[gmx-users] Pme on gpu performance

[Andrzej Rzepiela]

Dears,

I would like to ask what performance improvement is expected for  
future releases (e.g. 4.6) for PME calculations on gpu cards. Last  
week I sent benchmark results for dhfr to the list, which show no  
performance gain when the newest versions of tesla cards vs intel xeon  
R are used (more or less in agreement of what is presented on the  
gromacs website). However, for the same system  simulations with  
different gpu code, acemd,  on a very similar machine can be about 5  
times faster, as benchmarked recently by my colleagues, suggesting  
that performance of gromacs may soon improve. is that correct ?



Andrzej 
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[gmx-users] Adding ions using "genion"

[cuong nguyen]

Dear,

I create a box of water with 10 MIBC molecules on two opposite surfaces.
then I used the command "grompp -f input_min.mdp -o min.tpr -c box1.g96" to
creat .tpr file before using the command "genion -s min.tpr -o add.gro
-nname Cl -pname NA -nn 20 -np 20" to add 20 Na+ and 20 Cl- into this box.
I run the command "grompp -f input_min.mdp -o min.tpr -c add.gro" again and
appeared the warings :

Warning: atom name 176 in topol.top and add.gro does not match (CL - OW)
Warning: atom name 177 in topol.top and add.gro does not match (CL - HW1)
Warning: atom name 178 in topol.top and add.gro does not match (CL - HW2)
Warning: atom name 179 in topol.top and add.gro does not match (CL - OW)
Warning: atom name 180 in topol.top and add.gro does not match (CL - HW1)
(more than 20 non-matching atom names)

WARNING 1 [file topol.top, line 72]:
  21754 non-matching atom names
  atom names from topol.top will be used
  atom names from add.gro will be ignored
..
Fatal error:
Too many warnings (2), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.

then I tried with the command "grompp -f input_min.mdp -o min.tpr -c
add.gro -maxwarn 2000" and it run well.

However, when I kept working with the command "mdrun -s min -o min -c
min.g96 -x min -e min -g min", the errors appeared as follow:

Fatal error:
3 particles communicated to PME node 2 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Please help me to fix this problem.

Many thanks.


Nguyen Van Cuong
PhD student - Curtin University of Technology
Mobile: (+61) 452213981
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Re: [gmx-users] Adding ions using "genion"

[lina]

On Thu, Nov 24, 2011 at 5:16 PM, cuong nguyen  wrote:
> Dear,
> I create a box of water with 10 MIBC molecules on two opposite surfaces.
> then I used the command "grompp -f input_min.mdp -o min.tpr -c box1.g96" to
> creat .tpr file before using the command "genion -s min.tpr -o add.gro
> -nname Cl -pname NA -nn 20 -np 20" to add 20 Na+ and 20 Cl- into this box.
> I run the command "grompp -f input_min.mdp -o min.tpr -c add.gro" again and
> appeared the warings :
> Warning: atom name 176 in topol.top and add.gro does not match (CL - OW)
> Warning: atom name 177 in topol.top and add.gro does not match (CL - HW1)
> Warning: atom name 178 in topol.top and add.gro does not match (CL - HW2)
> Warning: atom name 179 in topol.top and add.gro does not match (CL - OW)
> Warning: atom name 180 in topol.top and add.gro does not match (CL - HW1)

There is a mis-match between your .top file and .gro file.

> (more than 20 non-matching atom names)
> WARNING 1 [file topol.top, line 72]:
>   21754 non-matching atom names
>   atom names from topol.top will be used
>   atom names from add.gro will be ignored
> ..
> Fatal error:
> Too many warnings (2), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> then I tried with the command "grompp -f input_min.mdp -o min.tpr -c add.gro
> -maxwarn 2000" and it run well.
> However, when I kept working with the command "mdrun -s min -o min -c
> min.g96 -x min -e min -g min", the errors appeared as follow:
> Fatal error:
> 3 particles communicated to PME node 2 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> Please help me to fix this problem.
> Many thanks.
>
> Nguyen Van Cuong
> PhD student - Curtin University of Technology
> Mobile: (+61) 452213981
>
>
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Re: [gmx-users] Adding ions using "genion"

[Mark Abraham]

On 24/11/2011 8:16 PM, cuong nguyen wrote:

Dear,

I create a box of water with 10 MIBC molecules on two opposite surfaces.
then I used the command "grompp -f input_min.mdp -o min.tpr -c 
box1.g96" to creat .tpr file before using the command "genion -s 
min.tpr -o add.gro -nname Cl -pname NA -nn 20 -np 20" to add 20 Na+ 
and 20 Cl- into this box.
I run the command "grompp -f input_min.mdp -o min.tpr -c add.gro" 
again and appeared the warings :


Warning: atom name 176 in topol.top and add.gro does not match (CL - OW)
Warning: atom name 177 in topol.top and add.gro does not match (CL - HW1)
Warning: atom name 178 in topol.top and add.gro does not match (CL - HW2)
Warning: atom name 179 in topol.top and add.gro does not match (CL - OW)
Warning: atom name 180 in topol.top and add.gro does not match (CL - HW1)
(more than 20 non-matching atom names)

WARNING 1 [file topol.top, line 72]:
  21754 non-matching atom names
  atom names from topol.top will be used
  atom names from add.gro will be ignored
..
Fatal error:
Too many warnings (2), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.

then I tried with the command "grompp -f input_min.mdp -o min.tpr -c 
add.gro -maxwarn 2000" and it run well.


No, it ran poorly, because you didn't understand what you were doing 
with -maxwarn. Your atom ordering must match between the .top and .gro 
files. Ignoring the warning doesn't fix the problem.


Mark



However, when I kept working with the command "mdrun -s min -o min -c 
min.g96 -x min -e min -g min", the errors appeared as follow:


Fatal error:
3 particles communicated to PME node 2 are more than 2/3 times the 
cut-off out of the domain decomposition cell of their charge group in 
dimension x.

This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors

Please help me to fix this problem.

Many thanks.

Nguyen Van Cuong
PhD student - Curtin University of Technology
Mobile: (+61) 452213981





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Re: [gmx-users] do remd in the npt ensemble:Warning: pressure scaling more than 1%, mu: 333821 333821 333821

[Mark Abraham]

On 24/11/2011 6:31 PM, 杜波 wrote:

dear teacher,
when i do remd in the npt ensemble.

