Re: [gmx-users] File input/output error: 1OTI.pdb

[Mark Abraham]

On 29/11/2011 4:10 PM, nbhut...@uci.edu wrote:

Hello all. I have just started research and will be using Gromacs. I am
not very command prompt or linux or programming savvy and I'm slowly
learning how to do certain things. I was trying to convert a pdb file
using pdb2gmx but keep getting the following error:

"File input/output error: 1OTI.pdb".

I'm not entirely sure how to solve this issue. The command I wrote is as
follows:

pdb2gmx -f 1OTI.pdb -o 1OTI_processed.gro -water spce

I am going through the lysozyme tutorial I found for gromacs. Any help
would be greatly appreciated! Thank you!



Something is wrong with that file, like inappropriate read/write 
permissions on it or the directory in which you are trying to work. The 
latter should be a subdirectory of your home directory. Do consider 
doing general linux tutorial material to acquire experience, if appropriate.


Mark
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[gmx-users] File input/output error: 1OTI.pdb

[nbhutwal]

Hello all. I have just started research and will be using Gromacs. I am
not very command prompt or linux or programming savvy and I'm slowly
learning how to do certain things. I was trying to convert a pdb file
using pdb2gmx but keep getting the following error:

"File input/output error: 1OTI.pdb".

I'm not entirely sure how to solve this issue. The command I wrote is as
follows:

pdb2gmx -f 1OTI.pdb -o 1OTI_processed.gro -water spce

I am going through the lysozyme tutorial I found for gromacs. Any help
would be greatly appreciated! Thank you!

-Neil

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RE: [gmx-users] how to know the pH of a solution

[Dallas Warren]

> Actually, I am trying to solve problem between C6H13COOH and C6H13COO-.
> I do want to know the different behaviours between this two molecules.
> however, I only can get the gro and top files from PRODRG server. I have

What you have here isn't a really difficult molecule, so changing the 
protonation state of the carboxylic acid to another one (if you already have 
the other) is not too difficult to do.  For someone starting out, it is 
certainly not trivial, but it isn't difficult.

Few pointers for you once you have your topology sorted; ensure you add in 
counter ions for the COO-, background salt may be appropriate or a variable to 
study, and do the molecules have to be at the two extremes of ionisation or is 
it only partially ionised?

> an idea is to add H+ ions to the solution and change the pH of this
> solution to push the H+ to the C6H13COO-.

Even if you could add protons to the system (and there was an appropriate 
forcefield to deal with it, which I am not sure there actually is that you can 
use with GROMACS), what is the concentration of "H+" in the system at the pH 
you want things to operate at?  How many atoms does that correspond to in the 
box size that you are looking at running?

To illustrate why this is an issue, at pH 2 the ratio of H2O molecules to "H+" 
is approximately 5500 to 1.  That isn't too bad, do able in a reasonable sized 
water box.  However, it is at more physiological concentrations, say pH 7, then 
the ratio changes to around 550,000,000 to 1.  That will require a very large 
system to get a statistically significant number of protons in there.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 
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Re: [gmx-users] how to know the pH of a solution

[Justin A. Lemkul]

cuong nguyen wrote:

Dear Justin,

Actually, I am trying to solve problem between C6H13COOH and C6H13COO-. 
I do want to know the different behaviours between this two molecules. 
however, I only can get the gro and top files from PRODRG server. I have 
an idea is to add H+ ions to the solution and change the pH of this 
solution to push the H+ to the C6H13COO-.




I sincerely doubt that any classical molecular mechanics force field can achieve 
this.  Bonds cannot be broken or formed without QM/MM, which is not feasible for 
a system of more than a few dozen (maybe a hundred) atoms.  There are titration 
MD algorithms that exist, but they are not available in Gromacs yet.


I have received your response about the FAQ of PRODRG and try to find 
out the solution. However, I just started using GROMACS 2 months ago and 
my english is not good enough. So I have not known how to get the gro 
and top files of C6H13COOH yet.




You need to run PRODRG once to get the atom names that the server uses, then run 
it again by providing the ADDHYD or DELHYD keywords for the atom that you want 
(de)protonated.  I think an example is provided online.


-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] how to know the pH of a solution

[Justin A. Lemkul]

cuong nguyen wrote:

Dear,

I have made a 10x10x10 box with 200 hexanoic acid molecules and fill 
full of water.


Please let me know how can I do to know and change the pH of this solution?



The concept of pH is ill-defined for molecular simulations, in the absence of 
the ability to transfer protons.  For classical MD, you have fixed protonation 
state and thus you can't really have "pH" in the classical sense.  I suppose you 
could get an idea of what the pH should be by measuring the ratio of 
deprotonated and protonated species in your system (i.e. Henderson-Hasselbalch).


