[gmx-users] add missing atom

[you zou]

Hi everyone,
I have one question about adding atoms that are missing in residue. This atom 
is OG in SER amino acid. I don't know how can I add this atom to my residue. If 
I have to add this atom manually how can I find coordinates of that? Or If 
there is server or software to do this I will be happy if you suggest me its.
Thank you

  
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Re: [gmx-users] Virial and Pressure

[Mark Abraham]

- Original Message -
From: hong bingbing 
Date: Friday, May 28, 2010 9:19
Subject: [gmx-users] Virial and Pressure
To: gmx-users@gromacs.org


---

> Hi, everyone,
> 
> Just ask if my interpretation is correct. Does the virial for pressure 
> calculation include all kinds of interactions, non-bonded and bonded? 

Yep. See appendix B1 for some details.
 
> Is there a way to self-defined virial with only specified interaction 
> components?

Not without writing code.

Mark
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RE: [gmx-users] [gmx-user]Error by pdb2gmx

[Dallas B. Warren]

You have no function types defined in your bonds, angles and dihedrals.

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. 

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of ???
> Sent: Friday, 28 May 2010 11:58 AM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] [gmx-user]Error by pdb2gmx
> 
> Dear Editors:
> I used gromacs version 4.0.7. I update ffG45a3.rtp to include my
> molecule with its rtp in the attached file DRG.txt.And the pdb file of
> my molecule is mol.txt and also attached. When I used the following
> command,there is an error! "pdb2gmx_mpi  -ff G45a3 -f  iso-C16.PDB"
> 
> Opening library file ffG45a3.rtp
> Opening library file /home/gromacs4/share/gromacs/top/aminoacids.dat
> Opening library file /home/gromacs4/share/gromacs/top/aminoacids.dat
> WARNING: masses will be determined based on residue and atom names,
>  this can deviate from the real mass of the atom type
> Opening library file /home/gromacs4/share/gromacs/top/atommass.dat
> Entries in atommass.dat: 178
> WARNING: vdwradii will be determined based on residue and atom names,
>  this can deviate from the real mass of the atom type
> Opening library file /home/gromacs4/share/gromacs/top/vdwradii.dat
> Entries in vdwradii.dat: 28
> Opening library file /home/gromacs4/share/gromacs/top/dgsolv.dat
> Entries in dgsolv.dat: 7
> Opening library file /home/gromacs4/share/gromacs/top/electroneg.dat
> Entries in electroneg.dat: 71
> Opening library file /home/gromacs4/share/gromacs/top/elements.dat
> Entries in elements.dat: 218
> Reading iso-C16.PDB...
> Read 81 atoms
> Opening library file /home/gromacs4/share/gromacs/top/xlateat.dat
> 26 out of 26 lines of xlateat.dat converted succesfully
> Analyzing pdb file
> There are 1 chains and 0 blocks of water and 1 residues with 81 atoms
> 
>   chain  #res #atoms
>   1 ' ' 1 81
> 
> All occupancies are one
> Opening library file /home/gromacs4/share/gromacs/top/ffG45a3.atp
> Atomtype 1
> Reading residue database... (ffG45a3)
> Opening library file ffG45a3.rtp
> Using default: not generating all possible dihedrals
> Using default: excluding 3 bonded neighbors
> Using default: generating 1,4 H--H interactions
> Using default: removing impropers on same bond as a proper
> Residue 96
> ---
> Program pdb2gmx_mpi, VERSION 4.0.7
> Source code file: resall.c, line: 344
> 
> Fatal error:
> in .rtp file in residue DRG at line:
> 
> What's up with the resall.c in line 344?
> I hope the problem won't bother you too much!
> Thank you very much!
> 
> Angel
> 
> 
> 
> 
> 
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[gmx-users] [gmx-user]Error by pdb2gmx

[佘安奇]

Dear Editors:
I used gromacs version 4.0.7. I update ffG45a3.rtp to include my molecule with 
its rtp in the attached file DRG.txt.And the pdb file of my molecule is mol.txt 
and also attached. When I used the following command,there is an error! 
"pdb2gmx_mpi  -ff G45a3 -f  iso-C16.PDB"

Opening library file ffG45a3.rtp
Opening library file /home/gromacs4/share/gromacs/top/aminoacids.dat
Opening library file /home/gromacs4/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
 this can deviate from the real mass of the atom type
Opening library file /home/gromacs4/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
 this can deviate from the real mass of the atom type
Opening library file /home/gromacs4/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /home/gromacs4/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /home/gromacs4/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /home/gromacs4/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading iso-C16.PDB...
Read 81 atoms
Opening library file /home/gromacs4/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 81 atoms

  chain  #res #atoms
  1 ' ' 1 81  

All occupancies are one
Opening library file /home/gromacs4/share/gromacs/top/ffG45a3.atp
Atomtype 1
Reading residue database... (ffG45a3)
Opening library file ffG45a3.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing impropers on same bond as a proper
Residue 96
---
Program pdb2gmx_mpi, VERSION 4.0.7
Source code file: resall.c, line: 344

Fatal error:
in .rtp file in residue DRG at line:

What's up with the resall.c in line 344?
I hope the problem won't bother you too much!
Thank you very much!
 
Angel
 
 


  [ DRG2  ]
  [ atoms ]
  CCN   CH3 0.0 1
  CCM   CH1 0.08300 2
  CCO   CH3 0.03300 2
  CCK   CH2 0.05000 2
  CCI   CH2 0.08300 2
  CCJ C 0.23500 2
  OCLOA-0.10600 2
  OCT O-0.37800 2
  NCHNR 0.07300 3
  HCH H-0.01100 3
  CCB C 0.22100 3
  OCD O-0.40200 3
  CCA   CH2 0.07600 3
  CCC   CH2 0.04300 3
  CCE   CH1 0.07500 4
  CCG   CH3 0.02500 4
  CCF   CH3 0.02700 4
  NBZNR 0.07200 4
  HBZ H-0.01100 4
  CBT C 0.21900 4
  OBV O-0.40700 4
  CBS   CH2 0.12900 5
  CBU   CH2 0.09200 5
  CBW C 0.33900 5
  OBYOM-0.28000 5
  OBXOM-0.28000 5
  NBRNR 0.06800 6
  HBR H-0.01200 6
  CBM C 0.20900 6
  OBO O-0.42600 6
  CBL   CH2 0.07000 6
  CBN   CH1 0.07000 6
  CBQ   CH3 0.02100 6
  CBP   CH3 0.01800 7
  NBKNR 0.06600 7
  HBK H-0.01200 7
  CBE C 0.20200 7
  OBG O-0.44100 7
  CBD   CH2 0.06600 7
  CBF   CH2 0.03500 7
  CBH   CH1 0.06600 7
  CBJ   CH3 0.0 8
  CBI   CH3 0.01800 9
  NBCNR 0.06600 9
  HBC H-0.01200 9
C C 0.20200 9
O O-0.44100 9
   CA   CH2 0.06600 9
   CB   CH2 0.03500 9
   CG   CH1 0.06600 9
  CD2   CH3 0.0220010
  CD1   CH3 0.0220010
NNR 0.0690010
H H-0.0120010
  CAX C 0.2110010
  OAY O-0.4220010
  CAW   CH2 0.0710010
  CAV   CH2 0.0390010
  CAU   CH2 0.1090011
  CAT C 0.3850011
  OBAOM-0.2470011
  OAZOM-0.2470011
  NBBNR 0.0630012
  HBB H-0.0130012
  CAA C 0.1960012
  OAG O-0.4550012
  CAB   CH2 0.0320012
  CAC   CH1 0.1140012
  CAD   CH2 0.0310012
  CAE   CH2 0.0320012
  CAF   CH2 0.013
  CAH   CH2 0.013
  CAI   CH2 0.013
  CAJ   CH2 0.013
  CAK   CH2 0.013
  CCP   CH2 0.013
  CCQ   CH2-0.0030014
  CCR   CH2-0.0020014
  CCS   CH1 0.0310014
  CCV   CH3-0.0260014
  CCU   CH3 0.015
  [ bonds ]
 CCM   CCN 0.1530   715.0
 CCM   CCO 0.1530   715.0
 CCM   CCK 0.1530   715.0
 CCI   CCK 0.1530   715.0
 CCI   CCJ 0.1390   866.0
 CCI   NCH 0.1480   764.0
 CCJ   OCL 0.1360  1020.0
 CCJ   OCT 0.1230  1660.0
 CAC   OCL 0.1440   610.0
 NCH   HCH 0.1000  1870.0
 CCB  