=md.mdp===
; Start time and timestep in ps
tinit = 0
dt = 0.01
nsteps = 5000
; For exact run continuation or redoing part of a run

; Temperature coupling
Tcoupl = nose-hoover
; Groups to couple separately
tc_grps = system
; Time constant (ps) and reference temperature (K)
tau_t = 0.3
ref_t = 800
; Pressure coupling
Pcoupl = berendsen
pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 0.5
compressibility = 6.5e-5
ref_p = 1.0
==error
step 00, will finish Mon Nov 28 00:11:22 2011
step 100, will finish Mon Nov 28 00:11:19 2011

Step 102 Warning: pressure scaling more than 1%, mu: 333821 333821 
333821


Step 102 Warning: pressure scaling more than 1%, mu: 455440 455440 
455440


---
Program mdrun_mpi_4.5.5, VERSION 4.5.5
Source code file: smalloc.c, line: 214

Fatal error:
Not enough memory. Failed to realloc -5476105916 bytes for grid->nra, 
grid->nra=0x38ce0

(called from file nsgrid.c, line 483)
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---
===command=
mpirun n8,8,8,11,11,11,11,2 -np $n_thread 
/export/software/bin/mdrun_mpi_4.5.5 -multidir ./0/ ./1/ ./2/ ./3/ 
./4/ ./5/ ./6/ ./7/ ./8/ ./9/ ./10/ ./11/ ./12/ ./13/ ./14/ ./15/ 
-replex 50 -nice 0 -s pmma.tpr -o md -c after_md -pd -v >& log1 &


how could i do except use the smaller dt or big/small tau_p ?



Surprisingly, the URL provided in the error message contains a useful 
source of information:

http://www.gromacs.org/Documentation/Errors#Pressure_scaling_more_than_1.25

Mark
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[gmx-users] centroid clustering

[Mark Abraham]

On 24/11/2011 5:07 PM, Robel Teklebrhan wrote:



  Dear gmx users,

  Is centroid to centroid clustering method available in Gromacs? I 
want to use this method to cluster my molecules?




When asking for help, please start a new email with a descriptive 
subject so that the people who you hope can help you can use their time 
effectively, and future users can find the discussion. Before asking for 
help, please search likely places for information - like g_cluster -h.


Mark
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[gmx-users] Umbrella Sampling tutorial

[Steven Neumann]

Hey Gmx Users,

I went through Justin tutorial of umbrella sampling with spacing of 0.2 nm:
Time  COM distance
   0  -  0.5
208 -  0.7
218 -  0.92
225 - 1.119
231 - 1.41
235 - 1.61
239 - 1.81
246 - 2.09
253 - 2.3
261 - 2.51
268 - 2.71
276 - 2.91
289 - 3.11
307 - 3.3
325 - 3.5
348 - 3.7
359 - 3.93
371 - 4.1
388 - 4.3
412 - 4.51
423 - 4.7
450 - 4.92
454 - 5

Together 22 windows. I obtained delatG= -37 kcal/mol

Do you have any clue why is that so far away from the value from tutorial
of -50.5 kcal./mol?

Thank you,

Steven
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Re: [gmx-users] grompp line too long error

[杨伟]

Here is the detailed info about my setup:
System:64-bit Linux
GMX version:4.5.4
I know that windows and linux have different line end format and I didn't edit 
my text files using editor on windows,but all on linux.
My goal is to simulate membrane protein embeded in lipid bilayer,I don't have 
experience working with gromacs before,so I followed the tutorial recommended 
by the official gromacs website:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
I downloaded the files offered by the tutorial and proceeded and then 
encountered some problems.
As there is no lipid molecular defenition in gromacs,the tutorial refered me to 
this link:
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
to download the so called "Berger lipids",I did exactly what the tutorial 
instucted.
When I called pdb2gmx,I found the nomenclature of atoms in "Berger lipids" is 
not consistent with that of the gromos53a6 forcefield.
I abandoned "Berger lipids" because I found the DPPC lipid model offered by 
Oxford lipidbook is consistent with gromos53a6 forcefield,then pdb2gmx 
worked.You can find the lipidbook here:
http://lipidbook.bioch.ox.ac.uk/package/show/id/14.html
After generating the .gro file,I called grompp to generate the .tpr file,and 
then,grompp throwed the very error message in my original mail.I didn't modify 
the files generated by the programs I called.
In order to re-generate the error message, I zipped the forcefield files I 
used, you can find it here:
http://ishare.iask.sina.com.cn/f/21401866.html?w='%20target='_blank'
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[gmx-users] Regarding KALP-15 Simulation

[Ravi Kumar Venkatraman]

Dear All,
 *Sorry folks* without following the subsequent lines I came to
wrong conclusion. But I got stuck with some other problem. After
concatenating the dppc128 periodicity corrected box and kalp box the
numbers indices of the atoms are not continuos so when I run the grompp
command I am getting an error. Is there any easy way to correct those
numbers in an easy way.

I am showing part of the final gro file to  explain my problem clearly
  16ALA CA  132   3.227   3.454   4.449
   16ALA CB  133   3.160   3.571   4.374
   16ALA  C  134   3.130   3.393   4.550
   16ALA  O  135   3.149   3.408   4.670
   17NH2  N  136   3.044   3.305   4.501
   17NH2 H1  137   3.046   3.283   4.404
  * 17NH2 H2  138   2.978   3.261   4.561**
1DPPCC11   1.577   5.265   0.920*
1DPPCC22   1.675   5.295   1.135
1DPPCC33   1.648   5.482   0.985
1DPPCN44   1.680   5.338   0.995
1DPPCC55   1.808   5.301   0.932
1DPPCC66   1.929   5.396   0.953

Thank you in Advance.

*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.

+91-9686933963.*
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Re: [gmx-users] grompp line too long error

[Gianluca Santoni]

Here is the detailed info about my setup:
System:64-bit Linux
GMX version:4.5.4
I know that windows and linux have different line end format and I 
didn't edit my text files using editor on windows,but all on linux.
Which editor? Problems in principle could arise from your encodings 
setup, even on linux.


My goal is to simulate membrane protein embeded in lipid bilayer,I 
don't have experience working with gromacs before,so I followed the 
tutorial recommended by the official gromacs website:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
I downloaded the files offered by the tutorial and proceeded and then 
encountered some problems.
As there is no lipid molecular defenition in gromacs,the tutorial 
refered me to this link:

http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
to download the so called "Berger lipids",I did exactly what the 
tutorial instucted.
When I called pdb2gmx,I found the nomenclature of atoms in "Berger 
lipids" is not consistent with that of the gromos53a6 forcefield.
I abandoned "Berger lipids" because I found the DPPC lipid model 
offered by Oxford lipidbook is consistent with gromos53a6 
forcefield,then pdb2gmx worked.You can find the lipidbook here:

http://lipidbook.bioch.ox.ac.uk/package/show/id/14.html
After generating the .gro file,I called grompp to generate the .tpr 
file,and then,grompp throwed the very error message in my original 
mail.I didn't modify the files generated by the programs I called.
In order to re-generate the error message, I zipped the forcefield 
files I used, you can find it here:
http://ishare.iask.sina.com.cn/f/21401866.html?w='%20target='_blank' 







--
Gianluca Santoni,
Institut de Biologie Structurale
41 rue Horowitz
Grenoble
_
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html

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[gmx-users] mdrun -rerun (not reproducible energy values?)

