Re: [gmx-users] Gromacs: Cloud Vs. Boinc Server?

[lloyd riggs]

Message: 1
Date: Tue, 11 Oct 2011 22:05:27 +0200
From: Szil?rd P?ll 
Subject: Re: [gmx-users] Gromacs: Cloud Vs. Boinc Server?
To: Discussion list for GROMACS users 
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1

Hi Gregory,

I am not very familiar with the could computing offerings, but as far
as I know, in general they are not a very cheap solution when it comes
to relatively low usage (non massive enterprise use).

If you would need it only for you own research, you might be better
off with applying for a grant to get cluster time at a compute center.

Alternatively, as the next Gromacs version will support GPU
acceleration and will have quite with decent performance, you could
consider investing in multi-GPU box with GeForce cards. Of course,
this is feasible only if you don't mind the maintenance overhead and
costs.

Cheers,
--
Szilárd

Radeons work as well.  You can put a 3-4 GPU board together with the highest 
end AMD or Intel chip for 3K, plus 16G RAM if you look around for a day or two, 
but the cooling is the main problem (with 1/4 the price radeons Vs. GTI cards), 
so one has to take cooling into account (h20 cost another 800$, or investing in 
4-6 good fans/cooling an additional 2-300$).  If you have a slightly higher 
budget you can get multi CPU boards with 4 GPU slots, ie 4 or 8 CPU's (direct 
via mail from Taiwan), but the CPU's and GPU's is where the money is spent.

As far as I have seen GPU Gromacs runs at around 1 Teraflop per Radeon 5900 
series (double percission, single is supposed to run around 4 tera flops per 
GPU, so depends on your needs, desires as far as simulations), and the latest 
Intel 970's are around 400-500 Gflops/chip.

Stephan Watkins

-- 
NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie!   
Jetzt informieren: http://www.gmx.net/de/go/freephone
-- 
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

Re: [gmx-users] Pressure very high with chloroform and gromacs-4.5.5

[Nuno Azoia]

Thank you Mark for your answer!

I agree with you when you say that the high pressure is not itself a
problem. To avoid that problem I change my system from 1000 molecules
to 27000 molecules, and the pressure change from several thousands to
several hundreds bar.
What I found very strange was the increasing volume (and pressure). My
system is very unstable, I know, because the density is very low, and
not the opposite, so I was expecting to see the box getting smaller.
Looking to the trajectory I can see a box almost empty (with empty I
mean empty space, with chloroform molecules aggregating in small
droplets), and that's why I found the system behavior very strange.

I will follow your suggestion concerning nsttcouple and nstpcouple and
the other initial conditions.