-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] how to know the pH of a solution

[Dallas Warren]

Ionisation state of the acid / base functional groups (based on the target pH 
and the pKa of the functional groups) within the system.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of cuong nguyen
Sent: Tuesday, 29 November 2011 2:28 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] how to know the pH of a solution

Dear,

I have made a 10x10x10 box with 200 hexanoic acid molecules and fill full of 
water.

Please let me know how can I do to know and change the pH of this solution?

Thank you very much.


Cheers,


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


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[gmx-users] how to know the pH of a solution

[cuong nguyen]

Dear,

I have made a 10x10x10 box with 200 hexanoic acid molecules and fill full
of water.

Please let me know how can I do to know and change the pH of this solution?

Thank you very much.


Cheers,


Nguyen Van Cuong
PhD student - Curtin University of Technology
Mobile: (+61) 452213981
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Re: [gmx-users] protein hydration shell water

[Justin A. Lemkul]

Yao Yao wrote:

Hi Gmxers,

Anyone knows any command or flag that can extract the water within some 
distance from the surface of a protein?




You can make an index file using g_select, or print a list with g_dist -dist.

-Justin

--


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


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[gmx-users] protein hydration shell water

[Yao Yao]

Hi Gmxers,

Anyone knows any command or flag that can extract the water within some 
distance from the surface of a protein?

thanks,

Yao Yao
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Re: [gmx-users] Pme on gpu performance

[Jones de Andrade]

Hi.

I'm another one waiting for the OpenCL version here.

4.6 will support only CUDA.
>
> OpenCL GPU implementations have yet match CUDA; on CPU it would hardly
> match the performance of the hand-tuned SSE kernels, moreover, CPU &
> GPU algorithms are not the same.
>

If you allow me, the (second and third!) argument is not strong enough,
since also cuda for cpu would not match the performance of all tricks from
gromacs. Also, I think that the cpu and cuda algorithms are not the same.
>From my point of view, the only really strong argument would be the first
one: "OpenCL GPU implementations have yet match CUDA!", despite the fact
that I would like to see it better explained if possible (even a link would
be suffice).

More important: does this mean that openMM and gromacs gpu development are
"breaking apart"? What can we really expect from that, other than easier
installation and usage?

Thanks a lot!

Sincerely yours,

Jones



>
> --
> Szilárd
>
>
>
> On Sun, Nov 27, 2011 at 11:25 PM, Alexey Shvetsov
>  wrote:
> > Hi!
> >
> > Will it use CUDA or OpenCL? Second one will be more common since it will
> > work with wider range of platfroms (cpu, gpu, fcpga)
> >
> > Szilárd Páll писал 27.11.2011 23:50:
> >>
> >> Native acceleration = not relying on external libraries. ;)
> >>
> >> --
> >> Szilárd
> >>
> >>
> >>
> >> On Sun, Nov 27, 2011 at 9:33 PM, Peter C. Lai  wrote:
> >>>
> >>> Random hijack:
> >>>
> >>> Will the CUDA acceleration support CMAP or will it still be limited to
> >>> the limitations of OpenMM that it currently has?
> >>>
> >>> On 2011-11-27 12:10:47PM -0600, Szilárd Páll wrote:
> 
>  Hi Andrzej,
> 
>  GROMACS 4.6 is work in progress, it will have native CUDA acceleration
>  with multi-GPU support along a few other improvements. You can expect
>  a speedup in the ballpark of 3x. We will soon have the code available
>  for testing.
> 
>  I'm a little skeptical about the 5x of ACEMD. What setting did you
>  use? AFAIR they were using large time-steps without contraints in
>  their benchmarks.
> 
>  Cheers,
>  --
>  Szilárd
> 
> 
> 
>  On Thu, Nov 24, 2011 at 9:53 AM, Andrzej Rzepiela
>   wrote:
>  > 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
>  > --
>  > gmx-users mailing listgmx-users@gromacs.org
>  > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  > Please search the archive at
>  > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>  > Please don't post (un)subscribe requests to the list. Use thewww
>  > interface
>  > or send it to gmx-users-requ...@gromacs.org.
>  > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>  >
>  --
>  gmx-users mailing listgmx-users@gromacs.org
>  http://lists.gromacs.org/mailman/listinfo/gmx-users
>  Please search the archive at
>  http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>  www interface or send it to gmx-users-requ...@gromacs.org.
>  Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>> --
> >>> ==
> >>> Peter C. Lai| University of Alabama-Birmingham
> >>> Programmer/Analyst  | KAUL 752A
> >>> Genetics, Div. of Research  | 705 South 20th Street
> >>> p...@uab.edu | Birmingham AL 35294-4461
> >>> (205) 690-0808|
> >>> ==
> >>>
> >>> --
> >>> gmx-users mailing listgmx-users@gromacs.org
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>> Please search the archive at
> >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >>> Please don't post (un)subscribe requests to the list. Use the
> >>> www interface or send it to gmx-users-requ...@gromacs.org.
> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >
> > --
> > Best Regards,
> > Alexey 'Alexxy' Shvetsov
> > Petersburg Nuclear Physics Institute, Russia
> > Department of Molecular and Radiation Biophysi