[Vasileios Tatsis]

Dear Gromacs Users,

I am using the -rerun option of mdrun to re-analyze a trajectory. Thus,  I 
tried to rerun the same trajectory (md.xtc) with exactly the same md.tpr. 
But the bonded interactions are not computed or written to the log file or to 
the .edr file, resulting to completely different energy values from the initial 
log and edr files.
I am using the following command, in order to read the coordinates stored in 
the .xtc file and compute the potential energy:
mdrun -rerun md.xtc -s md.tpr 


Thanks in advance for your help-- 
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[gmx-users] Reg : Simulating heterologous protein complex with bound ligand

[Rohit Farmer]

Dear Gromacs Users,

I am working on a protein complex with two subunits which are 
heterologous and I docked them using HADDOCK. Now, to one of the subunit 
I built a ligand covalently attached to one of the residue, which enters 
into the active site of the another subunit in the complex.


Now I want to simulate the entire complex i.e. the two subunits and the 
bound ligand. Does anyone know how it can be done.


Many thanks

Rohit

PhD Biosciences
University of Birmingham
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[gmx-users] multiple molecules simulations

[Gloria Saracino]

Dear all, 

I have performed a simulation on eight identical peptides (composed by 11 
residues) embedded in explicit water. Box dimensions (cube of 7.92nm) have been 
chosen to get a high concentration to accelerate the aggregation process. PME 
has been used and rvdw=rcoulomb=0.9. 
The trajectory has been centered on a residue of a chain with
trjconv -f *.xtc -center -pbc mol -s *.tpr -n *.ndx
During the first 16ns even if each peptide cannot see its periodic image, the 
whole set of peptides (Protein in the index file) see itself in some frames at 
distances below 2nm, and in a very few of them below 0.9nm.
Looking at the trajectory in vmd after less then 2ns I see the formation of an 
oligomer composed by six peptides, the other two peptides move around leaving 
the oligomer on a side and approaching on an other side. The oligomer never 
sees its periodic image as well as the two peptides never see their periodic 
image. The pi violations observed for the whole system correspond to the two 
peptides that, together or one at time, are placed between the oligomer and its 
pi. Considering 0.9nm as the distance below of which there is a direct 
interaction I found that when the minimum distance of the two peptides from one 
side of the oligomer is close to 0.9, the minimum distance from the other side 
is always above 1.4nm.
Moreover the LJ and coulomb trends don't show abnormalities.
Even if in simulations of a single molecule the effect of periodic image 
violation is a clear signal of a too small box to approximate a condition of 
infinite diluition, how I have to interpret such a violation for a system 
composed by multiple molecules and in which I want to reproduce a condition of 
high concentration? 
Can I use this simulation to study the behavior of the system at the chosen 
concentration? 
There are particular simulation settings or checks that I have to take into 
account to handle a high concentrated solution a
nd that I overlooked?

Any help will be appreciated (I apologize if some questions may seem trivial),

Gloria-- 
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[gmx-users] Time step problem on coarse-grained LJ chain

[Tomy van Batis]

Dear all

I am trying to simulate a Lennard-Jones coarse-grained polymer melt. Until
know I simulated only one chain, in order to check if the parameters I used
are OK.

I simulated one chain of 50 LJ particles with *ε=1KJ/mol, m=1gr/mol, σ=1nm*.
This means that my characteristic time of the system *τ=σ(m/ε)1/2* is *τ=1ps.
*

I am using RIGID bonds between the particles also with length *σ=1nm*.

I have seen in many papers which are using similar systems that the time
step they use is Dt=0.01τ.

When I use *Dt=0.01τ* I don't get any error messages in my *.log* file or
in the resulting *.gro* file.

The problem that I have is when I am trying to convert my *.xtc* file to *
.pdb* in order to visualize it in VMD.

When I use:

*trjconv -f  ***.xtc   -s  ***.tpr  -o  ***.pdb -pbc whole*

the trajectory looks fine.

BUT, when I use

*trjconv-f  ***.xtc-s ***.tpr   -o ***.pdb -pbc nojump*

, it seems the chain is blowing after few steps (the bonds break and the
particles spread in every direction).

I would think that for a single chain, these two options of trjconv should
not make such a difference.

I used a relatively big box for the simulation (10 X 10 X 60). The
*strange*think is that I don't have this problem when I increase the
box size (to
50X50X60) , or of course when I decrease the time step.

Is it possible that I am not able to use such a large time-step in GROMACS,
or is it something with the *trjconv* that I don't understand ?

Thanks in advance

Best Regards, Chrysostomos
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Re: [gmx-users] 2. Re: GROMACS/ORCA QMMM (Jose Tusell)

[Christoph Riplinger]

Dear Jose,

I just installed the 4.5.5. version and the calculation runs ok for me! 
But I did change the ORCAINFO file:

First of all you should clean your ORCAINFO file. Remove
!QMMMOpt COPT
and remove
!EnGrad
Otherwise the program might get confused about doing a single point and 
gradient calculation only. I.e. as stated in the manual, you should only 
give information on the electronic structure calculation method and 
basis set in the ORCAINFO file. Gromacs itself will put the

!QMMMOpt
keyword, if you request
bOpt = yes
Otherwise Gromacs puts
!EnGrad

Furthermore, you chose !COPT in the ORCAINFO file. Do you want to have 
the optimization done in cartesian coordinates? I would suggest you do 
the optimization in internal coordinates. This runs usually faster. Did 
you try the optimization in internal coordinates?


Hope that helps,
Christoph



On 11/22/2011 04:25 PM, Jose Tusell wrote:

I'm using GROMACS 4.5.5.  Here is my minim.mdp file:

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 500.0 ; Stop minimization when the maximum
force<  1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization)
steps to perform

; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor
list and long range forces
ns_type = grid  ; Method to determine neighbor list
(simple, grid)
rlist   = 1.0   ; Cut-off for making neighbor list
(short range forces)
coulombtype = PME   ; Treatment of long range
electrostatic interactions
rcoulomb= 1.0   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)
nstxout = 10; save coordinates every 0.2 ps
nstvout = 10; save velocities every 0.2 ps
nstenergy   = 10; save energies every 0.2 ps
nstlog  = 10; update log file every 0.2 ps

QMMM= yes
QMMM-grps   = Other
QMmethod= RHF
QMbasis = 3-21G
QMMMscheme  = Normal
QMcharge= -2
QMmult  = 1
SH  = no
bOpt= yes
bTS = no

Here is my ORCAINFO file:

!PAL8 Quick-DFT VerySlowConv TightSCF KDIIS VDW EnGrad NoUseSym
!QMMMOpt COPT
%scf
   Maxiter 5000
end
%pal nprocs 8
end

I think that all you need to reproduce the error.  Let me know what you find.