Nuno Azoia


On Wed, Oct 12, 2011 at 6:24 AM, Mark Abraham  wrote:
> On 12/10/2011 2:22 AM, Nuno Azoia wrote:
>>
>> Hello!
>>
>> I found something very strange while making a CHCl3 box using
>> gromacs-4.5.5.
>> A look the mailing list, the manual and some release notes for
>> gromacs-4.5 and I couldn't found the answer for my problem. It's
>> possible that I'm doing something wrong, but I can not find what, so
>> I'm describe my problem.
>>
>> I start a chloroform box from scratch, using genconf, and I get o
>> chloroform box with 1000 molecules. I get energy minimization without
>> problems.
>> Then I've run some equilibration steps in a NVT ensemble and in the
>> end I get pressure in the order of hundreds of bar.
>
> The high pressure is not itself a problem - small numbers of molecules and
> short simulation times lead to doubtful statistics for pressure.
>
>>  Then I change to
>> NPT conditions and both the pressure and the volume keep increasing
>> with time.
>
> Be sure to visualize your trajectory to confirm its behaviour matches what
> you expect from the trends in P and V.
>
>>
>> To discard the possibility of a size problem, I repeat everything with
>> a box of 27000 molecules, with a volume of ~13800 nm^3. The problem
>> was the same. Very high pressures (150-200 bar) and very low densities
>> (<  200 g/L) after 750 ps simulation time. And both volume and pressure
>> increasing with time.
>>
>>
>> I'm doing now the same procedure, but using gromacs-4.0.7 and I'm
>> getting very different (and better) results. After energy minimization
>> I run 5 steps in a nvt ensemble and I got pressure around -30 bar
>> (Ok for me). After that I start to run the simulations in npt ensemble
>> and the pressure start to increase slowly, with negative values
>> because the system have very low densities (~400 g/L), and the volume
>> is decreasing. So I'm getting the normal reaction from the system.
>>
>>
>>
>> Where is the problem? There are some different parameters to set in
>> the mdp file and I didn't realize that, or is this a problem in
>> gromacs-4.5?
>
> It seems you are generating some numerical instability with your choice of
> initial and simulation conditions, and that gromacs-4.0 was luckier in
> avoiding the problem. If this is a parallel simulation, then the way
> communication is managed in order to organize T and P coupling changed going
> up to 4.5. For equilibration, I would encourage setting nsttcouple and
> nstpcouple to 1. Using a shorter time step can help with numerical
> instability. Berendsen T coupling or a larger coupling time constant might
> also help. After gentler NVT, then switch to NPT, let the box size
> stabilize, and finally move to larger coupling periods, time steps and
> v-rescale T coupling.
>
> Mark
>
>>
>>
>> In both cases I used this parameters:
>> -
>> integrator          =  md
>> dt                    =  0.002
>> nsteps              =  5
>> nstcomm          =  1
>> nstxtcout           =  500
>> xtc-precision      =  1000
>> nstxout             =  0
>> nstvout             =  0
>> nstfout             =  0
>> nstlog              =  500
>> nstenergy           =  500
>>
>> nstlist               =  5
>> ns_type             =  grid
>>
>> ;Reaction field
>> rlist               = 0.8
>> coulombtype         = Reaction-field
>> rcoulomb            = 1.4
>> epsilon_r           = 1.0
>> epsilon_rf          = 4.8
>> vdwtype             = cut-off
>> rvdw                = 1.4
>>
>> ; temperature coupling
>> Tcoupl              =  v-rescale
>> tc-grps             =  CHCL3
>> tau_t               =  0.05
>> ld_seed             =  -1
>> ref_t               =  300
>>
>> ; Energy monitoring
>> energygrps          =  CHCl3
>>
>> ; Isotropic pressure
>> Pcoupl              =  no
>> Pcoupltype          =  isotropic
>> tau_p               =  0.5
>> compressibility     =  4.5e-5
>> ref_p               =  1.0
>>
>> ; Generate velocites is on at 300 K.
>> gen_vel             =  yes
>> gen_temp            =  300
>> gen_seed            =  -1
>>
>> constraint_algorithm=lincs
>> lincs_order         =  4
>> lincs-warnangle     = 90
>> constraints         = 

[gmx-users] R: Re: H-bond lifetime with g_hbond

[Anna Marabotti]

Dear all,
any other suggestions on how to operate with g_hbond in order to allow
convergence of the autocorrelation function (see message below)? 

Moreover, I have another question. On the same trajectories, I'm using
g_hbonds also to infer the contacts between the protein and the ligand (and
possibly infer van der Waals interactions). This is the command I used:

g_hbond -f protein-GLA_mdC.xtc -s protein-GLA_md.tpr -g
protein-GLA_md_vdw.log -contact -r 1.4 -num protein-GLA_md_vdwnum.xvg

The printout of the command is:
 
Select a group: 1
Selected 1: 'Protein'
Select a group: 15
Selected 15: 'GLA'
Checking for overlap in atoms between Protein and GLA
Calculating contacts between Protein (5935 atoms) and GLA (24 atoms)
Found 24 donors and 5935 acceptors
Making hbmap structure...done.
Reading frame   0 time0.000   
Will do grid-seach on 6x6x4 grid, rcut=1.4
Last frame   3000 time 3.000   
Found 38017 different contacts in trajectory
Found 0 different atom-pairs within hydrogen bonding distance
Average number of contacts per timeframe 0.000 out of 71220 possible

However, the .log file gives me a list of interactions such as:
#  Donor  Hydrogen  Acceptor
  GLA395O4   PRO35O
  GLA395O4   GLY36N
  GLA395O4   GLY36CA
  GLA395O4   GLY36HA1
  GLA395O4   GLY36HA2
  GLA395O4   GLY36C
  GLA395O4   GLY36O
  GLA395O4   ARG37N
  GLA395O4   ARG37H


Moreover, I found previously several hBonds in this trajectory, therefore, I
don't understand why the printout tells "Found 0 different atom-pairs within
hydrogen bonding distance" and "Average number of contacts per timeframe
0.000 out of 71220 possible". I also used flag -r2 instead of -r, but the
result is the same. Maybe this is a trivial question, but...what is the
correct way to use the flags -contact and -r (or -r2) within g_hbond
command?