Re: [gmx-users] analysis of MD energy terms

[Justin A. Lemkul]

Moeed wrote:

Hello Justin,


[Actually, the reason I posted some parts of my mdp file was because you 
said I am sending redundant information so I just deleted the first 
lines of mdp file :) ]




What I was referring to was the meaningless grompp outputs, EM results, etc.  An 
.mdp file should always be posted in full if it is relevant.




To get the xtc file initially I used nrexcl=3 in the top file. Then I 
used mdrun -rerun to breakdown energies on this xtc file with new top 
file nrexcl=7 to exclude all intramolecular nonbonded interactions (you 
definitely recall all these details :)



1- Does it matter in the first run (to get xtc) what option I use for 
nrexcl in top file. Actually, I thought maybe in the normal run I have 
to set this option to zero. I did that and I got lincs warning (the same 
applies for nrexcl=1). So I tried nrexcl=2 and I noticed the results are 
not the same as nrexcl 3. However, this means I am still having 
nonbonded intramolecular interaction between atoms that are less than 2 
bonds away. Am I right?




Haphazardly setting different values for nrexcl will break down the physics! 
You must understand the intrinsic assumptions in most MD force fields before 
playing with these values.  If you set nrexcl = 1 or 2 then nonbonded 
interactions are being calculated for atom pairs that are normally governed only 
by bonded interactions.  Anything less than 3 (or greater than three in most 
cases, for that matter) is going to lead to a breakdown and unreasonable 
results, if you manage to get the simulation running at all.  That's why your 
nrexcl = 7 has to be done as a rerun.  If you tried this kind of simulation on 
its own, the results would be gibberish.




2- I am wondering why in this breakdown I still see LJ and coloumb 1-4 
interactions while I have nrexcl=2.




Because 1-4 interactions are separated by three bonds.  Using nrexcl = 2 has no 
effect here.




3- In the second set of results (nrexcl=3) potential energy is 2766 > 
2156 (the value for nrexcl==2). Logically, when 3 bonds away are 
excluded potential energy should be less I think!..




Hard to say.  You're completely changing the balance of power between bonded and 
nonbonded interactions.




4- Regarding the units, in chapter 2 of manual the units for energy is 
in KJ/mol. Here is this table I see heat capacity is given in J/mol K. 
Could you please kindly tell me the units what is the unit for energy 
temrs  LJ or coulomb?




The heat capacity you get is not useful.  I believe the method for calculating 
it has been updated in the development code, but basically you'll get the same 
result (or nearly so) for just about every simulation that you run, regardless 
of what's in it :)




5- Very important question: If I want to compute the interaction 
energies BETWEEN molecuels, do I have to sum up LJ (SR) =(-3026 e.g) and 
coloumb (SR)=74 ? and can I conclude that there is a net attraction 
energy in the system?




That depends.  Are there long range interactions?  PME?  Dispersion correction?



6- If I want to assure that equilibrium is reached, can I make the 
simulation time long enough such that T reaches 300 K? now it is 297 K.




You can make run for as much time as you want.  Sounds to me like you're 
relatively close to where you need to be, but you've got to reach the target 
temperature, ensure that it's stable, and then and only then should you be 
collecting data.


-Justin



I appreciate your help.

Thanks

Moeed



_mdrun -rerun on trajectory for nrexcl=2 in top file_


Energy  Average   RMSD Fluct.  Drift  
Tot-Drift


 


---

 

Angle   4286.19258.765231.37840.1269
401.349


 

Ryckaert-Bell.  722.96669.061661.167711.1046
111.068


 

*LJ-14   498.43231.289130.91381.67344
16.7378*


* *

*Coulomb-14 -322.26411.505610.1507
1.87612 18.765*


* *

*LJ (SR)-3026.0345.519838.61068.35011
83.5178*


* *

*Coulomb (SR)74.45642.536052.535370.02034   
0.203441*


 

Coul. recip.   -77.5276 2.37091.31777  -0.682623
-6.8276


 

Potential   2156.22335.429282.80762.4689
624.814


 

Kinetic En.   0  0  0  
0  0


 

Total Energy2156.22335.429282.80762.4689
624.814


 

Temperature   0  0  0  
0  0


 

Pressure (bar)  1563.28161.924161.4754.17097 
41.718


 

Cons. rmsd () 0  0  0  
0  0


 

Mu-X -0.00385475   0.893851   0.893682 -0.00602335 
-0.0602456


 


Heat Capacity Cv:  nan J/mol K (fac

[gmx-users] Solvation Free Energy Calculation

[Emanuel Birru]

Hi 

I am using Gromacs to calculate solvation of free energy calculation. First I 
tried the tutorial I found on the following link and run all the simulations 
for different lambda values 36 run for both in water and in vacuum and I got 
25215.67 is gromacs calculate this in J or KJ? Even if it in J its way far from 
the toluene solvation of free energy (-3.1KJ/mol). I got some warnings while I 
was running the g_analyze which says  "tau2 is longer than the length of the 
data (100) invalid fit (statistics might be bad) will fix tau2 at the total 
time 100", I got this warning for few runs not for all the runs.

Any suggestion,
Cheers
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[gmx-users] analysis of MD energy terms

[Moeed]

Hello Justin,


[Actually, the reason I posted some parts of my mdp file was because you
said I am sending redundant information so I just deleted the first lines of
mdp file :) ]


To get the xtc file initially I used nrexcl=3 in the top file. Then I used
mdrun -rerun to breakdown energies on this xtc file with new top file nrexcl=7
to exclude all intramolecular nonbonded interactions (you definitely recall
all these details :)


1- Does it matter in the first run (to get xtc) what option I use for nrexcl
in top file. Actually, I thought maybe in the normal run I have to set this
option to zero. I did that and I got lincs warning (the same applies
for nrexcl=1).
So I tried nrexcl=2 and I noticed the results are not the same as nrexcl 3.
However, this means I am still having nonbonded intramolecular interaction
between atoms that are less than 2 bonds away. Am I right?


2- I am wondering why in this breakdown I still see LJ and coloumb 1-4
interactions while I have nrexcl=2.


3- In the second set of results (nrexcl=3) potential energy is 2766 > 2156
(the value for nrexcl==2). Logically, when 3 bonds away are excluded
potential energy should be less I think!..