[gmx-users] Using walls and user defined potentials

[Olivia Waring]

Hi all,

I am simulating a self-assembled monolayer of alkanethiols under the
influence of a 12-3 surface potential. I have been trying to implement this
potential function using the "walls" and "tables" features of GROMACS.
There are four atom types in my system: CH3, CH2, S, and wall0. The
following three interaction types - CH3 + wall0, CH2 + wall0, and S + wall0
- are governed by tables that I provided. All other interaction types are
taken care of by a default table.xvg file (which corresponds to a standard
LJ potential). My production runs are crashing, and I'm really not sure
why, although my first guess is that it might have something to do with the
wall_r_linpot value. I'm also not sure why the log file has the following
two entries:
   wall_atomtype[0] = 3
   wall_atomtype[1] = -1
when my input .mdp file said wall_atomtype = wall0.

The log file is shown in full below. Any advice would be greatly
appreciated.

Thanks so much!
Olivia


Input Parameters:
   integrator   = md
   nsteps   = 50
   init_step= 0
   ns_type  = Grid
   nstlist  = 5
   ndelta   = 2
   nstcomm  = 10
   comm_mode= Linear
   nstlog   = 1000
   nstxout  = 1000
   nstvout  = 1000
   nstfout  = 0
   nstcalcenergy= 5
   nstenergy= 1000
   nstxtcout= 1000
   init_t   = 0
   delta_t  = 0.002
   xtcprec  = 1000
   nkx  = 0
   nky  = 0
   nkz  = 0
   pme_order= 4
   ewald_rtol   = 1e-05
   ewald_geometry   = 0
   epsilon_surface  = 0
   optimize_fft = FALSE
   ePBC = xy
   bPeriodicMols= FALSE
   bContinuation= TRUE
   bShakeSOR= FALSE
   etc  = V-rescale
   nsttcouple   = 5
   epc  = No
   epctype  = Isotropic
   nstpcouple   = -1
   tau_p= 2
   ref_p (3x3):
  ref_p[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   compress (3x3):
  compress[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   refcoord_scaling = No
   posres_com (3):
  posres_com[0]= 0.0e+00
  posres_com[1]= 0.0e+00
  posres_com[2]= 0.0e+00
   posres_comB (3):
  posres_comB[0]= 0.0e+00
  posres_comB[1]= 0.0e+00
  posres_comB[2]= 0.0e+00
   andersen_seed= 815131
   rlist= 1
   rlistlong= 1
   rtpi = 0.05
   coulombtype  = Cut-off
   rcoulomb_switch  = 0
   rcoulomb = 1
   vdwtype  = User
   rvdw_switch  = 0
   rvdw = 1
   epsilon_r= 1
   epsilon_rf   = 1
   tabext   = 2
   implicit_solvent = No
   gb_algorithm = Still
   gb_epsilon_solvent   = 80
   nstgbradii   = 1
   rgbradii = 1
   gb_saltconc  = 0
   gb_obc_alpha = 1
   gb_obc_beta  = 0.8
   gb_obc_gamma = 4.85
   gb_dielectric_offset = 0.009
   sa_algorithm = Ace-approximation
   sa_surface_tension   = 2.05016
   DispCorr = No
   free_energy  = no
   init_lambda  = 0
   delta_lambda = 0
   n_foreign_lambda = 0
   sc_alpha = 0
   sc_power = 0
   sc_sigma = 0.3
   sc_sigma_min = 0.3
   nstdhdl  = 10
   separate_dhdl_file   = yes
   dhdl_derivatives = yes
   dh_hist_size = 0
   dh_hist_spacing  = 0.1
   nwall= 1
   wall_type= table
   wall_atomtype[0] = 3
   wall_atomtype[1] = -1
   wall_density[0]  = 0
   wall_density[1]  = 0
   wall_ewald_zfac  = 3
   pull = no
   disre= No
   disre_weighting  = Conservative
   disre_mixed  = FALSE
   dr_fc= 1000
   dr_tau   = 0
   nstdisreout  = 100
   orires_fc= 0
   orires_tau   = 0
   nstorireout  = 100
   dihre-fc = 1000
   em_stepsize  = 0.01
   em_tol   = 10
   niter= 20
   fc_stepsize  = 0
   nstcgsteep   = 1000
   nbfgscorr= 10
   ConstAlg = Lincs
   shake_tol= 0.0001
   lincs_order  = 4
   lincs_warnangle  = 30
   lincs_iter   = 1
   bd_fric  = 0
   ld_seed  = 1993
   cos_accel= 0
   deform (3x3):
  deform[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  deform[1]={ 0.0e+00,  0.0e+00,  0.0

Re: [gmx-users] Pme on gpu performance

[Matt Larson]

Szilárd,

 Version 4.6, GPU without OpenMM sounds fantastic.  I am very excited!
I was having trouble getting simulations to work equivalently well on
the GPU as CPU because of having to make different choices with
cutoffs and mainly not being able to use the V-rescale thermostat.