Thanks for you input,

Jose R Tusell

On Tue, Nov 22, 2011 at 8:06 AM, Christoph Riplinger
  wrote:

Dear Jose,

Also our calculations using bOpt with ORCA are fine.
ORCA does not give the coordinates in nm, but in Angstrom.
Which version of gromacs are you using?
Christoph

On 11/22/2011 03:53 PM, Jose Tusell wrote:

When GROMACS takes care of the optimization this doesn't happen.

Jose R Tusell


On Tue, Nov 22, 2011 at 12:35 AM, Gerrit Groenhofwrote:

  On 11/22/2011 04:02 AM,gmx-users-requ...@gromacs.org  wrote:

gmx-users@gromacs.org

To subscribe or unsubscribe via the World Wide Web, visit

  2. Re: GROMACS/ORCA QMMM (Jose Tusell)

Does anyone know what is going on with the coordinates of the QM
region?  Why are they not converted to the correct units?  Could
anyone point me to the error?

I have not experienced this myself. The only thing I can think of is that
ORCA returns the atom coordinates in nm?
Does this happen also when you let Gromacs take care of the optimization?

Gerrit



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Re: [gmx-users] pyroglutamate in gromos53a6

[Henry Hocking]

Thank you Tsjerk,

I am now trying with amber99.ff but have encountered the following  
problem:


My PCA is at the N-terminus. I have an entry for [ NPCA ] in  
aminoacids.rtp and have updated aminoacids.r2b to include NPCA and  
I've even added an entry in aminoacids.hdb for NPCA. Yet when I  
generate my itp/gro files using pdb2gmx, the NPCA is recognises (all  
atoms are there) but the second residue [ GLY ] is now changed to  
[ NGLY ] in the itp file despite still being the second residue in the  
gro file. As a test, if I remove NGLY from aminoacids.r2b it complains  
that 'there is no residue type for 'GLY' as a starting terminus' thus  
ignoring that the first residue of my chain is in fact NPCA.


What could be going on here? The -ter flag has no effect here as I  
noticed that for all amber99XX.ff the aminoacids.n.tdb files are empty.


Cheers,

Henry



On 22 Nov 2011, at 18:17, Tsjerk Wassenaar wrote:


Hi Henry,

That would be a bit of a wild west approach. A better approximation
would be taking the charges from the backbone amide group, as it is
just an amide with on either side aliphatic carbons. Doing it properly
is a bit more involved, as for the G53a6 FF you need to choose
parameters giving the right free enthalpy of solvation.

Groetjes,

Tsjerk

On Tue, Nov 22, 2011 at 5:10 PM, Henry Hocking   
wrote:

Dear all,
Where can I find gromos53a6.ff parameters for pyroglutamate (PCA/  
PGLU/ PGA)

?
Alternatively, given that I have them in amber99.ff and oplsaa.ff  
is there a

way I could adapt these to gromos53a6.ff?
Can I use, for example, the gromos53a6.ff atom types from glutamine,
add/remove appropriate bonds / angles / impropers and then take the
corresponding charge values from my amber99.ff/aminoacid.rtp file.  
I assume
that what I've just suggested is the cowboy method and that in  
reality it is

not that straightforward, right?
Kind regards,
Henry

Henry Hocking, PhD
Utrecht University
Bijvoet Center for Biomolecular Research
Padualaan 8
3584 CH Utrecht, The Netherlands
Phone: +31-30-2532875
Fax: +31-30-253 7623
E-mail: h.g.hock...@uu.nl





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--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Bijvoet Center for Biomolecular Research
Padualaan 8
3584 CH Utrecht, The Netherlands

Phone: +31-30-2532875
Fax: +31-30-253 7623
E-mail: h.g.hock...@uu.nl





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Re: [gmx-users] Time step problem on coarse-grained LJ chain

[Tsjerk Wassenaar]

Hi Chrysostomos,

To understand this, you have to understand how jumps are removed. I
explained that before, and it's in the archive somewhere. The bottom
line is that jumps can't be removed properly when intervals between
frames are too large, or the changes in position are too large
relative to the size of the box.

Cheers,

Tsjerk

2011/11/24 Tomy van Batis :
> Dear all
>
> I am trying to simulate a Lennard-Jones coarse-grained polymer melt. Until
> know I simulated only one chain, in order to check if the parameters I used
> are OK.
>
> I simulated one chain of 50 LJ particles with ε=1KJ/mol, m=1gr/mol, σ=1nm.
> This means that my characteristic time of the system τ=σ(m/ε)1/2 is τ=1ps.
>
> I am using RIGID bonds between the particles also with length σ=1nm.
>
> I have seen in many papers which are using similar systems that the time
> step they use is Dt=0.01τ.
>
> When I use Dt=0.01τ I don't get any error messages in my .log file or in the
> resulting .gro file.
>
> The problem that I have is when I am trying to convert my .xtc file to .pdb
> in order to visualize it in VMD.
>
> When I use:
>
> trjconv -f  ***.xtc   -s  ***.tpr  -o  ***.pdb -pbc whole
>
> the trajectory looks fine.
>
> BUT, when I use
>
> trjconv-f  ***.xtc-s ***.tpr   -o ***.pdb -pbc nojump
>
> , it seems the chain is blowing after few steps (the bonds break and the
> particles spread in every direction).
>
> I would think that for a single chain, these two options of trjconv should
> not make such a difference.
>
> I used a relatively big box for the simulation (10 X 10 X 60). The strange
> think is that I don't have this problem when I increase the box size (to
> 50X50X60) , or of course when I decrease the time step.
>
> Is it possible that I am not able to use such a large time-step in GROMACS,
> or is it something with the trjconv that I don't understand ?
>
> Thanks in advance
>
> Best Regards, Chrysostomos
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] pyroglutamate in gromos53a6

[Tsjerk Wassenaar]

Hi Henry,

Apparently NPCA is not listed as being protein, so pdb2gmx assumes
that the chain begins with GLY. Add NPCA to the file residuetypes.dat
one directory up, with the designation 'Protein'. I think that should
solve it.