4- Regarding the units, in chapter 2 of manual the units for energy is in
KJ/mol. Here is this table I see heat capacity is given in J/mol K. Could
you please kindly tell me the units what is the unit for energy temrs  LJ or
coulomb?


5- Very important question: If I want to compute the interaction energies
BETWEEN molecuels, do I have to sum up LJ (SR) =(-3026 e.g) and coloumb
(SR)=74 ? and can I conclude that there is a net attraction energy in the
system?


6- If I want to assure that equilibrium is reached, can I make the
simulation time long enough such that T reaches 300 K? now it is 297 K.


I appreciate your help.

Thanks

Moeed



*mdrun -rerun on trajectory for nrexcl=2 in top file*


Energy  Average   RMSD Fluct.  Drift
Tot-Drift



---



Angle   4286.19258.765231.37840.1269
401.349



Ryckaert-Bell.  722.96669.061661.167711.1046
111.068



*LJ-14   498.43231.289130.91381.67344
16.7378*

* *

*Coulomb-14 -322.26411.505610.15071.87612
18.765*

* *

*LJ (SR)-3026.0345.519838.61068.35011
83.5178*

* *

*Coulomb (SR)74.45642.536052.535370.02034
0.203441*



Coul. recip.   -77.5276 2.37091.31777  -0.682623
-6.8276



Potential   2156.22335.429282.80762.4689
624.814



Kinetic En.   0  0  0  0
0



Total Energy2156.22335.429282.80762.4689
624.814



Temperature   0  0  0  0
0



Pressure (bar)  1563.28161.924161.4754.17097
41.718



Cons. rmsd () 0  0  0  0
0



Mu-X -0.00385475   0.893851   0.893682 -0.00602335
-0.0602456



Heat Capacity Cv:  nan J/mol K (factor = nan)




*
*

*mdrun -rerun on trajectory for nrexcl=3 in top file*



Statistics over 5001 steps [ 0. thru 10. ps ], 14 data sets

All averages are over 501 frames





Energy  Average   RMSD Fluct.  Drift
Tot-Drift

---

Angle   4400.09284.259237.26854.2184
542.293

Ryckaert-Bell.  1009.62124.46894.037928.2417
282.474

*LJ-14   648.41140.6844 39.9262.70793
27.0848*

**

*Coulomb-14 -278.65434.422711.807111.1987
112.01*

**

*LJ (SR)-3010.16 47.96842.53887.67736
76.789*

**

*Coulomb (SR)74.7846 2.51862.47007   0.170417
1.70451*

Coul. recip.   -78.04362.586061.54725  -0.717662
-7.17805

Potential   2766.05454.268342.141103.497
1035.18

Kinetic En.   0  0  0  0
0

Total Energy2766.05454.268342.141103.497
1035.18

Temperature   0  0  0  0
0

Pressure (bar)  1973.01177.068172.80313.3792
133.819

Cons. rmsd () 0  0  0  0
0

Mu-X -0.0523974   0.826473   0.826318 -0.00553723
-0.0553834

Heat Capacity Cv:  nan J/mol K (factor = nan)




;Run control
integrator  =  md
dt  =  0.002; ps !
nsteps  =  5000; total 1.0 ps.
nstcomm =  1; frequency for center of mass motion
removal

;Output control
nstenergy   =  10; fr

[gmx-users] Virial and Pressure

[hong bingbing]

Hi, everyone,

Just ask if my interpretation is correct. Does the virial for pressure 
calculation include all kinds of interactions, non-bonded and bonded? 

Is there a way to self-defined virial with only specified interaction 
components?

Thank you
Bingster


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Re: [gmx-users] XTC Error!!!

[Justin A. Lemkul]

deisy yurley rodriguez sarmiento wrote:

Hi Everyone!!!
As you begin to operate the mdrun, appear time after

Fatal Error:
XTC Error



Is this the full error message?  Usually an XTC error has more text after it.


To this happen?
As can be fixed?



Do you have enough disk space?  Did the simulation crash?  Did the .xtc file get 
corrupted (use gmxcheck)?


-Justin


Thanks in advance

Deisy Y. Rodriguez S.
Practicante de Computos Avanzados
Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX
Tel. 6344000  ext. 2792
Universidad Industrial de Santander




--


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] XTC Error!!!

[deisy yurley rodriguez sarmiento]

Hi Everyone!!!
As you begin to operate the mdrun, appear time after

Fatal Error:
XTC Error

To this happen?
As can be fixed?

Thanks in advance

Deisy Y. Rodriguez S.
Practicante de Computos Avanzados
Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX
Tel. 6344000  ext. 2792
Universidad Industrial de Santander



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Re: [gmx-users] OPLS-AA forcefield

[Justin A. Lemkul]

Erik Marklund wrote:

Justin A. Lemkul skrev:



you zou wrote:

Hi everyone,

I have one simple question. I don't know is there any different 
between OPLS-AA forcefield and OPLS-AA/L forcefield? I think these 
are different but when I use pdb2gmx tool there is no OPLS-AA 
forcefield to choose.




There is no difference.  The presence of "/L" simply indicates it is 
for liquid simulations.  I am unaware of a vacuum or gas phase 
OPLS-AA, certainly not within Gromacs.


-Justin
I think that's incorrect. The 'L' in OPLS stands for 'Liquid'. The 
trailing /L was added when some parameters were reparameteriezd 
(dihedrals I think) at some point, but I don't know what it stands for.




Oops, you're quite right!  My mistake.  I was thinking of the wrong L :)  The /L 
indicates the use of local MP2 (LMP2) for parameterization.


-Justin


Erik



Thank you


Hotmail: Free, trusted and rich email service. Get it now. 










--


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] OPLS-AA forcefield

[Erik Marklund]

Justin A. Lemkul skrev:



you zou wrote:

Hi everyone,

I have one simple question. I don't know is there any different 
between OPLS-AA forcefield and OPLS-AA/L forcefield? I think these 
are different but when I use pdb2gmx tool there is no OPLS-AA 
forcefield to choose.




There is no difference.  The presence of "/L" simply indicates it is 
for liquid simulations.  I am unaware of a vacuum or gas phase 
OPLS-AA, certainly not within Gromacs.


-Justin
I think that's incorrect. The 'L' in OPLS stands for 'Liquid'. The 
trailing /L was added when some parameters were reparameteriezd 
(dihedrals I think) at some point, but I don't know what it stands for.


Erik



Thank you


Hotmail: Free, trusted and rich email service. Get it now. 








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

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Re: [gmx-users] OPLS-AA forcefield

[Justin A. Lemkul]

you zou wrote:

Hi everyone,

I have one simple question. I don't know is there any different 
between OPLS-AA forcefield and OPLS-AA/L forcefield? I think these are 
different but when I use pdb2gmx tool there is no OPLS-AA forcefield to 
choose.




There is no difference.  The presence of "/L" simply indicates it is for liquid 
simulations.  I am unaware of a vacuum or gas phase OPLS-AA, certainly not 
within Gromacs.


-Justin


Thank you


Hotmail: Free, trusted and rich email service. Get it now. 





--


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] OPLS-AA forcefield

[you zou]

Hi everyone,
I have one simple question. I don't know is there any different between OPLS-AA 
forcefield and OPLS-AA/L forcefield? I think these are different but when I use 
pdb2gmx tool there is no OPLS-AA forcefield to choose.
Thank you 
_
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Re: [gmx-users] vibrational spectra of glucose

[Justin A. Lemkul]

Nilesh Dhumal wrote:

I used the opls parameters in gromacs.