 -Matt

On Sun, Nov 27, 2011 at 6:01 PM, Szilárd Páll  wrote:
> Hi,
>
> 4.6 will support only CUDA.
>
> OpenCL GPU implementations have yet match CUDA; on CPU it would hardly
> match the performance of the hand-tuned SSE kernels, moreover, CPU &
> GPU algorithms are not the same.
>
> --
> Szilárd
>
>
>
> On Sun, Nov 27, 2011 at 11:25 PM, Alexey Shvetsov
>  wrote:
>> Hi!
>>
>> Will it use CUDA or OpenCL? Second one will be more common since it will
>> work with wider range of platfroms (cpu, gpu, fcpga)
>>
>> Szilárd Páll писал 27.11.2011 23:50:
>>>
>>> Native acceleration = not relying on external libraries. ;)
>>>
>>> --
>>> Szilárd
>>>
>>>
>>>
>>> On Sun, Nov 27, 2011 at 9:33 PM, Peter C. Lai  wrote:

 Random hijack:

 Will the CUDA acceleration support CMAP or will it still be limited to
 the limitations of OpenMM that it currently has?

 On 2011-11-27 12:10:47PM -0600, Szilárd Páll wrote:
>
> Hi Andrzej,
>
> GROMACS 4.6 is work in progress, it will have native CUDA acceleration
> with multi-GPU support along a few other improvements. You can expect
> a speedup in the ballpark of 3x. We will soon have the code available
> for testing.
>
> I'm a little skeptical about the 5x of ACEMD. What setting did you
> use? AFAIR they were using large time-steps without contraints in
> their benchmarks.
>
> Cheers,
> --
> Szilárd
>
>
>
> On Thu, Nov 24, 2011 at 9:53 AM, Andrzej Rzepiela
>  wrote:
> > 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
> > --
> > 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 thewww
> > interface
> > or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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Re: [gmx-users] questions about steer molecular dynamics by using gromacs4

[Justin A. Lemkul]

mirc...@sjtu.edu.cn wrote:

Dear All:

I am trying to use steer molecular dynamics simulations to pull a ligand 
along a channel pore (along the Z axis) by constant rate. I know how to 
realize this by GROMACS3, however, it seemed that in gromacs4, there are 
some changes regarding this issues, so I am pasting my pull code 
parameters and some of my questions here, Could any one be so kind to 
answer my questions? Thanks in advance.



My pull code parameters
---
pull=umbrella
pull_dim=N N Y
pull_start=yes

### if the pull_start is set to "yes", it means that, the distance 
between the pull group and the reference group of the starting structure 
will be calculated and the value will be added to the pull_init1 and the 
final result will be used a the inital distance between the pull group 
and the reference group in the simulations, am i right?###


pull_nstxout=500

###  if the pull_nstxout is set to 500, the COM of the pull group 
will be write every 500 steps (i.e. 1ps,if the time step is 
2fs)?


pull_nstfout=500
pull_group0=Protein
pull_group1=Ligand
pull_vec1=0 0 1
pull_init1=0
pull_rate1= 0.025
pull_k1= 1000

how can I make sure the pull_rate1 and the pull_k1 I used is 
appropriate?###3

__

  what is the out put of the pulling code?  #

Does the above parameters can pull the ligand along the Z axis with a 
constant rate successfully? Are there any problem the my pull code 
parameters?


Thanks very much for your time and your kind!



Please try the steered MD/umbrella sampling tutorial.  Your questions should be 
largely answered.


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

-Justin

--


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


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Re: [gmx-users] restoration of crashed simulation

[Justin A. Lemkul]

Saba Ferdous wrote:
Dear Justin, 

I have been simulation a protein complex on 10ns. about 
4100,000/5000,000 of nsteps had been completed that my system got off 
due to electric cut-off. 
Now I want to resume this simulation. Is it possible to resume from the 
step it got ceased. 
Can you please tell me the proper command for the restoration?
 As this simulation was running since 6 days and I cant afford to 
restart it from the beginning:(


Kindly tell me the full command to get it start from where it was stopped.



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

-Justin

--


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


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[gmx-users] questions about steer molecular dynamics by using gromacs4

[mircial]

Dear All:

I am trying to use steer molecular dynamics simulations to pull a  
ligand along a channel pore (along the Z axis) by constant rate. I  
know how to realize this by GROMACS3, however, it seemed that in  
gromacs4, there are some changes regarding this issues, so I am  
pasting my pull code parameters and some of my questions here, Could  
any one be so kind to answer my questions? Thanks in advance.