Groetjes,

Tsjerk

On Thu, Nov 24, 2011 at 6:59 PM, Henry Hocking  wrote:
> Thank you Tsjerk,
> I am now trying with amber99.ff but have encountered the following problem:
> My PCA is at the N-terminus. I have an entry for [ NPCA ] in aminoacids.rtp
> and have updated aminoacids.r2b to include NPCA and I've even added an entry
> in aminoacids.hdb for NPCA. Yet when I generate my itp/gro files using
> pdb2gmx, the NPCA is recognises (all atoms are there) but the second residue
> [ GLY ] is now changed to [ NGLY ] in the itp file despite still being the
> second residue in the gro file. As a test, if I remove NGLY from
> aminoacids.r2b it complains that 'there is no residue type for 'GLY' as a
> starting terminus' thus ignoring that the first residue of my chain is in
> fact NPCA.
> What could be going on here? The -ter flag has no effect here as I noticed
> that for all amber99XX.ff the aminoacids.n.tdb files are empty.
> Cheers,
> Henry
>
>
>
> On 22 Nov 2011, at 18:17, Tsjerk Wassenaar wrote:
>
> Hi Henry,
>
> That would be a bit of a wild west approach. A better approximation
> would be taking the charges from the backbone amide group, as it is
> just an amide with on either side aliphatic carbons. Doing it properly
> is a bit more involved, as for the G53a6 FF you need to choose
> parameters giving the right free enthalpy of solvation.
>
> Groetjes,
>
> Tsjerk
>
> On Tue, Nov 22, 2011 at 5:10 PM, Henry Hocking  wrote:
>
> Dear all,
>
> Where can I find gromos53a6.ff parameters for pyroglutamate (PCA/ PGLU/ PGA)
>
> ?
>
> Alternatively, given that I have them in amber99.ff and oplsaa.ff is there a
>
> way I could adapt these to gromos53a6.ff?
>
> Can I use, for example, the gromos53a6.ff atom types from glutamine,
>
> add/remove appropriate bonds / angles / impropers and then take the
>
> corresponding charge values from my amber99.ff/aminoacid.rtp file. I assume
>
> that what I've just suggested is the cowboy method and that in reality it is
>
> not that straightforward, right?
>
> Kind regards,
>
> Henry
>
> 
>
> Henry Hocking, PhD
>
> Utrecht University
>
> Bijvoet Center for Biomolecular Research
>
> Padualaan 8
>
> 3584 CH Utrecht, The Netherlands
>
> Phone: +31-30-2532875
>
> Fax: +31-30-253 7623
>
> E-mail: h.g.hock...@uu.nl
>
>
>
>
>
> --
>
> gmx-users mailing list    gmx-users@gromacs.org
>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
>
> Please search the archive at
>
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>
> Please don't post (un)subscribe requests to the list. Use the
>
> www interface or send it to gmx-users-requ...@gromacs.org.
>
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing list    gmx-users@gromacs.org
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>
> 
> Henry Hocking, PhD
> Utrecht University
> Bijvoet Center for Biomolecular Research
> Padualaan 8
> 3584 CH Utrecht, The Netherlands
> Phone: +31-30-2532875
> Fax: +31-30-253 7623
> E-mail: h.g.hock...@uu.nl
>
>
>
>
>
> --
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] pyroglutamate in gromos53a6

[Henry Hocking]

Thank you Tsjerk,

Now it works !

Cheers,

Henry

On 24 Nov 2011, at 23:11, Tsjerk Wassenaar wrote:


Hi Henry,

Apparently NPCA is not listed as being protein, so pdb2gmx assumes
that the chain begins with GLY. Add NPCA to the file residuetypes.dat
one directory up, with the designation 'Protein'. I think that should
solve it.

Groetjes,

Tsjerk

On Thu, Nov 24, 2011 at 6:59 PM, Henry Hocking   
wrote:

Thank you Tsjerk,
I am now trying with amber99.ff but have encountered the following  
problem:
My PCA is at the N-terminus. I have an entry for [ NPCA ] in  
aminoacids.rtp
and have updated aminoacids.r2b to include NPCA and I've even added  
an entry
in aminoacids.hdb for NPCA. Yet when I generate my itp/gro files  
using
pdb2gmx, the NPCA is recognises (all atoms are there) but the  
second residue
[ GLY ] is now changed to [ NGLY ] in the itp file despite still  
being the

second residue in the gro file. As a test, if I remove NGLY from
aminoacids.r2b it complains that 'there is no residue type for  
'GLY' as a
starting terminus' thus ignoring that the first residue of my chain  
is in

fact NPCA.
What could be going on here? The -ter flag has no effect here as I  
noticed

that for all amber99XX.ff the aminoacids.n.tdb files are empty.
Cheers,
Henry



On 22 Nov 2011, at 18:17, Tsjerk Wassenaar wrote:

Hi Henry,

That would be a bit of a wild west approach. A better approximation
would be taking the charges from the backbone amide group, as it is
just an amide with on either side aliphatic carbons. Doing it  
properly

is a bit more involved, as for the G53a6 FF you need to choose
parameters giving the right free enthalpy of solvation.

Groetjes,

Tsjerk

On Tue, Nov 22, 2011 at 5:10 PM, Henry Hocking   
wrote:


Dear all,

Where can I find gromos53a6.ff parameters for pyroglutamate (PCA/  
PGLU/ PGA)


?

Alternatively, given that I have them in amber99.ff and oplsaa.ff  
is there a


way I could adapt these to gromos53a6.ff?

Can I use, for example, the gromos53a6.ff atom types from glutamine,

add/remove appropriate bonds / angles / impropers and then take the

corresponding charge values from my amber99.ff/aminoacid.rtp file.  
I assume


that what I've just suggested is the cowboy method and that in  
reality it is


not that straightforward, right?

Kind regards,

Henry



Henry Hocking, PhD

Utrecht University

Bijvoet Center for Biomolecular Research

Padualaan 8

3584 CH Utrecht, The Netherlands

Phone: +31-30-2532875

Fax: +31-30-253 7623

E-mail: h.g.hock...@uu.nl





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--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Henry Hocking, PhD
Utrecht University
Bijvoet Center for Biomolecular Research
Padualaan 8
3584 CH Utrecht, The Netherlands
Phone: +31-30-2532875
Fax: +31-30-253 7623
E-mail: h.g.hock...@uu.nl





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--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Utrecht University
Bijvoet Center for Biomolecular Research
Padu

Re: [gmx-users] Umbrella Sampling tutorial

[Justin A. Lemkul]

Steven Neumann wrote:

Hey Gmx Users,
 
I went through Justin tutorial of umbrella sampling with spacing of 0.2 nm:

Time  COM distance
   0  -  0.5
208 -  0.7
218 -  0.92
225 - 1.119
231 - 1.41
235 - 1.61
239 - 1.81
246 - 2.09
253 - 2.3
261 - 2.51
268 - 2.71
276 - 2.91
289 - 3.11
307 - 3.3
325 - 3.5
348 - 3.7
359 - 3.93
371 - 4.1
388 - 4.3
412 - 4.51
423 - 4.7
450 - 4.92
454 - 5
 
Together 22 windows. I obtained delatG= -37 kcal/mol
 
Do you have any clue why is that so far away from the value from 
tutorial of -50.5 kcal./mol?
 