...and what parameters would those be?  I don't know of any "standard" glucose 
parameters that are included in the Gromacs distribution, at least not for OPLS-AA.


Also, what was the outcome of energy minimization?  Did it converge?  Did it 
crash?  Why are you using such a large emstep?  I suspect that 0.1 may lead to 
instability.


-Justin


NIlesh

On Thu, May 27, 2010 1:17 pm, Erik Marklund wrote:

Where did you get the parameters for glucose? Those are my first
suspects.

Erik


Nilesh Dhumal skrev:


After energy minimzation, I visualized the pdb and all atoms are really
 far  from each other.

NIlesh


On Thu, May 27, 2010 1:10 pm, Erik Marklund wrote:



Bonds don't break in gromacs without qm/mm ...yet. Why do you think
they're broken?

Erik



Nilesh Dhumal skrev:




Hello,



I am trying to calculate the normal vibrational spectra of glcuose
molecule in vaccum. After the energy minimization,  I found all the
bonds are broken. I have pasted the input file for energy
minimzation. WHy all bonds are geting broken.
Nilesh



define   = -DFLEXIBLE

constraints  = all-bonds

integrator   = L-BFGS


nsteps   = 15000

nbfgscorr= 50

emtol= .001

emstep   = 0.1

gen_vel  = yes

gen-temp = 300

nstcomm  =  1

; NEIGHBORSEARCHING PARAMETERS



; nblist update frequency



nstlist  =10

; ns algorithm (simple or grid)



ns-type  = simple

; Periodic boundary conditions: xyz (default), no (vacuum)



; or full (infinite systems only)



pbc  = no

; nblist cut-off



rlist= 0

domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW



; Method for doing electrostatics



coulombtype  = Cut-Off

rcoulomb-switch  = 0

rcoulomb = 0

; Dielectric constant (DC) for cut-off or DC of reaction field




; Method for doing Van der Waals



vdw-type = Cut-off

; Periodic boundary conditions: xyz (default), no (vacuum)



; or full (infinite systems only)



pbc  = no

; nblist cut-off



rlist= 0

domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW



; Method for doing electrostatics



coulombtype  = Cut-Off

rcoulomb-switch  = 0

rcoulomb = 0

; Dielectric constant (DC) for cut-off or DC of reaction field




; Method for doing Van der Waals



vdw-type = Cut-off


















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

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

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--


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] vibrational spectra of glucose

[Erik Marklund]

And what's the output from the EM?

Erik

Nilesh Dhumal skrev:

I used the opls parameters in gromacs.
NIlesh

On Thu, May 27, 2010 1:17 pm, Erik Marklund wrote:
  

Where did you get the parameters for glucose? Those are my first
suspects.

Erik


Nilesh Dhumal skrev:



After energy minimzation, I visualized the pdb and all atoms are really
 far  from each other.

NIlesh


On Thu, May 27, 2010 1:10 pm, Erik Marklund wrote:


  

Bonds don't break in gromacs without qm/mm ...yet. Why do you think
they're broken?

Erik



Nilesh Dhumal skrev:





Hello,



I am trying to calculate the normal vibrational spectra of glcuose
molecule in vaccum. After the energy minimization,  I found all the
bonds are broken. I have pasted the input file for energy
minimzation. WHy all bonds are geting broken.
Nilesh



define   = -DFLEXIBLE

constraints  = all-bonds

integrator   = L-BFGS


nsteps   = 15000

nbfgscorr= 50

emtol= .001

emstep   = 0.1

gen_vel  = yes

gen-temp = 300

nstcomm  =  1

; NEIGHBORSEARCHING PARAMETERS



; nblist update frequency



nstlist  =10

; ns algorithm (simple or grid)



ns-type  = simple

; Periodic boundary conditions: xyz (default), no (vacuum)



; or full (infinite systems only)



pbc  = no

; nblist cut-off



rlist= 0

domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW



; Method for doing electrostatics



coulombtype  = Cut-Off

rcoulomb-switch  = 0

rcoulomb = 0

; Dielectric constant (DC) for cut-off or DC of reaction field




; Method for doing Van der Waals



vdw-type = Cut-off

; Periodic boundary conditions: xyz (default), no (vacuum)



; or full (infinite systems only)



pbc  = no

; nblist cut-off



rlist= 0

domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW



; Method for doing electrostatics



coulombtype  = Cut-Off

rcoulomb-switch  = 0

rcoulomb = 0

; Dielectric constant (DC) for cut-off or DC of reaction field




; Method for doing Van der Waals



vdw-type = Cut-off

















  

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

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

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

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[gmx-users] Constraint causing system to explode

[chris . neale]

Dear Warren:

I don't have your answer, but I'll point out that when you ask: "Is it  
possible that this is a problem that arises because of domain  
decomposition over multiple nodes" that you are probably the person in  
the best position to address this. 300ps should not take too long to  
simulate so why not try it on a single node and also on multiple nodes  
with mdrun -pd and report back?


Somebody may have your answer, but the system blowing up question is  
so common that it is probably faster for you to rule out some things  
first.


Chris.

-- original message --

	I am looking at the the free energy profile of end-to end distances  
of various peptides, but I am consistently getting a system blow-up  
when running simulations with that distance constrained by a type 2  
constraint.


	I run a simulation of the unconstrained peptide in a box of tip4p  
water, Na+ and Cl- ions, and it runs with no problem.


	Then I grab a frame of that simulation in which the end-to-end  
distance is 0.8 nm (full frame including water) as a .gro file.  Then  
I add a type 2 constraint between the N-terminal nitrogen atom and the  
C-terminal carboxyl carbon, create a new .tpr file using the revised  
topology and the already equilibrated frame as starting files and a  
.mdp file that now has the free_energy set to on, and then launch mdrun.


	About 189 ps into the simulation I start getting warnings as follows,  
ultimately leading to blow-up and the run failing (fragment of error  
file output shown at end of message).


	I am obviously missing something about how the constraint is handled.  
 Is it possible that this is a problem that arises because of domain  
decomposition over multiple nodes, ir is there something more basic  
that needs to be dealt with when imposing a type 2 constraint?


Warren Gallin

Step 94636, time 189.272 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.041028, max 0.161215 (between atoms 217 and 219)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 94637, time 189.274 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.018884, max 0.100333 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length



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Re: [gmx-users] vibrational spectra of glucose

[Nilesh Dhumal]

I used the opls parameters in gromacs.
NIlesh

On Thu, May 27, 2010 1:17 pm, Erik Marklund wrote:
> Where did you get the parameters for glucose? Those are my first
> suspects.
>
> Erik
>
>
> Nilesh Dhumal skrev:
>
>> After energy minimzation, I visualized the pdb and all atoms are really
>>  far  from each other.
>>
>> NIlesh
>>
>>
>> On Thu, May 27, 2010 1:10 pm, Erik Marklund wrote:
>>
>>
>>> Bonds don't break in gromacs without qm/mm ...yet. Why do you think
>>> they're broken?
>>>
>>> Erik
>>>
>>>
>>>
>>> Nilesh Dhumal skrev:
>>>
>>>
>>>
 Hello,



