


and of course, in a more practical way:

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

L


--



--



Luca Mollica
Protein Dynamics and Flexibility by NMR
Institut de Biologie Structurale
41 Rue Jules Horowitz
Grenoble
38027
France

E-mail: luca.moll...@ibs.fr (lucamoll...@gmail.com)

Telephone: +33.438783889


--


Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a pack of 
cigarettes, it's dark, and we're wearing sunglasses.
Jake: Hit it.

(The Blues Brothers)

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Re: [gmx-users] Essential Dynamics

[Luca Mollica]

On 05/20/2010 10:40 AM, Carla Jamous wrote:

Hi everyone,

Please I need a piece of information not related to gromacs.
I'm searching for a document or article that may explain Essential 
Dynamics to beginners.


Thanks
Carla


http://www.ncbi.nlm.nih.gov/pubmed/8108382
AKA "how the molecular dynamics simulations were decomposed into 
essential motions for the first time".
I don't know if it's suitable for beginners or not: for sure it 
represents the begin of the story ...

:)


Luca


--



--



Luca Mollica
Protein Dynamics and Flexibility by NMR
Institut de Biologie Structurale
41 Rue Jules Horowitz
Grenoble
38027
France

E-mail: luca.moll...@ibs.fr (lucamoll...@gmail.com)

Telephone: +33.438783889


--


Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a pack of 
cigarettes, it's dark, and we're wearing sunglasses.
Jake: Hit it.

(The Blues Brothers)

--
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[gmx-users] Essential Dynamics

[Carla Jamous]

Hi everyone,

Please I need a piece of information not related to gromacs.
I'm searching for a document or article that may explain Essential Dynamics
to beginners.

Thanks
Carla
-- 
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[gmx-users] g_helixorient issue

[Anirban Ghosh]

Hi ALL,

I am trying to find out the tilt of a helix during a simulation. I am using
g_helixorient with the -otilt option. However I am getting the following
output, which when plotted using xmgrace, gives a straight along y=0.
---
#
# g_helixorient is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@title "Cumulative local helix tilt"
@xaxis  label "Time(ps)"
@yaxis  label "Tilt (degrees)"
@TYPE xy
  2 03.595408201224.23953723907
5.74576044083 5.64022207262.993204355243.96751046181
6.915472984316.317507743845.708302021031.80687570572
7.904520511635.554297924044.3107757568413.4955091476
10.86933803566.696783542631.318642735488.81209087372
15.092011451716.443498611513.575768470812.6605091095
9.89414119725.959523200992.222523212434.23878717422
11.912554740915.239257812510.13733291632.50473761559
2.987089633940
  4 0   0.1932501047851.85375285149
4.660104274755.734657764433.596650362013.71966171265
5.862170696265.205702304844.286367416385.67181348801
11.8561506271 10.8149480825.253306865693.01665711403
3.188149690636.1265802383410.878685951213.1984567642
15.8662624359 17.9544162759.977549552923.82837629318
7.255657672884.875072002413.158228397375.81644439697
6.565203189857.591495513925.399117946622.35803961754
4.941868305210
  6.0047684 02.78084087372 2.5538725853
3.536648511898.4336194992114.915288925213.8589410782
6.6992340087911.7872600555 17.235452652 10.804684639
12.89069366468.979190826425.7719144821210.7680120468
9.713017463688.8874626159711.251163482710.2795152664
8.691395759587.554894447333.242376565931.74266982079
2.973826408394.069952487953.690156698232.21045541763
2.921667337424.463324546814.281089782713.39760541916
4.103402614590
  8 0 5.4110045433 5.6742272377
8.93139266968  11.787487038.761271476755.92636489868
2.527382135396.2623438835110.01829242712.88692927361
8.243747711184.966527462018.7450408935517.1016178131
14.6491327286 8.43484878549.4807758331311.1341199875
11.373338699314.302871704112.88017845157.42469358444
3.84174942974.058297157291.937186241152.07590007782
6.721652030949.818412780769.60572147369 6.2793135643
4.37946939468
---

How to visualize this file properly? Why is the .xvg file written in this
manner? Any suggestion is welcome.