My pull code parameters
---
pull=   umbrella
pull_dim=   N N Y
pull_start  =   yes

### if the pull_start is set to "yes", it means that, the distance  
between the pull group and the reference group of the starting  
structure will be calculated and the value will be added to the  
pull_init1 and the final result will be used a the inital distance  
between the pull group and the reference group in the simulations, am  
i right?###


pull_nstxout=   500

###  if the pull_nstxout is set to 500, the COM of the pull group  
will be write every 500 steps (i.e. 1ps,if the time step is  
2fs)?


pull_nstfout=   500
pull_group0 =   Protein
pull_group1 =   Ligand
pull_vec1   =   0 0 1
pull_init1  =   0
pull_rate1  = 0.025
pull_k1 =1000

how can I make sure the pull_rate1 and the pull_k1 I used  
is appropriate?###3

__

  what is the out put of the pulling code?  #

Does the above parameters can pull the ligand along the Z axis with a  
constant rate successfully? Are there any problem the my pull code  
parameters?


Thanks very much for your time and your kind!

Best Regards

R.-X. Gu


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Re: [gmx-users] restoration of crashed simulation

[Mark Abraham]

On 28/11/2011 11:46 PM, Saba Ferdous wrote:

Dear Justin,

I have been simulation a protein complex on 10ns. about 
4100,000/5000,000 of nsteps had been completed that my system got off 
due to electric cut-off.
Now I want to resume this simulation. Is it possible to resume from 
the step it got ceased.

Can you please tell me the proper command for the restoration?
 As this simulation was running since 6 days and I cant afford to 
restart it from the beginning:(


Kindly tell me the full command to get it start from where it was stopped.


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

Mark
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[gmx-users] restoration of crashed simulation

[Saba Ferdous]

Dear Justin,

I have been simulation a protein complex on 10ns. about 4100,000/5000,000
of nsteps had been completed that my system got off due to electric
cut-off.
Now I want to resume this simulation. Is it possible to resume from the
step it got ceased.
Can you please tell me the proper command for the restoration?
 As this simulation was running since 6 days and I cant afford to restart
it from the beginning:(

Kindly tell me the full command to get it start from where it was stopped.

Many thanks

Regards

-- 
Saba Ferdous
Research Scholar (M. Phil)
National Center for Bioinformatics
Quaid-e-Azam University, Islamabad
Pakistan
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Re: [gmx-users] remd in the npt ensemble: When the exchange, the temperature abruptly surge .

[Mark Abraham]

On 28/11/2011 10:37 PM, ?? wrote:

dear teacher,
i find the answer of that  letter "Subject: Re: [gmx-users] REMD: NPT 
being +-Infinity or NaN",
ifind that "when the exchange, the temperature abruptly surge .",as 
follows,

dt=0.002ps  -replex 4000

@ s0 legend "Temperature"
@ s1 legend "Pressure"
0.00  546.497375   60.637791
1.00  556.582397  244.328201
..
   94.00  557.564453  -17.035589
   95.00  543.882629   57.111996
   96.00  523.336548  -25.745819
   97.00  555.043335  254.709778
   98.00  555.595886  -39.830761
   99.00  542.395325   49.084045
  100.00  550.955261  -149.259979
  101.00  134372.953125  4419.518066
  102.00  156382.859375  -17109.099609
  103.00  138660.156250  -11395.237305
  104.00  165148.265625  20807.541016
...

But if change the replex to 4,so i can not exchange.
Then the system is ok.
&& The initial conformation has been done a long time MD


If this is the same system as previously reported, then you're probably 
observing the system velocities exploding on one replica then being 
exchanged to a new replica.


Mark



thanks for your help !!
Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303 ; +8613820062885
E-mail: 2008d...@gmail.com  ; 
dubo2...@tju.edu.cn 






===
Message: 4
Date: Sun, 27 Nov 2011 22:36:08 -0500
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] REMD: NPT being +-Infinity or NaN
To: Discussion list for GROMACS users >

Message-ID: <4ed301a8.9070...@vt.edu >
Content-Type: text/plain; charset=UTF-8; format=flowed



?? wrote:
> dear teacher,
> when i do remd  in the  npt ensemble.
>
> REMD: NPT -replex 4000
> dt= 0.0001
>
> step 172000, will finish Sat Dec 31 18:44:12 2011
>
> ---
> Program mdrun_mpi_4.5.5, VERSION 4.5.5
> Source code file: nsgrid.c, line: 549
>
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with 
some

> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
>
> how could  i do except using the small dt ?
>

Your system is not stable, as is often the case with NPT REMD at high 
temperature.


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

-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] Atom not found in residue while adding hydrogens

[Mark Abraham]

On 28/11/2011 10:40 PM, yp sun wrote:

Dear professor,
Is there any simple way to resolve my problem? Thanks!



Yes. If you've read the first link I suggested then you will have some 
leads for solving your problem. If they don't help you, then you will 
need to follow the advice in my second link before anyone here can begin 
help you.