 I am trying to calculate the normal vibrational spectra of glcuose
 molecule in vaccum. After the energy minimization,  I found all the
 bonds are broken. I have pasted the input file for energy
 minimzation. WHy all bonds are geting broken.
 Nilesh



 define   = -DFLEXIBLE

 constraints  = all-bonds

 integrator   = L-BFGS


 nsteps   = 15000

 nbfgscorr= 50

 emtol= .001

 emstep   = 0.1

 gen_vel  = yes

 gen-temp = 300

 nstcomm  =  1

 ; NEIGHBORSEARCHING PARAMETERS



 ; nblist update frequency



 nstlist  =10

 ; ns algorithm (simple or grid)



 ns-type  = simple

 ; Periodic boundary conditions: xyz (default), no (vacuum)



 ; or full (infinite systems only)



 pbc  = no

 ; nblist cut-off



 rlist= 0

 domain-decomposition = no

 ; OPTIONS FOR ELECTROSTATICS AND VDW



 ; Method for doing electrostatics



 coulombtype  = Cut-Off

 rcoulomb-switch  = 0

 rcoulomb = 0

 ; Dielectric constant (DC) for cut-off or DC of reaction field




 ; Method for doing Van der Waals



 vdw-type = Cut-off

 ; Periodic boundary conditions: xyz (default), no (vacuum)



 ; or full (infinite systems only)



 pbc  = no

 ; nblist cut-off



 rlist= 0

 domain-decomposition = no

 ; OPTIONS FOR ELECTROSTATICS AND VDW



 ; Method for doing electrostatics



 coulombtype  = Cut-Off

 rcoulomb-switch  = 0

 rcoulomb = 0

 ; Dielectric constant (DC) for cut-off or DC of reaction field




 ; Method for doing Van der Waals



 vdw-type = Cut-off

















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

[Erik Marklund]

Where did you get the parameters for glucose? Those are my first suspects.

Erik

Nilesh Dhumal skrev:

After energy minimzation, I visualized the pdb and all atoms are really
far  from each other.

NIlesh

On Thu, May 27, 2010 1:10 pm, Erik Marklund wrote:
  

Bonds don't break in gromacs without qm/mm ...yet. Why do you think
they're broken?

Erik


Nilesh Dhumal skrev:



Hello,


I am trying to calculate the normal vibrational spectra of glcuose
molecule in vaccum. After the energy minimization,  I found all the
bonds are broken. I have pasted the input file for energy minimzation.
WHy all bonds are geting broken.
Nilesh


define   = -DFLEXIBLE

constraints  = all-bonds

integrator   = L-BFGS


nsteps   = 15000

nbfgscorr= 50

emtol= .001

emstep   = 0.1

gen_vel  = yes

gen-temp = 300

nstcomm  =  1

; NEIGHBORSEARCHING PARAMETERS


; nblist update frequency


nstlist  =10

; ns algorithm (simple or grid)


ns-type  = simple

; Periodic boundary conditions: xyz (default), no (vacuum)


; or full (infinite systems only)


pbc  = no

; nblist cut-off


rlist= 0

domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW


; Method for doing electrostatics


coulombtype  = Cut-Off

rcoulomb-switch  = 0

rcoulomb = 0

; Dielectric constant (DC) for cut-off or DC of reaction field



; Method for doing Van der Waals


vdw-type = Cut-off

; Periodic boundary conditions: xyz (default), no (vacuum)


; or full (infinite systems only)


pbc  = no

; nblist cut-off


rlist= 0

domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW


; Method for doing electrostatics


coulombtype  = Cut-Off

rcoulomb-switch  = 0

rcoulomb = 0

; Dielectric constant (DC) for cut-off or DC of reaction field



; Method for doing Van der Waals


vdw-type = Cut-off
















  

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

--
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Please search the archive at http://www.gromacs.org/search before posting!
 Please don't post (un)subscribe requests to the list. Use the
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http://www.gromacs.org/mailing_lists/users.php







  



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

--
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] vibrational spectra of glucose

[Nilesh Dhumal]

After energy minimzation, I visualized the pdb and all atoms are really
far  from each other.

NIlesh

On Thu, May 27, 2010 1:10 pm, Erik Marklund wrote:
> Bonds don't break in gromacs without qm/mm ...yet. Why do you think
> they're broken?
>
> Erik
>
>
> Nilesh Dhumal skrev:
>
>> Hello,
>>
>>
>> I am trying to calculate the normal vibrational spectra of glcuose
>> molecule in vaccum. After the energy minimization,  I found all the
>> bonds are broken. I have pasted the input file for energy minimzation.
>> WHy all bonds are geting broken.
>> Nilesh
>>
>>
>> define   = -DFLEXIBLE
>>
>> constraints  = all-bonds
>>
>> integrator   = L-BFGS
>>
>>
>> nsteps   = 15000
>>
>> nbfgscorr= 50
>>
>> emtol= .001
>>
>> emstep   = 0.1
>>
>> gen_vel  = yes
>>
>> gen-temp = 300
>>
>> nstcomm  =  1
>>
>> ; NEIGHBORSEARCHING PARAMETERS
>>
>>
>> ; nblist update frequency
>>
>>
>> nstlist  =10
>>
>> ; ns algorithm (simple or grid)
>>
>>
>> ns-type  = simple
>>
>> ; Periodic boundary conditions: xyz (default), no (vacuum)
>>
>>
>> ; or full (infinite systems only)
>>
>>
>> pbc  = no
>>
>> ; nblist cut-off
>>
>>
>> rlist= 0
>>
>> domain-decomposition = no
>>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>>
>>
>> ; Method for doing electrostatics
>>
>>
>> coulombtype  = Cut-Off
>>
>> rcoulomb-switch  = 0
>>
>> rcoulomb = 0
>>
>> ; Dielectric constant (DC) for cut-off or DC of reaction field
>>
>>
>>
>> ; Method for doing Van der Waals
>>
>>
>> vdw-type = Cut-off
>>
>> ; Periodic boundary conditions: xyz (default), no (vacuum)
>>
>>
>> ; or full (infinite systems only)
>>
>>
>> pbc  = no
>>
>> ; nblist cut-off
>>
>>
>> rlist= 0
>>
>> domain-decomposition = no
>>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>>
>>
>> ; Method for doing electrostatics
>>
>>
>> coulombtype  = Cut-Off
>>
>> rcoulomb-switch  = 0
>>
>> rcoulomb = 0
>>
>> ; Dielectric constant (DC) for cut-off or DC of reaction field
>>
>>
>>
>> ; Method for doing Van der Waals
>>
>>
>> vdw-type = Cut-off
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
>
> --
> ---
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 4537fax: +46 18 511 755
> er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/
>
> --
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Re: [gmx-users] vibrational spectra of glucose

[Erik Marklund]

Bonds don't break in gromacs without qm/mm ...yet. Why do you think 
they're broken?