Regards,

Anirban
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Re: [gmx-users] DSSP

[Carsten Kutzner]

Hi Shahid,

I have fixed the problem in do_dssp. You can either pull the
newest release-4-0-patches branch from the git repository
or change ./src/tools/do_dssp.c, line 80 from

snew(ssbuf,nres+10); 

to:

snew(ssbuf, 2*nres-1);


Carsten



On May 19, 2010, at 9:48 AM, Carsten Kutzner wrote:

> Hi,
> 
> there was a problem in do_dssp when used on proteins with more
> than 10 chains. Is this the case? I just saw that I
> only fixed that in the head, but not in 4.0.x.  
> 
> Carsten
> 
> 
> 
> On May 18, 2010, at 3:49 PM, shahid nayeem wrote:
> 
>> Hi
>> When I run  dssp alone with a .pdb file it works well. But when I run with 
>> Gromacs as do_dssp it gives segmentation fault and does not do any 
>> calculation except giving some intermediate files as follows.
>> 
>> Opening library file /usr/local/gromacs/share/gromacs/top/ss.map
>> Reading frame   0 time0.000
>> Warning: if there are broken molecules in the trajectory file,
>> they can not be made whole without a run input file
>> 
>> 
>> Back Off! I just backed up dd8G1JXX to ./#dd8G1JXX.1#
>> Segmentation fault
>> 
>> shahid 
>> 
>> 
>> 
>> On 5/18/10, Justin A. Lemkul  wrote:
>> 
>> 
>> shahid nayeem wrote:
>> Hi
>> After posting this mail I did some google search and after changing the 
>> executible name to dssp I moved it in /usr/local/bin/ After this when I did 
>> do_dssp it starts running asks to select a group I choose main chain 5, then 
>> it generates some intermediate file and gives error as segmentation fault. I 
>> though this problem was because of the executible in /usr/local/bin/ and 
>> rest of file in another directory say /home/shahid/software/dssp/. For this 
>> first I set the path in ~/.bascrc 
>> 
>> Other files should be irrelevant.  The only file you need is the dssp binary.
>> 
>> as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got 
>> the same intermediate file generated backing up the previous one. 
>> 
>> Intermediate files are not an issue.  When the executable is in this 
>> directory, does the calculation otherwise work?
>> 
>> Then I moved all the files of dssp directory to /usr/local/bin/ and then 
>> tried to run do_dssp I am in the same situation.
>> 
>> If the executable in your home directory structure works, but in 
>> /usr/local/bin it fails, then it could be some sort of permission error.  It 
>> ultimately doesn't matter where your executable is, /usr/local/bin is 
>> default, but you can set any other location you like with the DSSP 
>> environment variable.
>> 
>> -Justin
>> 
>> waiting for your help
>> shahid nayeem
>> 
>> On 5/18/10, *Justin A. Lemkul* mailto:jalem...@vt.edu>> 
>> wrote:
>> 
>> 
>> 
>>   shahid nayeem wrote:
>> 
>>   Dear All
>>   I downloaded dsspcmbi.tar.gz, and compiled  using command
>>   ./DsspCompileGCC as given in Readme.txt file. when I try to run
>>   do_dssp command in gromacs I get error
>> 
>> 
>>   Well, what happened?
>> 
>> 
>>   Fatal error:
>>   DSSP executable (/usr/local/bin/dssp) does not exist (use setenv
>>   DSSP)
>> 
>>   I checked for DSSP executible in /usr/local/bin/ and I couldnt
>>   find. I
>> 
>> 
>>   It won't be there unless you put it there and you have re-named it.
>>I believe the default name of the dssp program is "dsspcmbi," which
>>   you need to change when you move the executable.
>> 
>>   http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp
>> 
>>   -Justin
>> 
>>   even tried dsspcmbi.zip file but again I got the same error. I
>>   compiled dssp as root. Now what shoul I do in order to run do_dssp
>>   comand of gromacs.
>>   Shahid nayeem
>> 
>> 
>>   -- 
>> 
>>   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/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/mailing_lists/users.php
>> 
>> 
>> 
>> -- 
>> 
>> 
>> 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.groma