Mark



Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

--- *11?11?28?,??, Mark Abraham //* ??:


???: Mark Abraham 
??: Re: [gmx-users] Atom not found in residue while adding hydrogens
???: "Discussion list for GROMACS users" 
??: 2011?11?28?,??,??7:25

On 28/11/2011 10:13 PM, yp sun wrote:

Dear Sir,
When I run pdb2gmx, I encounter the following error information:

Program pdb2gmx, VERSION 3.3.1
Source code file: genhydro.c, line: 304
Fatal error:
Atom CB not found in residue ASP223 while adding hydrogens

What should I do?



Probably update to a much faster GROMACS version, check out

http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry,
and follow the guidelines here for making posts
http://www.gromacs.org/Support :-)

Mark

-???-

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.
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Re: [gmx-users] .top to .itp file conversion

[Tsjerk Wassenaar]

Hi,

You can print the moleculetype definition, up to the system tag using sed:

sed -n -e '/^\s*\[\s*system\s*\]\s*$/q' -e
'/^\s*\[\s*moleculetype\s*\]\s*$/,$p' TOP > ITP

First expression: quit at [ system ], allowing spaces before, in between
and after
Second expression: print everything from [ moleculetype ] to end of file.

This does assume there is only a single moleculetype definition and no
rubbish (#includes) in between.

Hope it helps,

Tsjerk

On Mon, Nov 28, 2011 at 12:22 PM, Mark Abraham wrote:

>  On 28/11/2011 10:09 PM, yp sun wrote:
>
>   I think by running pdb2gmx you can get .itp file.
>
>
> ... only if there are corresponding .rtp entries, which is likely not the
> case for GTP. pdb2gmx is not magic.
>
> Mark
>
>
>
> Yeping Sun
> CAS Key Laboratory of Pathogenic Microbiology & Immunology
> INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
> NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
>
> --- *11年11月28日，周一, David van der Spoel 
> 
> * 写道：
>
>
> 发件人: David van der Spoel  
> 主题: Re: [gmx-users] .top to .itp file conversion
> 收件人: "Discussion list for GROMACS users" 
> 
> 日期: 2011年11月28日,周一,下午4:22
>
> On 2011-11-28 09:20, neeru sharma wrote:
> > Dear gromacs users,
> >
> > I have generated Amber topology and coordinate files for GTP molecule.
> > Then, I converted them into the corresponding gromacs topology (.top)
> > and coordinate files (.gro). Now, I need to convert this gromacs .top
> > file into .itp format.
> > Is there any command in gromacs or any other tool to do so.
> > Thanks
> >
> > 
> > Neeru Sharma
> > CDAC,Pune (India)
> >
> >
> >
> emacs or vi. your choice.
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.se
>   http://folding.bmc.uu.se
> --
> gmx-users mailing list
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> .
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>
>
>
>
>
> --
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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] Atom not found in residue while adding hydrogens

[yp sun]

Dear professor,
 
Is there any simple way to resolve my problem? Thanks!

Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES 
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

--- 11年11月28日，周一, Mark Abraham  写道：


发件人: Mark Abraham 
主题: Re: [gmx-users] Atom not found in residue while adding hydrogens
收件人: "Discussion list for GROMACS users" 
日期: 2011年11月28日,周一,下午7:25



On 28/11/2011 10:13 PM, yp sun wrote: 





Dear Sir,
 
When I run pdb2gmx, I encounter the following error information: 

Program pdb2gmx, VERSION 3.3.1
Source code file: genhydro.c, line: 304
Fatal error:
Atom CB not found in residue ASP223 while adding hydrogens

What should I do?
Probably update to a much faster GROMACS version, check out 
http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry,
 and follow the guidelines here for making posts http://www.gromacs.org/Support 
:-)

Mark

-下面为附件内容-


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[gmx-users] remd in the npt ensemble: When the exchange, the temperature abruptly surge .

[杜波]

dear teacher,
i find the answer of that  letter "Subject: Re: [gmx-users] REMD: NPT being
+-Infinity or NaN",
ifind that "when the exchange, the temperature abruptly surge .",as follows,
dt=0.002ps  -replex 4000

@ s0 legend "Temperature"
@ s1 legend "Pressure"
0.00  546.497375   60.637791
1.00  556.582397  244.328201
..
   94.00  557.564453  -17.035589
   95.00  543.882629   57.111996
   96.00  523.336548  -25.745819
   97.00  555.043335  254.709778
   98.00  555.595886  -39.830761
   99.00  542.395325   49.084045
  100.00  550.955261  -149.259979
  101.00  134372.953125  4419.518066
  102.00  156382.859375  -17109.099609
  103.00  138660.156250  -11395.237305
  104.00  165148.265625  20807.541016
...