Not really.  You don't have the even 0.2-nm spacing that the tutorial calls for, 
but I know others have reproduced the value, so it should certainly be possible.


-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] Regarding KALP-15 Simulation

[Justin A. Lemkul]

Ravi Kumar Venkatraman wrote:

Dear All,
 *Sorry folks* without following the subsequent lines I came 
to wrong conclusion. But I got stuck with some other problem. After 
concatenating the dppc128 periodicity corrected box and kalp box the 
numbers indices of the atoms are not continuos so when I run the grompp 
command I am getting an error. Is there any easy way to correct those 
numbers in an easy way.




What error are you getting?  The numbering in the .gro file should not cause a 
problem.  Non-consecutive numbering in the .top can cause a fatal error, but 
should not be relevant here.


-Justin


I am showing part of the final gro file to  explain my problem clearly
  16ALA CA  132   3.227   3.454   4.449
   16ALA CB  133   3.160   3.571   4.374
   16ALA  C  134   3.130   3.393   4.550
   16ALA  O  135   3.149   3.408   4.670
   17NH2  N  136   3.044   3.305   4.501
   17NH2 H1  137   3.046   3.283   4.404
  * 17NH2 H2  138   2.978   3.261   4.561**
1DPPCC11   1.577   5.265   0.920*
1DPPCC22   1.675   5.295   1.135
1DPPCC33   1.648   5.482   0.985
1DPPCN44   1.680   5.338   0.995
1DPPCC55   1.808   5.301   0.932
1DPPCC66   1.929   5.396   0.953

Thank you in Advance.

*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.

+91-9686933963.*



--


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


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Re: [gmx-users] Reg : Simulating heterologous protein complex with bound ligand

[Justin A. Lemkul]

Rohit Farmer wrote:

Dear Gromacs Users,

I am working on a protein complex with two subunits which are 
heterologous and I docked them using HADDOCK. Now, to one of the subunit 
I built a ligand covalently attached to one of the residue, which enters 
into the active site of the another subunit in the complex.


Now I want to simulate the entire complex i.e. the two subunits and the 
bound ligand. Does anyone know how it can be done.




Multiple proteins should be automatically processed with pdb2gmx, provided you 
give some indication where new chains should start (see pdb2gmx -chainsep for 
options).  Novel residues have to be parameterized and implemented in the parent 
force field.  See:


http://www.gromacs.org/Documentation/How-tos/Parameterization
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Justin

--


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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] Reg : Simulating heterologous protein complex with bound ligand

[Rohit Farmer]

Dear Gromacs Users,

I am working on a protein complex with two subunits which are
heterologous and I docked them using HADDOCK. Now, to one of the subunit
I built a ligand covalently attached to one of the residue, which enters
into the active site of the another subunit in the complex.

Now I want to simulate the entire complex i.e. the two subunits and the
bound ligand. Does anyone know how it can be done.

Many thanks

Rohit

PhD Biosciences
University of Birmingham

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Re: [gmx-users] amber99sb in GROMACS vs amber99sb in AMBER

[Thomas Evangelidis]

Hi Oliver,

Apologies for the late reply. The comparison you have showed us has been
done for a DNA fragment. Do you believe that negligible errors can also be
obtained for proteins using the amber99sb force field?

thanks,
Thomas



On 22 November 2011 11:58, Oliver Grant  wrote:

> Hi there,
>
> Acpype does the conversion for you and the results from their own testing
> are here:
> http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx
>
> For reproducing experimental data I would look in the original force-field
> publications.
>
> Oliver
>
>
> On Mon, Nov 21, 2011 at 8:21 PM, Michael Shirts wrote:
>
>> > Is anyone aware of any benchmark analysis about the implementation of
>> the
>> > amber99sb force field (or any of its variants: 99sb-ildn, 99sb-nmr) in
>> > GROMACS and AMBER. I am interested to know in what extend the energies
>> > correlate and if the results agree with experimental data.
>>
>> Whether the results compare agree with experimental data is irrelevant
>> to the correctness of the implementation -- that has to do with the
>> validity of AMBER99sb to begin with.  The only question is, do GROMACS
>> and AMBER give the same energies for the same configurations?
>>
>> I actually do not know the answer, and would be interested to hear if
>> it's been tested.  http://ffamber.cnsm.csulb.edu/ does not appear to
>> have the very comprehensive tests that appear for earlier models at
>> the current time.  I SUSPECT there should not be a problem, since
>> AMBER99sb just changed a couple of torsions, so errors are unlikely
>> (though in theory possible).
>> --
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>>
>
>
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-- 

==

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tev...@bioacademy.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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Re: [gmx-users] mdrun -rerun (not reproducible energy values?)

[Mark Abraham]

On 25/11/2011 2:28 AM, Vasileios Tatsis wrote:

Dear Gromacs Users,

I am using the -rerun option of mdrun to re-analyze a trajectory. 
Thus, I tried to rerun the same trajectory (md.xtc) with exactly the 
same md.tpr.
But the bonded interactions are not computed or written to the log 
file or to the .edr file, resulting to completely different energy 
values from the initial log and edr files.


That does not sound possible if the .tpr is the same. With bond or angle 
constraints, some bonded terms would not appear in either version, of 
course.


Mark


I am using the following command, in order to read the coordinates stored in 
the .xtc file and compute the potential energy:
mdrun -rerun md.xtc -s md.tpr

Thanks in advance for your help




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[gmx-users] Pressure stabilization during NPT phase

[James Starlight]

Dear Gromacs Users!


At the present time I'm simulating small peptide (11 a.c in coiled
conformation) in water.

I've desided to use parameters from Lysozyme simmulation ( opls ff for
parametrisation and all mdp parameters from that simulation).

Because my peptide was smaller than typical globular protein I've desided
to use bigger periodical box than in tutorial

I've used editconf  -c -d 1.5 -bt cubic instead of 1.0 nm in tutorial wich
resulted in bigger box relative peptide size.

so i have this box vectors5.39318   5.39318   5.39318

My experiment was in full agreement with the above tutorial until NVP phase
was conducted. I have conducted 100ps equilibration but When I've checked
average pressure it was 0.75 atm instead of 1 BAR and have big RMSD- 200.
(also I've checked my system visually but it looks fine- I have not
pointed any artifacts linked with unstable pressure like voids in the
solvent etc). Should I equilibrate my sustem longer until pressure would
not be stabilized to reference BAR?  What another options should i take
into account during simulation of the small peptides ?