Re: [gmx-users] asking help for simulation of protein in 8M urea

[Tsjerk Wassenaar]

Hi Caty,

In addition to Luca's comments, also consider what you mean with 8M.
Molarity is defined as mole per liter, but the addition of urea may
have an effect on the volume, such that adding a volume x urea to a
volume y water does not yield a volume x+y. Especially with such high
concentrations you might be better off with molalities (mole/kg).
Then you probably want to first generate a box of urea in water by
adding a adding a box of water to a box of urea and letting it diffuse
(at a high temperature). But only after you figured out the answers to
Luca's questions :)

Cheers,

Tsjerk

On Thu, May 20, 2010 at 9:32 AM, Luca Mollica  wrote:
> On 05/20/2010 09:05 AM, caty hacker wrote:
>>
>> Dear all,
>>            I want to a protein simulation in 8M urea. Can anyone suggest
>> me any introductory tutorial on that. Thank you in advance.
>
> I think a "tutorial" is useless for such a simulation. Papers are the best
> reference depending on what you want to simulate
> and on what you want to "see": if you are trying to simulate the unfolding
> there are several publications that discuss the major issues of the field,
> i.e.
>
> a. which ff and/or urea topology to use
> b. which computational technique (REMD, MD, MetaMD ...) to use
>
> So ... what's your goal ? :)
> At the moment I am too working on some systems that require the usage of
> urea and doing a bit of set up for AMBER FF, whereas in the past I have used
> a
> topology for the last GROMOS FF.
>
> Cheers
>
> Luca
>
>
> --
>
> 
>
> --
>
>
>
> Luca Mollica
> Protein Dynamics and Flexibility by NMR
> Institut de Biologie Structurale
> 41 Rue Jules Horowitz
> Grenoble
> 38027
> France
>
> E-mail: luca.moll...@ibs.fr (lucamoll...@gmail.com)
>
> Telephone: +33.438783889
>
>
> --
>
>
> Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a pack of
> cigarettes, it's dark, and we're wearing sunglasses.
> Jake: Hit it.
>
> (The Blues Brothers)
>
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> or send it to gmx-users-requ...@gromacs.org.
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
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[gmx-users] g_helixorient issue

[Anirban Ghosh]

Hi ALL,

I am trying to find out the tilt of a helix during a simulation. I am using
g_helixorient with the -otilt option. However I am getting the following
output, which when plotted using xmgrace, gives a straight along y=0.
---
#
# g_helixorient is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@title "Cumulative local helix tilt"
@xaxis  label "Time(ps)"
@yaxis  label "Tilt (degrees)"
@TYPE xy
  2 03.595408201224.23953723907
5.74576044083 5.64022207262.993204355243.96751046181
6.915472984316.317507743845.708302021031.80687570572
7.904520511635.554297924044.3107757568413.4955091476
10.86933803566.696783542631.318642735488.81209087372
15.092011451716.443498611513.575768470812.6605091095
9.89414119725.959523200992.222523212434.23878717422
11.912554740915.239257812510.13733291632.50473761559
2.987089633940
  4 0   0.1932501047851.85375285149
4.660104274755.734657764433.596650362013.71966171265
5.862170696265.205702304844.286367416385.67181348801
11.8561506271 10.8149480825.253306865693.01665711403
3.188149690636.1265802383410.878685951213.1984567642
15.8662624359 17.9544162759.977549552923.82837629318
7.255657672884.875072002413.158228397375.81644439697
6.565203189857.591495513925.399117946622.35803961754
4.941868305210
  6.0047684 02.78084087372 2.5538725853
3.536648511898.4336194992114.915288925213.8589410782
6.6992340087911.7872600555 17.235452652 10.804684639
12.89069366468.979190826425.7719144821210.7680120468
9.713017463688.8874626159711.251163482710.2795152664
8.691395759587.554894447333.242376565931.74266982079
2.973826408394.069952487953.690156698232.21045541763
2.921667337424.463324546814.281089782713.39760541916
4.103402614590
  8 0 5.4110045433 5.6742272377
8.93139266968  11.787487038.761271476755.92636489868
2.527382135396.2623438835110.01829242712.88692927361
8.243747711184.966527462018.7450408935517.1016178131
14.6491327286 8.43484878549.4807758331311.1341199875
11.373338699314.302871704112.88017845157.42469358444
3.84174942974.058297157291.937186241152.07590007782
6.721652030949.818412780769.60572147369 6.2793135643
4.37946939468
---