Erik

Nilesh Dhumal skrev:

Hello,

I am trying to calculate the normal vibrational spectra of glcuose
molecule in vaccum. After the energy minimization,  I found all the bonds
are broken.
I have pasted the input file for energy minimzation.
WHy all bonds are geting broken.
Nilesh

define   = -DFLEXIBLE

constraints  = all-bonds

integrator   = L-BFGS


nsteps   = 15000

nbfgscorr= 50

emtol= .001

emstep   = 0.1

gen_vel  = yes

gen-temp = 300

nstcomm  =  1

; NEIGHBORSEARCHING PARAMETERS

; nblist update frequency

nstlist  =10

; ns algorithm (simple or grid)

ns-type  = simple

; Periodic boundary conditions: xyz (default), no (vacuum)

; or full (infinite systems only)

pbc  = no

; nblist cut-off

rlist= 0

domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype  = Cut-Off

rcoulomb-switch  = 0

rcoulomb = 0

; Dielectric constant (DC) for cut-off or DC of reaction field


; Method for doing Van der Waals

vdw-type = Cut-off

; Periodic boundary conditions: xyz (default), no (vacuum)

; or full (infinite systems only)

pbc  = no

; nblist cut-off

rlist= 0

domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype  = Cut-Off

rcoulomb-switch  = 0

rcoulomb = 0

; Dielectric constant (DC) for cut-off or DC of reaction field


; Method for doing Van der Waals

vdw-type = Cut-off















  



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

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[gmx-users] vibrational spectra of glucose

[Nilesh Dhumal]

Hello,

I am trying to calculate the normal vibrational spectra of glcuose
molecule in vaccum. After the energy minimization,  I found all the bonds
are broken.
I have pasted the input file for energy minimzation.
WHy all bonds are geting broken.
Nilesh

define   = -DFLEXIBLE

constraints  = all-bonds

integrator   = L-BFGS


nsteps   = 15000

nbfgscorr= 50

emtol= .001

emstep   = 0.1

gen_vel  = yes

gen-temp = 300

nstcomm  =  1

; NEIGHBORSEARCHING PARAMETERS

; nblist update frequency

nstlist  =10

; ns algorithm (simple or grid)

ns-type  = simple

; Periodic boundary conditions: xyz (default), no (vacuum)

; or full (infinite systems only)

pbc  = no

; nblist cut-off

rlist= 0

domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype  = Cut-Off

rcoulomb-switch  = 0

rcoulomb = 0

; Dielectric constant (DC) for cut-off or DC of reaction field


; Method for doing Van der Waals

vdw-type = Cut-off

; Periodic boundary conditions: xyz (default), no (vacuum)

; or full (infinite systems only)

pbc  = no

; nblist cut-off

rlist= 0

domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype  = Cut-Off

rcoulomb-switch  = 0

rcoulomb = 0

; Dielectric constant (DC) for cut-off or DC of reaction field


; Method for doing Van der Waals

vdw-type = Cut-off















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[gmx-users] Re: Compile gromacs 4.0.7 with mopac

[Stefan Hoorman]

>
> >
> >
> >  1. Re: Non-conservation of total energy while using structure
> > file to resume the simulation (Mark Abraham)
> >  2. Compile gromacs 4.0.7 with mopac (Stefan Hoorman)
>
> Try linking with g2c.
> Best wishes,
>
> Gerrit
>
>
>
> Thank you for the tip Gerrit. There is just one problem, I don't know how
to do that. I've looked it over the internet, but didn't find anything that
would enlighten my way. Could you be a bit more specific?

Thank you in advance
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[gmx-users] PMF in vacuum

[chris . neale]

Dear Eudes:
To answer your pbc vs no-pbc question, I suggest that you use pbc=no  
and set nstlist=0 rlist=0 rvdw=0 rcoulomb=0 so that you calculate all  
interactions in direct space with no cutoffs.


## Major comments that you should still investigate

1. There is no need to use a virtual atom, the pull code will use the  
center of mass. I strongly suggest that you stop using a virtual atom  
and just use the entire benzene as an argument to the pull code group.  
I have had difficulties with slightly more complicated setups of this  
type.


2. In test2.jpg, the system without pbc shows a flat PMF after the  
cut-off -- exactly what one would expect. The pbc system shows  
continued interaction -- again what I would expect. So there is  
nothing actually all that strange here. One would not expect to see  
such a drastic difference in a high dielectric such as water, but in  
vacuum I suspect that this is expected.


3. Please clarify what your cutoff was. I don't see a cut-off listed  
in your .mdp options and leaving this to the default of 1.0 nm is a  
bad idea because it can lead to confusion a times like this. I might  
assume that it was 0.7 nm based on test2.jpg, but then see the point  
#3 below.


4a. I have no idea what -DPOSRES is actually doing for you since I  
can't see your topology.


4b. Are you sure that "pull_dim = N N Y" is really what you want?  
Sometimes one wants to average over X and Y, but I am not sure that  
you do in this case.


4c. What exactly do you believe pull_r0 and pull_r1 are doing for you?

### More minor notes:

5. regarding test1.jpg: a PMF is correct to an additive constant,  
meaning that you can shift two PMFs relative to one another. These 2  
PMFs are therefore less different than they appear in your compaison  
plot, but they do differ in the slope between 1.0 - 2.0 nm. This is  
probably just a convergence issue and you will always need to do tests  
like this.


6. regarding histo.png: can you confirm that the few very short  
gaussians are due to less sampling in a few windows? In any event, the  
overlap looks good.


Chris

-- original message --

Hello Chris, thanks for your attention.
I'm sending you some links to some tests
I performed. As I said you will notice that
depending on the parameter used my simulation
shows PMF profiles quite different. Especially what
concerns to the difference between the use or not of the PBC.

https://sites.google.com/site/fileti/files/test1.jpg
https://sites.google.com/site/fileti/files/test2.jpg
https://sites.google.com/site/fileti/files/histo.png

I have constructed two very similar topologies (ben-a.itp and ben-b.itp)
where I put a virtual site in the center of benzene.
This sites were restrained to keep my molecules
fixed distance desired.

The basic details of the simulations are given below:1000

define   = -DPOSRES
integrator   = sd
tinit= 0
dt   = 0.002
nsteps   = 500 or 50
comm-mode= angular
nstcomm  = 1
comm-grps= System
bd-fric  = 1
ld-seed  = 1993
nstlist  = 5
ns_type  = simple
pbc  = no or xyz
periodic_molecules   = no
rlist= 0
coulombtype  = Cut-off
vdw-type = Cut-off
rvdw = 0
DispCorr = no
Tcoupl   = Nose-Hoover
tc_grps  = system
tau_t= 0.1
ref_t= 300
Pcoupl   = no
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0
constraints  = all-bonds
constraint_algorithm = lincs

; COM PULLING
pull = umbrella
pull_geometry= distance
pull_dim = N N Y
pull_r1  = 1
pull_r0  = 1.5
pull_constr_tol  = 1e-06
pull_start   = yes
pull_nstxout = 10
pull_nstfout = 10
pull_ngroups = 1
pull_group0  = BENa
pull_weights0=
pull_pbcatom0= 0
pull_group1  = BENb
pull_weights1=
pull_pbcatom1= 0
pull_vec1= 0 0 1
pull_init1   = 0
pull_rate1   = 0.0
pull_k1  = 1700 or


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[gmx-users] Constraint causing system to explode

[Warren Gallin]

Hi,

I am looking at the the free energy profile of end-to end distances of 
various peptides, but I am consistently getting a system blow-up when running 
simulations with that distance constrained by a type 2 constraint.

I run a simulation of the unconstrained peptide in a box of tip4p 
water, Na+ and Cl- ions, and it runs with no problem.

Then I grab a frame of that simulation in which the end-to-end distance 
is 0.8 nm (full frame including water) as a .gro file.  Then I add a type 2 
constraint between the N-terminal nitrogen atom and the C-terminal carboxyl 
carbon, create a new .tpr file using the revised topology and the already 
equilibrated frame as starting files and a .mdp file that now has the 
free_energy set to on, and then launch mdrun.

About 189 ps into the simulation I start getting warnings as follows, 
ultimately leading to blow-up and the run failing (fragment of error file 
output shown at end of message).