Thanks,

James
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[gmx-users] about relaxation protocol

[Albert]

Dear all:

  I am a new Gromacs user and I would like to relax my membrane system 
by linear force constant:


NPT with protein and ligand heavy atoms annealing, force constant was 
removed from 10.0-->0 Kal/mol during 10 ns.


Is it possible for Gromacs to introduced such kind of relaxation in a 
.mdp file?


Thank you very much

Best wishes
Albert

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Re: [gmx-users] about relaxation protocol

[Tsjerk Wassenaar]

Hi Albert,

You can use the free energy perturbation stuff. Check the manual.

Cheers,

Tsjerk

On Nov 25, 2011 7:43 AM, "Albert"  wrote:



Dear all:

 I am a new Gromacs user and I would like to relax my membrane system by
linear force constant:

NPT with protein and ligand heavy atoms annealing, force constant was
removed from 10.0-->0 Kal/mol during 10 ns.

Is it possible for Gromacs to introduced such kind of relaxation in a .mdp
file?

Thank you very much

Best wishes
Albert

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Re: [gmx-users] Pressure stabilization during NPT phase

[Mark Abraham]

On 25/11/2011 5:22 PM, James Starlight wrote:

Dear Gromacs Users!


At the present time I'm simulating small peptide (11 a.c in coiled 
conformation) in water.


I've desided to use parameters from Lysozyme simmulation ( opls ff for 
parametrisation and all mdp parameters from that simulation).


Because my peptide was smaller than typical globular protein I've 
desided to use bigger periodical box than in tutorial


I've used editconf  -c -d 1.5 -bt cubic instead of 1.0 nm in tutorial 
wich resulted in bigger box relative peptide size.


so i have this box vectors5.39318   5.39318   5.39318

My experiment was in full agreement with the above tutorial until NVP 
phase was conducted. I have conducted 100ps equilibration but When 
I've checked average pressure it was 0.75 atm instead of 1 BAR and 
have big RMSD- 200. (also I've checked my system visually but it looks 
fine- I have not  pointed any artifacts linked with unstable pressure 
like voids in the solvent etc).


Seems normal for a tiny simulation - 
http://www.gromacs.org/Documentation/Terminology/Pressure


Should I equilibrate my sustem longer until pressure would not be 
stabilized to reference BAR?  What another options should i take into 
account during simulation of the small peptides ?


Seek to reproduce conditions that other published studies have shown 
perform well.


Mark
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Re: [gmx-users] Pressure stabilization during NPT phase

[Tsjerk Wassenaar]

Hi James,

There have been extensive discussions about this on the list. Check the
archives. In short, smaller systems give larger fluctuations, and shorter
simulations give larger deviations from the expected average.

Cheers,

Tsjerk

On Nov 25, 2011 7:23 AM, "James Starlight"  wrote:

Dear Gromacs Users!


At the present time I'm simulating small peptide (11 a.c in coiled
conformation) in water.

I've desided to use parameters from Lysozyme simmulation ( opls ff for
parametrisation and all mdp parameters from that simulation).

Because my peptide was smaller than typical globular protein I've desided
to use bigger periodical box than in tutorial

I've used editconf  -c -d 1.5 -bt cubic instead of 1.0 nm in tutorial wich
resulted in bigger box relative peptide size.

so i have this box vectors5.39318   5.39318   5.39318

My experiment was in full agreement with the above tutorial until NVP phase
was conducted. I have conducted 100ps equilibration but When I've checked
average pressure it was 0.75 atm instead of 1 BAR and have big RMSD- 200.
(also I've checked my system visually but it looks fine- I have not
pointed any artifacts linked with unstable pressure like voids in the
solvent etc). Should I equilibrate my sustem longer until pressure would
not be stabilized to reference BAR?  What another options should i take
into account during simulation of the small peptides ?

Thanks,

James

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Re: [gmx-users] Pressure stabilization during NPT phase

[James Starlight]

Mark, Tsjerk thanks!

I've check my uncompleated produced MD run by G_energy and find that
average pressure is 1.1 Bar that is most close to ref.


By the way could you tell me about extra possible ways of checking running
simmulation? ( E.g I'm calculating long produce trajectory and want to
check my uncompleated system ).

As I understood One of the possible way is the ussage of G_energy but how I
could obtain GRO and TPR file from uncompleated MD trajectory ( .trr)
(recently I've asked about this but I've missed that topic ;o)  ?



Thanks again

James

2011/11/25 Tsjerk Wassenaar 

> Hi James,
>
> There have been extensive discussions about this on the list. Check the
> archives. In short, smaller systems give larger fluctuations, and shorter
> simulations give larger deviations from the expected average.
>
> Cheers,
>
> Tsjerk
>
> On Nov 25, 2011 7:23 AM, "James Starlight"  wrote:
>
> Dear Gromacs Users!
>
>
> At the present time I'm simulating small peptide (11 a.c in coiled
> conformation) in water.
>
> I've desided to use parameters from Lysozyme simmulation ( opls ff for
> parametrisation and all mdp parameters from that simulation).
>
> Because my peptide was smaller than typical globular protein I've desided
> to use bigger periodical box than in tutorial
>
> I've used editconf  -c -d 1.5 -bt cubic instead of 1.0 nm in tutorial wich
> resulted in bigger box relative peptide size.
>
> so i have this box vectors5.39318   5.39318   5.39318
>
> My experiment was in full agreement with the above tutorial until NVP
> phase was conducted. I have conducted 100ps equilibration but When I've
> checked average pressure it was 0.75 atm instead of 1 BAR and have big
> RMSD- 200. (also I've checked my system visually but it looks fine- I have
> not  pointed any artifacts linked with unstable pressure like voids in the
> solvent etc). Should I equilibrate my sustem longer until pressure would
> not be stabilized to reference BAR?  What another options should i take
> into account during simulation of the small peptides ?
>
> Thanks,
>
> James
>
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Re: [gmx-users] Pressure stabilization during NPT phase

[Mark Abraham]

On 25/11/2011 6:38 PM, James Starlight wrote:

Mark, Tsjerk thanks!

I've check my uncompleated produced MD run by G_energy and find that 
average pressure is 1.1 Bar that is most close to ref.



By the way could you tell me about extra possible ways of checking 
running simmulation? ( E.g I'm calculating long produce trajectory and 
want to check my uncompleated system ).


As I understood One of the possible way is the ussage of G_energy but 
how I could obtain GRO and TPR file from uncompleated MD trajectory ( 
.trr) (recently I've asked about this but I've missed that topic ;o)  ?