Thanks a lot
Anna


Message: 1
Date: Tue, 11 Oct 2011 10:25:32 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] H-bond lifetime with g_hbond
To: Discussion list for GROMACS users 
Message-ID: <4e9451dc.6010...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Anna Marabotti wrote:
> Dear gmx-users,
> I have a protein with 5 different ligands. For each system I made 30ns 
> simulation and I calculated the lifetime of the H-bonds between protein 
> and ligand with the command:
>  
> g_hbond -f traj.xtc -s topol.tpr -hbm hbmap.xpm -hbn hbond.ndx -ac 
> hbac.xvg -life hblife.xvg
>  
> During all calculations, the printout of the command gave the same
warning:
> 
>  
> 
> WARNING: Correlation function is probably not long enough
> 
> because the standard deviation in the tail of C(t) > 0.001
> 
>  
> 
> and as a matter of fact, the tail of C(t) (average C(t) over second half 
> of acf) reported below this warning was always > 0.001, generally 
> comprised between 0.45 and 0.74 with two exceptions: a value of 
> 0.02+/-0.03 and a value of 0.04+/-0.01.
> 

The warning doesn't complain about the value of C(t), it is telling you that
the 
standard deviation in the value is unacceptable.

> Therefore, I'm asking if the forward values considered as lifetimes are 
> reliable or not, and in case, what can I do to avoid this warning.
> 

I can't directly comment on this, but it would seems as if the values are
not 
adequately converged.

-Justin

>  
> 
> Thank you very much and best regards
> 
> Anna
> 
>  
> 
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science, CNR
> Via Roma, 64
> 83100 Avellino (Italy)
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> Email: anna.marabo...@isa.cnr.it 
> Skype account: annam1972
> Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
>  
> "When a man with a gun meets a man with a pen, the man with a gun is a 
> dead man"
> (Roberto Benigni, about Roberto Saviano)
>  
> 

-- 


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





-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/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

Re: [gmx-users] Pressure very high with chloroform and gromacs-4.5.5

[Mark Abraham]

On 12/10/2011 8:04 PM, Nuno Azoia wrote:

Thank you Mark for your answer!

I agree with you when you say that the high pressure is not itself a
problem. To avoid that problem I change my system from 1000 molecules
to 27000 molecules, and the pressure change from several thousands to
several hundreds bar.
What I found very strange was the increasing volume (and pressure). My
system is very unstable, I know, because the density is very low, and
not the opposite, so I was expecting to see the box getting smaller.
Looking to the trajectory I can see a box almost empty (with empty I
mean empty space, with chloroform molecules aggregating in small
droplets), and that's why I found the system behavior very strange.


Sounds like your initial density might be far too low. grompp reports 
it, so do check.


Mark


I will follow your suggestion concerning nsttcouple and nstpcouple and
the other initial conditions.

Nuno Azoia


On Wed, Oct 12, 2011 at 6:24 AM, Mark Abraham  wrote:

On 12/10/2011 2:22 AM, Nuno Azoia wrote:

Hello!

I found something very strange while making a CHCl3 box using
gromacs-4.5.5.
A look the mailing list, the manual and some release notes for
gromacs-4.5 and I couldn't found the answer for my problem. It's
possible that I'm doing something wrong, but I can not find what, so
I'm describe my problem.

I start a chloroform box from scratch, using genconf, and I get o
chloroform box with 1000 molecules. I get energy minimization without
problems.
Then I've run some equilibration steps in a NVT ensemble and in the
end I get pressure in the order of hundreds of bar.

The high pressure is not itself a problem - small numbers of molecules and
short simulation times lead to doubtful statistics for pressure.


  Then I change to
NPT conditions and both the pressure and the volume keep increasing
with time.

Be sure to visualize your trajectory to confirm its behaviour matches what
you expect from the trends in P and V.