I am obviously missing something about how the constraint is handled.  
Is it possible that this is a problem that arises because of domain 
decomposition over multiple nodes, ir is there something more basic that needs 
to be dealt with when imposing a type 2 constraint?

Warren Gallin



Step 94636, time 189.272 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.041028, max 0.161215 (between atoms 217 and 219)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 94637, time 189.274 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.018884, max 0.100333 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 94638, time 189.276 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.039664, max 0.168134 (between atoms 217 and 219)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 94639, time 189.278 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.009052, max 0.046170 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 94640, time 189.28 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.010107, max 0.040597 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 114146, time 228.292 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.018616, max 0.132800 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 114147, time 228.294 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.067800, max 0.404060 (between atoms 217 and 219)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 114148, time 228.296 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004950, max 0.032340 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 114149, time 228.298 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.003656, max 0.020543 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 139429, time 278.858 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.023892, max 0.091259 (between atoms 211 and 217)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 139430, time 278.86 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.023116, max 0.102488 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 139431, time 278.862 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.031945, max 0.132323 (between atoms 211 and 217)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 139432, time 278.864 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.023118, max 0.104278 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 139433, time 278.866 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.024565, max 0.101936 (between atoms 211 and 217)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 139434, time 278.868 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.013388, max 0.058925 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 139435, time 278.87 (ps)  LINCS WARNIN

[gmx-users] Re: the output of do_dssp

[Hsin-Lin Chiang]

Hi ,Mark:

I had announced that my system is a dimer with each peptides have 6 
residues in my first post.

I'm sorry if I didn't express it  to be understood easily.
Can you please tell me why 13 coils are reasonable if my systems is a dimer?

regards,
Hsin-Lin

Hi, Justin:

I post my coordinate with protein translated by trjconv
By this gro file, I get 0 structure and 13 coils.


Haven't you been saying for what seems like weeks now that you have 12 residues in your 
"protein"? If so...




C   70   2.223   2.893
1.484 -0.0883  0.1244 -0.1837
 6ASN O1
71   2.111   2.941   1.505 -0.2557
-0.4837 -0.1041
 6ASN O2
72   2.313   2.953   1.419 -
0.5561  0.0660  0.4455


Here, there's quite clearly an internal COO and NH3... hence it seems that you 
have two 6-residue chains. That's important data to be aware of, and to 
communicate to people who might help... Our belief that you really had a 
12-residue peptide excludes this kind of issue from trouble-shooting, which 
ends up wasting everyone's time.

Mark



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Re: [gmx-users] CG (MARTINI) parameters for RNA

[Thomas Piggot]

Hi,

The DNA parameters for use with the MARTINI forcefield are not publicly 
available to download at the moment, however they will be available very 
soon. I (or someone else from the Khalid group) will let the list know 
when and where they have been made available.


Cheers

Tom

Itamar Kass wrote:

Shalom all,

I wish to try and simulate a protein with few RNA bases attached. As I
favour speed over accuracy in this case I wish to use the MARTINI model.
I could not find RNA/DNA parameters, but noticed that on the site there
is a reference to Khalid S, Bond PJ, Holyoake J, Hawtin RW, Sansom MSP.
DNA and lipid bilayers: self-assembly and insertion. J. Royal Soc. Int.
  5, S241-S250, 2008.

I wonder if someone had those parameters already implemented into the
model? It will be nice to get it nicely packed. Or maybe even better,
are there any beta parameters to RNA/DNA in a new MARTINI force field?

All the best,
Itamar



--
Dr Thomas Piggot
University of Southampton, UK.
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Re: [gmx-users] coinstraint bond length changes

[Justin A. Lemkul]

Sebastian Waltz wrote:

Hi all,

I constrained in the .top file some bonds 


[ constraints ]
;ai aj  typedistance
   4041 2   0.1430
   4748 2   0.1430
   5455 2   0.1430
   6162 2   0.1430

After running the simulation for 5ns I get a bond length of
0.23(out of the .trr file). So I am not sure whats
going wrong. This bonds are C O double bonds which have an
equilibrium bond length of 0.143nm.



Since these are actual chemical bonds, why are you using constraint type 2 
instead of 1?  See the manual, section 5.4 regarding the proper function type.


-Justin


Thanks a lot

Sebastian  


--


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] coinstraint bond length changes

[Sebastian Waltz]

Hi all,

I constrained in the .top file some bonds 

[ constraints ]
;ai aj  typedistance
   4041 2   0.1430
   4748 2   0.1430
   5455 2   0.1430
   6162 2   0.1430

After running the simulation for 5ns I get a bond length of
0.23(out of the .trr file). So I am not sure whats
going wrong. This bonds are C O double bonds which have an
equilibrium bond length of 0.143nm.

Thanks a lot

Sebastian  
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Re: [gmx-users] Re: gmx-users Digest, Vol 73, Issue 177

[Justin A. Lemkul]

Hsin-Lin Chiang wrote:

Hi ,Mark:

I had announced my system is a dimer with each peptides have 6 residues.
I'm sorry if I didn't express it  to be understood easily.
Can you please tell me why 13 coils are reasonable if my systems is a 
dimer?




It's not.  I already answered this:

http://lists.gromacs.org/pipermail/gmx-users/2010-May/051311.html

-Justin


regards,
Hsin-Lin

Hi, Justin:

I post my coordinate with protein translated by trjconv
By this gro file, I get 0 structure and 13 coils.
 
Haven't you been saying for what seems like weeks now that you have 12 
residues in your "protein"? If so...



  

C   70   2.223   2.893  1.484 -0.0883  0.1244 -0.1837
 6ASN O1  71   2.111   2.941   1.505 -0.2557
-0.4837 -0.1041
 6ASN O2  72   2.313   2.953   1.419 -
0.5561  0.0660  0.4455
 
Here, there's quite clearly an internal COO and NH3... hence it seems 
that you have two 6-residue chains. That's important data to be aware 
of, and to communicate to people who might help... Our belief that you 
really had a 12-residue peptide excludes this kind of issue from 
trouble-shooting, which ends up wasting everyone's time.


Mark

   


--


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


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[gmx-users] Re: gmx-users Digest, Vol 73, Issue 177

[Hsin-Lin Chiang]

Hi ,Mark:

I had announced my system is a dimer with each peptides have 6 residues.
I'm sorry if I didn't express it  to be understood easily.
Can you please tell me why 13 coils are reasonable if my systems is a dimer?

regards,
Hsin-Lin

Hi, Justin:

I post my coordinate with protein translated by trjconv
By this gro file, I get 0 structure and 13 coils.
 

Haven't you been saying for what seems like weeks now that you have 12 residues in your 
"protein"? If so...


   
C   70   2.223   2.893  
1.484 -0.0883  0.1244 -0.1837
 6ASN O1  
71   2.111   2.941   1.505 -0.2557

-0.4837 -0.1041
 6ASN O2  
72   2.313   2.953   1.419 -

0.5561  0.0660  0.4455
 

Here, there's quite clearly an internal COO and NH3... hence it seems that you 
have two 6-residue chains. That's important data to be aware of, and to 
communicate to people who might help... Our belief that you really had a 
12-residue peptide excludes this kind of issue from trouble-shooting, which 
ends up wasting everyone's time.