Choose a length of time in advance that you are happy to risk being 
wasted. Run that length of time, make a backup, check whatever you want 
to check, then continue the simulation. As you acquire confidence, you 
will want to increase that time (and like everyone you will regret that 
decision at least once!)


Mark





Thanks again

James

2011/11/25 Tsjerk Wassenaar mailto:tsje...@gmail.com>>

Hi James,

There have been extensive discussions about this on the list.
Check the archives. In short, smaller systems give larger
fluctuations, and shorter simulations give larger deviations from
the expected average.

Cheers,

Tsjerk


On Nov 25, 2011 7:23 AM, "James Starlight"
mailto:jmsstarli...@gmail.com>> wrote:

Dear Gromacs Users!


At the present time I'm simulating small peptide (11 a.c in
coiled conformation) in water.

I've desided to use parameters from Lysozyme simmulation ( opls
ff for parametrisation and all mdp parameters from that simulation).

Because my peptide was smaller than typical globular protein I've
desided to use bigger periodical box than in tutorial

I've used editconf  -c -d 1.5 -bt cubic instead of 1.0 nm in
tutorial wich resulted in bigger box relative peptide size.

so i have this box vectors5.39318   5.39318   5.39318

My experiment was in full agreement with the above tutorial until
NVP phase was conducted. I have conducted 100ps equilibration but
When I've checked average pressure it was 0.75 atm instead of 1
BAR and have big RMSD- 200. (also I've checked my system visually
but it looks fine- I have not  pointed any artifacts linked with
unstable pressure like voids in the solvent etc). Should I
equilibrate my sustem longer until pressure would not be
stabilized to reference BAR?  What another options should i take
into account during simulation of the small peptides ?

Thanks,

James

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Re: [gmx-users] multiple molecules simulations

[Gloria Saracino]

Dear all,
I did not get an answer yet.
I really want know your opinion. 

If you need other details about the simulation I'm willing to give it to you.
Thank you in advance,

Gloria





 Da: Gloria Saracino 
A: "gmx-users@gromacs.org"  
Inviato: Giovedì 24 Novembre 2011 17:06
Oggetto: [gmx-users] multiple molecules simulations
 

Dear all, 

I have performed a simulation on eight identical peptides (composed by 11 
residues) embedded in explicit water. Box dimensions (cube of 7.92nm) have been 
chosen to get a high concentration to accelerate the aggregation process. PME 
has been used and rvdw=rcoulomb=0.9. 
The trajectory has been centered on a residue of a chain with
trjconv -f *.xtc -center -pbc mol -s *.tpr -n *.ndx
During the first 16ns even if each peptide cannot see its periodic image, the 
whole set of peptides (Protein in the index file) see itself in some frames at 
distances below
 2nm, and in a very few of them below 0.9nm.
Looking at the trajectory in vmd after less then 2ns I see the formation of an 
oligomer composed by six peptides, the other two peptides move around leaving 
the oligomer on a side and approaching on an other side. The oligomer never 
sees its periodic image as well as the two peptides never see their periodic 
image. The pi violations observed for the whole system correspond to the two 
peptides that, together or one at time, are placed between the oligomer and its 
pi. Considering 0.9nm as the distance below of which there is a direct 
interaction I found that when the minimum distance of the two peptides from one 
side of the oligomer is close to 0.9, the minimum distance from the other side 
is always above 1.4nm.
Moreover the LJ and coulomb trends don't show abnormalities.
Even if in simulations of a single molecule the effect of periodic image 
violation is a clear signal of a too small box to
 approximate a condition of infinite diluition, how I have to interpret such a 
violation for a system composed by multiple molecules and in which I want to 
reproduce a condition of high concentration? 
Can I use this simulation to study the behavior of the system at the chosen 
concentration? 
There are particular simulation settings or checks that I have to take into 
account to handle a high concentrated solution a
nd that I overlooked?

Any help will be appreciated (I apologize if some questions may seem trivial),

Gloria


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Re: [gmx-users] Pressure stabilization during NPT phase

[James Starlight]

This way I've already used but is this possible to extract Gro and trp
files from uncompleated runs and not stopping this simulation ?


James

2011/11/25 Mark Abraham 

>  On 25/11/2011 6:38 PM, James Starlight wrote:
>
> Mark, Tsjerk thanks!
>
> I've check my uncompleated produced MD run by G_energy and find that
> average pressure is 1.1 Bar that is most close to ref.
>
>
> By the way could you tell me about extra possible ways of checking running
> simmulation? ( E.g I'm calculating long produce trajectory and want to
> check my uncompleated system ).
>
> As I understood One of the possible way is the ussage of G_energy but how
> I could obtain GRO and TPR file from uncompleated MD trajectory ( .trr)
> (recently I've asked about this but I've missed that topic ;o)  ?
>
>
> Choose a length of time in advance that you are happy to risk being
> wasted. Run that length of time, make a backup, check whatever you want to
> check, then continue the simulation. As you acquire confidence, you will
> want to increase that time (and like everyone you will regret that decision
> at least once!)
>
> Mark
>
>
>
>
>
> Thanks again
>
> James
>
> 2011/11/25 Tsjerk Wassenaar 
>
>> Hi James,
>>
>> There have been extensive discussions about this on the list. Check the
>> archives. In short, smaller systems give larger fluctuations, and shorter
>> simulations give larger deviations from the expected average.
>>
>> Cheers,
>>
>> Tsjerk
>>
>>  On Nov 25, 2011 7:23 AM, "James Starlight" 
>> wrote:
>>
>> Dear Gromacs Users!
>>
>>
>> At the present time I'm simulating small peptide (11 a.c in coiled
>> conformation) in water.
>>
>> I've desided to use parameters from Lysozyme simmulation ( opls ff for
>> parametrisation and all mdp parameters from that simulation).
>>
>> Because my peptide was smaller than typical globular protein I've desided
>> to use bigger periodical box than in tutorial
>>
>> I've used editconf  -c -d 1.5 -bt cubic instead of 1.0 nm in tutorial
>> wich resulted in bigger box relative peptide size.
>>
>> so i have this box vectors5.39318   5.39318   5.39318
>>
>> My experiment was in full agreement with the above tutorial until NVP
>> phase was conducted. I have conducted 100ps equilibration but When I've
>> checked average pressure it was 0.75 atm instead of 1 BAR and have big
>> RMSD- 200. (also I've checked my system visually but it looks fine- I have
>> not  pointed any artifacts linked with unstable pressure like voids in the
>> solvent etc). Should I equilibrate my sustem longer until pressure would
>> not be stabilized to reference BAR?  What another options should i take
>> into account during simulation of the small peptides ?
>>
>> Thanks,
>>
>> James
>>
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