But if change the replex to 4,so i can not exchange.
Then the system is ok.
&& The initial conformation has been done a long time MD

thanks for your help !!
Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303 ; +8613820062885
E-mail: 2008d...@gmail.com ; dubo2...@tju.edu.cn





===
Message: 4
Date: Sun, 27 Nov 2011 22:36:08 -0500
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] REMD: NPT being +-Infinity or NaN
To: Discussion list for GROMACS users 
Message-ID: <4ed301a8.9070...@vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed



杜波 wrote:
> dear teacher,
> when i do remd  in the  npt ensemble.
>
> REMD: NPT -replex 4000
> dt= 0.0001
>
> step 172000, will finish Sat Dec 31 18:44:12 2011
>
> ---
> Program mdrun_mpi_4.5.5, VERSION 4.5.5
> Source code file: nsgrid.c, line: 549
>
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
>
> how could  i do except using the small dt ?
>

Your system is not stable, as is often the case with NPT REMD at high
temperature.

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

-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] Atom not found in residue while adding hydrogens

[Mark Abraham]

On 28/11/2011 10:13 PM, yp sun wrote:

Dear Sir,
When I run pdb2gmx, I encounter the following error information:

Program pdb2gmx, VERSION 3.3.1
Source code file: genhydro.c, line: 304
Fatal error:
Atom CB not found in residue ASP223 while adding hydrogens

What should I do?



Probably update to a much faster GROMACS version, check out 
http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry, 
and follow the guidelines here for making posts 
http://www.gromacs.org/Support :-)


Mark
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Re: [gmx-users] .top to .itp file conversion

[Mark Abraham]

On 28/11/2011 10:09 PM, yp sun wrote:

I think by running pdb2gmx you can get .itp file.



... only if there are corresponding .rtp entries, which is likely not 
the case for GTP. pdb2gmx is not magic.


Mark



Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

--- *11?11?28?,??, David van der Spoel //* ??:


???: David van der Spoel 
??: Re: [gmx-users] .top to .itp file conversion
???: "Discussion list for GROMACS users" 
??: 2011?11?28?,??,??4:22

On 2011-11-28 09:20, neeru sharma wrote:
> Dear gromacs users,
>
> I have generated Amber topology and coordinate files for GTP
molecule.
> Then, I converted them into the corresponding gromacs topology
(.top)
> and coordinate files (.gro). Now, I need to convert this gromacs
.top
> file into .itp format.
> Is there any command in gromacs or any other tool to do so.
> Thanks
>
> 
> Neeru Sharma
> CDAC,Pune (India)
>
>
>
emacs or vi. your choice.

-- 
David van der Spoel, Ph.D., Professor of Biology

Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
sp...@xray.bmc.uu.se
 
http://folding.bmc.uu.se

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.
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[gmx-users] Atom not found in residue while adding hydrogens

[yp sun]

Dear Sir,
 
When I run pdb2gmx, I encounter the following error information: 

Program pdb2gmx, VERSION 3.3.1
Source code file: genhydro.c, line: 304
Fatal error:
Atom CB not found in residue ASP223 while adding hydrogens

What should I do?

Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES 
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china-- 
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Re: [gmx-users] .top to .itp file conversion

[yp sun]

I think by running pdb2gmx you can get .itp file.

Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES 
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

--- 11年11月28日，周一, David van der Spoel  写道：


发件人: David van der Spoel 
主题: Re: [gmx-users] .top to .itp file conversion
收件人: "Discussion list for GROMACS users" 
日期: 2011年11月28日,周一,下午4:22


On 2011-11-28 09:20, neeru sharma wrote:
> Dear gromacs users,
>
> I have generated Amber topology and coordinate files for GTP molecule.
> Then, I converted them into the corresponding gromacs topology (.top)
> and coordinate files (.gro). Now, I need to convert this gromacs .top
> file into .itp format.
> Is there any command in gromacs or any other tool to do so.
> Thanks
>
> 
> Neeru Sharma
> CDAC,Pune (India)
>
>
>
emacs or vi. your choice.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
sp...@xray.bmc.uu.se    http://folding.bmc.uu.se
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Re: [gmx-users] g_rdf -com

[mohammad agha]

Dear Prof. Spoel

Thanks for your reply. 

I used g_clustsize and after it, I used g_rdf but it is not true, because the 
plot of g(r) for tails of surfactants relative to COM of micelle starts from 0 
but it is not true!

Best Regards
Sara




 From: David van der Spoel 
To: Discussion list for GROMACS users  
Sent: Sunday, November 27, 2011 3:08 PM
Subject: Re: [gmx-users] g_rdf -com
 
On 2011-11-27 12:27, mohammad agha wrote:
> Dear Prof.
>
> I have a question about g_rdf.
> I have a box consists of 500 surfactants that make 10 micelle. I want to
> compute rdf for surfactant relative to the center of mass of micelle.
> When I do g_rdf, the program ask me 2 groups that the first one is COM,
> but it is COM of molecules that I defined in index file.
> If I select the surfactant molecules as the first group for COM, this
> means the COM of micelle or just surfactants?
> If it select just COM of surfactants, then what do I do for selection of
> COM of micelle?
> Please help me.
>
> Best Regards
> Sara
>
>
you first have to define which surfactants belong together before g_rdf 
can do this - make an appropriate index file, maybe g_clustsize can help.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
sp...@xray.bmc.uu.se    http://folding.bmc.uu.se
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Re: [gmx-users] g(r) and <ρB>local