Mark

   

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[gmx-users] Re: Compile gromacs 4.0.7 with mopac (Stefan Hoorman)

[Gerrit Groenhof]

> 
> 
>  1. Re: Non-conservation of total energy while using structure
> file to resume the simulation (Mark Abraham)
>  2. Compile gromacs 4.0.7 with mopac (Stefan Hoorman)

Try linking with g2c.
Best wishes,

Gerrit


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[gmx-users] Re: stepsize too small: help to solve problem in GROMACS installation

[Anna Marabotti]

 
Dear Mark,
many thanks for your suggestions. At present, the problem I reported here
seems to be solved using the gcc442 compilers, we are doing a lot of checks
on the machine and we will take into account all your observations.
Many thanks also for the correction on the web site.

Anna
--

Message: 4
Date: Thu, 27 May 2010 17:28:48 +1000
From: Mark Abraham 
Subject: Re: [gmx-users] Re: stepsize too small: help to solve problem
in  GROMACS installation
To: Discussion list for GROMACS users 
Message-ID: 
Content-Type: text/plain; CHARSET=US-ASCII

- Original Message -
From: Anna Marabotti 
Date: Thursday, May 27, 2010 16:55
Subject: [gmx-users] Re: stepsize too small: help to solve problem in
GROMACS installation
To: gmx-users@gromacs.org

> Dear Justin, dear all,
> sorry for not having seen the warning before asking the question about
> compilers (just a little justification, however: the warning 
> appears only on
> the Download page, not on the Installation page; I went directly 
> to the
> installation page and I did not notice it).

Fixed.
 
> The only other possibility we have is to try compiling GROMACS 
> with gcc-442
> compiler. This time I checked more carefully (at least, I hope 
> so!) on the
> site and it seems to me that no problems are reported. For your 
> experience,is it a good choice or we can expect other problems? 
> In this last case, what
> do you suggest as the best compiler for Gromacs?

GROMACS performance is pretty insensitive to compiler version so long as you
are using assembly-language inner loops (e.g. always true by default on
x86). Most of the compute time is spent there, so most of the rest is
irrelevant.

The main side issue is the FFT performance for PME. Make sure you're using
either vendor FFT libraries, or suitably well-compiled FFTW. Even there,
FFTW with gcc -O5 (making sure the SSE(n) optimization is used) was only a
hair behind icc+mkl in some tests I did a year ago.

Mark



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Re: Re[2]: [gmx-users] Non-conservation of total energy while using structure file to resume the simulation

[Mark Abraham]

- Original Message -
From: Dmitri Dubov 
Date: Thursday, May 27, 2010 19:11
Subject: Re[2]: [gmx-users] Non-conservation of total energy while using 
structure file to resume the simulation
To: Discussion list for GROMACS users 

> > I expect that either 

> > grompp -f new -o newtpr
> > mdrun -s newtpr -cpi old_state.cpt

> No, this way is unsuccessful, maybe due to somewhat contradictive 
> instructions:
> grompp supplies newtpr with usual options
> tinit                    = 0
> nsteps                   = 10
> simulation_part          = 1

> and from old_state.cpt the system finds itself on 10th step already and 
> stops.

OK. Presumably some more cunning choice of .mdp options would work, or using 
grompp, tbconv -extend and then mdrun.

> > grompp -f new -t old_state.cpt -o newtpr
> > mdrun -s newtpr
> > will do what you want. Please report back if one or both work :-)

> And the latter variant is working! More precisely I use
> grompp -f new -t old_state.cpt -c oldtpr -o newtpr 
> mdrun_d -s newtpr


Mark
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Re[2]: [gmx-users] Non-conservation of total energy while using structure file to resume the simulation

[Dmitri Dubov]

Dear Mark,

thank you for your prompt reply.

> - Original Message -
> From: Dmitri Dubov 
> Date: Thursday, May 27, 2010 15:41
> Subject: [gmx-users] Non-conservation of total energy while using
> structure file to resume the simulation
> To: Discussion list for GROMACS users 

>> Dear GMX'ers!

>> I simulate system of about hundreds of water molecules in NVE ensemble with 
>> md integrator. Every 100 ps I need to change slightly some parameters, say, 
>> electric field and to continue the simulation from this point. As I realize 
>> I cannot go on my run using the checkpointing and tpbconv in this case. 
>> Therefore I try to use the output structure file confout.gro which contains 
>> both coordinates and velocities at the end of the previous step. 

>> The problem is in the total energy. Within every 100-ps run the energy drift 
>> is quite low. But when I start the next step, at its very beginning I see 
>> the considerable jump in the total energy and the temperature comparing with 
>> the end values of previuos step. 

>> NOTE that it is the case even when I change NOTHING in my job.mdp file! 

> Sure, discontinuity is guaranteed from the loss of precision.

>> To my knowledge the coordinates and velocities define exactly the energy and 
>> the temperature. Now I suspect the only reason - low precision of 
>> confout.gro. So, my questions are:

>> Is there another reason for the total energy non-conservation in my 
>> simulation?

> Probably not.

>>How can I get the full precision in output structure file RIGTH after mdrun? 
>>Or it is mandatory to use trjconv with -ndec option?

> I expect that either 

> grompp -f new -o newtpr
> mdrun -s newtpr -cpi old_state.cpt

No, this way is unsuccessful, maybe due to somewhat contradictive instructions:
grompp supplies newtpr with usual options
tinit= 0
nsteps   = 10
simulation_part  = 1
and from old_state.cpt the system finds itself on 10th step already and 
stops.

> or

> grompp -f new -t old_state.cpt -o newtpr
> mdrun -s newtpr
> will do what you want. Please report back if one or both work :-)
And the latter variant is working! More precisely I use

grompp -f new -t old_state.cpt -c oldtpr -o newtpr 
mdrun_d -s newtpr

Thanks one more for the fruitful suggestion!

> Or, maybe you can use old-style .trr and .edr output as input to
> grompp, so long as you planned that in advance. A checkpoint-file approach is 
> superior, however.

>> What is the default precision of .trr trajectory file in single and double 
>> precision modes?

> Machine precision.

> Mark

-- 
Sincerely,
 Dmitri  mailto:ddu...@ngs.ru-- 
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Re: [gmx-users] Re: stepsize too small: help to solve problem in GROMACS installation

[Mark Abraham]

- Original Message -
From: Anna Marabotti 
Date: Thursday, May 27, 2010 16:55
Subject: [gmx-users] Re: stepsize too small: help to solve problem in   GROMACS 
installation
To: gmx-users@gromacs.org

> Dear Justin, dear all,
> sorry for not having seen the warning before asking the question about
> compilers (just a little justification, however: the warning 
> appears only on
> the Download page, not on the Installation page; I went directly 
> to the
> installation page and I did not notice it).

Fixed.
 
> The only other possibility we have is to try compiling GROMACS 
> with gcc-442
> compiler. This time I checked more carefully (at least, I hope 
> so!) on the
> site and it seems to me that no problems are reported. For your 
> experience,is it a good choice or we can expect other problems? 
> In this last case, what
> do you suggest as the best compiler for Gromacs?

GROMACS performance is pretty insensitive to compiler version so long as you 
are using assembly-language inner loops (e.g. always true by default on x86). 
Most of the compute time is spent there, so most of the rest is irrelevant.

The main side issue is the FFT performance for PME. Make sure you're using 
either vendor FFT libraries, or suitably well-compiled FFTW. Even there, FFTW 
with gcc -O5 (making sure the SSE(n) optimization is used) was only a hair 
behind icc+mkl in some tests I did a year ago.

Mark
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