How to visualize this file properly? Why is the .xvg file written in this
manner? Any suggestion is welcome.

Regards,

Anirban
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[gmx-users] adding constraints

[subarna thakur]

Hi all,
I want to add constraints for bond length of a ligand.Where do I place the 
constraints statement in the .rtp file or in the .top file? 
 Subarna Thakur


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Re: [gmx-users] asking help for simulation of protein in 8M urea

[Luca Mollica]

On 05/20/2010 09:05 AM, caty hacker wrote:

Dear all,
I want to a protein simulation in 8M urea. Can anyone 
suggest me any introductory tutorial on that. Thank you in advance.


I think a "tutorial" is useless for such a simulation. Papers are the 
best reference depending on what you want to simulate
and on what you want to "see": if you are trying to simulate the 
unfolding there are several publications that discuss the major issues 
of the field, i.e.


a. which ff and/or urea topology to use
b. which computational technique (REMD, MD, MetaMD ...) to use

So ... what's your goal ? :)
At the moment I am too working on some systems that require the usage of 
urea and doing a bit of set up for AMBER FF, whereas in the past I have 
used a

topology for the last GROMOS FF.

Cheers

Luca


--



--



Luca Mollica
Protein Dynamics and Flexibility by NMR
Institut de Biologie Structurale
41 Rue Jules Horowitz
Grenoble
38027
France

E-mail: luca.moll...@ibs.fr (lucamoll...@gmail.com)

Telephone: +33.438783889


--


Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a pack of 
cigarettes, it's dark, and we're wearing sunglasses.
Jake: Hit it.

(The Blues Brothers)

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Re: [gmx-users] Re: [gmx-user]Error by pdb2gmx (Mark Abraham)

[Mark Abraham]

Hi,

Please leave some context in your email replies. Whoever replied last time has 
their own work and probably responded to other people's problems on here... 
They won't remember your context as well as you do :-).

IIRC, I pointed out the problem was probably in what you'd done with the .rtp 
file. Your DRG content looks OK at a glance, but if you've dumped in that file 
with (say) inappropriate line-endings, then that could be your problem.

Mark

- Original Message -
From: 佘安奇   
Date: Thursday, May 20, 2010 11:32
Subject: [gmx-users] Re: [gmx-user]Error by pdb2gmx (Mark Abraham)
To: gmx-users@gromacs.org

---
| > Dear Mark: > I used gromacs version 3.3.1. I update ffG45a3.rtp to include 
my molecule. And the rtp of my molecule is in the attached file DRG.txt. >   > 
Thank you very much! >   > Angel |
---
> 
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[gmx-users] asking help for simulation of protein in 8M urea

[caty hacker]

Dear all,
I want to a protein simulation in 8M urea. Can anyone suggest me
any introductory tutorial on that. Thank you in advance.
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