[Gianluca Santoni]

On 11/28/11 9:34 AM, anna_grom...@libero.it wrote:


Dear all,

I've got a question:

in the equation of g(r), is <ρB>local a surface density or a volume 
density


It seems to be a surface density. (check the dimensions of the different 
quantities involved)


I think there is a mistake in gromacs' manual  (gromacs_manual_4.5pdf 
page 201):  "...<ρB>local the particle density of type B averaged over 
all spheres around particle A with radius rmax ..."


because if we consider <ρB>local  as a volume density in (8.3) 
equation,  in my opinion there isn't the possibility to have g(r) --> 
1 at rmax.



You can help me?  I am in error?

Thanks


Anna







--
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Institut de Biologie Structurale
41 rue Horowitz
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_
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[gmx-users] Dual Processor Intel Xeon X5650 (6 core) versus Quad Processor Opteron series 6100 (12 core)

[Claudio M. Soares]

Dear All,

We are in the process of buying new machines for calculation (mostly
GROMACS, but also Gaussian 09, MEAD and other codes) to add to our
cluster. We have the option of buying Dual Processor Intel Xeon X5650
with 6 cores or Quad processor AMD Opteron series 6100 (12 cores) or
series 6200 (16 cores). The Quad processor machines (with Opteron 6274
- around 4200 euros plus VAT) are a bit cheaper than two machines with
Dual processor Xeons (X5650 - around 5300 euros plus VAT).

I would like to ear about your experience with the Quad processor
Opterons of this kind. Our cluster is used by a substantial number of
people, which means that the machines will not likely be devoted to
one job only at the time; sharing is probably going to occur (at least
this is the optimum way to squeeze the most of our present Dual Dual
Processor Intel Xeon X5650 (2 jobs at the same time)).

Additionally, we would like to have benchmarks of GROMACS in the
Opteron architectures. Or even better, if there is a kind soul having
one of these Opteron machines around, we would be very happy to run
our own benchmark (a tar file with an easy-to-run shell script that
runs without supervision). Sellers/representatives of this type of
machines should be kind to provide such possibility, but here in
Portugal this is not usually possible.

Thanks in advance,

Cláudio

-- 

Claudio M. Soares
Instituto de Tecnologia Química e Biológica
Universidade Nova de Lisboa
Av. da República,
2780-157 Oeiras
PORTUGAL
Phone:(351)214469610/214469100
Fax :(351)214411277
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[gmx-users] g(r) and <ρB>local

[anna_grom...@libero.it]

Dear all,

I've got a question:  in the equation of g(r), is <ρB>local  a surface density 
or a volume density?I think there is a mistake in gromacs' manual  
(gromacs_manual_4.5pdf page 201):  "...<ρB>local the particle density of type B 
averaged over all spheres around particle A with radius rmax  ..."because if we 
consider <ρB>local  as a volume density in (8.3) equation,  in my opinion there 
isn't the possibility to have g(r) --> 1 at rmax.
You can help me?  I am in error? Thanks
Anna

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Re: [gmx-users] .top to .itp file conversion

[Mark Abraham]

On 28/11/2011 7:22 PM, David van der Spoel wrote:

On 2011-11-28 09:20, neeru sharma wrote:

Dear gromacs users,

I have generated Amber topology and coordinate files for GTP molecule.
Then, I converted them into the corresponding gromacs topology (.top)
and coordinate files (.gro). Now, I need to convert this gromacs .top
file into .itp format.
Is there any command in gromacs or any other tool to do so.
Thanks


Neeru Sharma
CDAC,Pune (India)




emacs or vi. your choice.



See http://www.gromacs.org/Documentation/File_Formats/.itp_File and 
examples in chapter 5 of the manual.


Mark
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Re: [gmx-users] .top to .itp file conversion

[David van der Spoel]

On 2011-11-28 09:20, neeru sharma wrote:

Dear gromacs users,

I have generated Amber topology and coordinate files for GTP molecule.
Then, I converted them into the corresponding gromacs topology (.top)
and coordinate files (.gro). Now, I need to convert this gromacs .top
file into .itp format.
Is there any command in gromacs or any other tool to do so.
Thanks


Neeru Sharma
CDAC,Pune (India)




emacs or vi. your choice.

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

[neeru sharma]

Dear gromacs users,

I have generated Amber topology and coordinate files for GTP molecule.
Then, I converted them into the corresponding gromacs topology (.top) and
coordinate files (.gro). Now, I need to convert this gromacs .top file into
.itp format.
Is there any command in gromacs or any other tool to do so.
Thanks


Neeru Sharma
CDAC, Pune (India)
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