To discard the possibility of a size problem, I repeat everything with
a box of 27000 molecules, with a volume of ~13800 nm^3. The problem
was the same. Very high pressures (150-200 bar) and very low densities
(<200 g/L) after 750 ps simulation time. And both volume and pressure
increasing with time.


I'm doing now the same procedure, but using gromacs-4.0.7 and I'm
getting very different (and better) results. After energy minimization
I run 5 steps in a nvt ensemble and I got pressure around -30 bar
(Ok for me). After that I start to run the simulations in npt ensemble
and the pressure start to increase slowly, with negative values
because the system have very low densities (~400 g/L), and the volume
is decreasing. So I'm getting the normal reaction from the system.



Where is the problem? There are some different parameters to set in
the mdp file and I didn't realize that, or is this a problem in
gromacs-4.5?

It seems you are generating some numerical instability with your choice of
initial and simulation conditions, and that gromacs-4.0 was luckier in
avoiding the problem. If this is a parallel simulation, then the way
communication is managed in order to organize T and P coupling changed going
up to 4.5. For equilibration, I would encourage setting nsttcouple and
nstpcouple to 1. Using a shorter time step can help with numerical
instability. Berendsen T coupling or a larger coupling time constant might
also help. After gentler NVT, then switch to NPT, let the box size
stabilize, and finally move to larger coupling periods, time steps and
v-rescale T coupling.

Mark



In both cases I used this parameters:
-
integrator  =  md
dt=  0.002
nsteps  =  5
nstcomm  =  1
nstxtcout   =  500
xtc-precision  =  1000
nstxout =  0
nstvout =  0
nstfout =  0
nstlog  =  500
nstenergy   =  500

nstlist   =  5
ns_type =  grid

;Reaction field
rlist   = 0.8
coulombtype = Reaction-field
rcoulomb= 1.4
epsilon_r   = 1.0
epsilon_rf  = 4.8
vdwtype = cut-off
rvdw= 1.4

; temperature coupling
Tcoupl  =  v-rescale
tc-grps =  CHCL3
tau_t   =  0.05
ld_seed =  -1
ref_t   =  300

; Energy monitoring
energygrps  =  CHCl3

; Isotropic pressure
Pcoupl  =  no
Pcoupltype  =  isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0

; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300
gen_seed=  -1

constraint_algorithm=lincs
lincs_order =  4
lincs-warnangle = 90
constraints =  all-bonds


and of course, for the npt ensemble I just change
___

[gmx-users] Umbrella sampling COM distance

[nahren manuel]

Dear Gromacs Users,

I am trying to study the free energy of binding in a protein-ligand complex. 

I use the following pull input in my mdp file:
; Pull code
pull    = umbrella
pull_geometry   = distance  
pull_dim    = N Y N
pull_start  = yes   
pull_ngroups    = 1
pull_group0 = Protein
pull_group1 = GLC
pull_rate1  = 0.005  
pull_k1 = 1000 


if I am pulling in 'Y' direction, is it necessary to make sure that the 
distance between the COM (of the protein and ligand) = distance between the Y 
coordinates,  i.eY(pro)-Y(lig),  ?

 VMD commands 

set pro [atomselect top "protein"]

set glc [atomselect top "resname GLC"]

set A [measure center $pro weight mass]
40.33518600463867 35.01163101196289 38.7291374206543

set B [measure center $glc weight mass]
40.591331481933594 39.440189361572266 38.494876861572266

vecdist $A $B
4.4421411021009884

Y(pro)-Y(lig) = 4.42855835

Best,
nahren
-- 
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

Re: [gmx-users] Pressure very high with chloroform and gromacs-4.5.5

[Nuno Azoia]

I know that from the beginning. That's why I found very strange the
increasing on the system volume. My initial setup have a density of
~400g/L, and for liquid chloroform is ~1400g/L.
Using gromacs-4.5 I get densities of about 200 after 750ps simulation
time, and using 4.0 I get almost 500 after 1ns.

And I was using such low densities because I build the box using
genconf with the options -nbox and -dist, starting with one molecule
of chloroform. If I used small distance values I get LINCS warnings in
the energy minimization step. Using genbox to solvate one empty box
with chloroform, I get very strange behaviors, with a very large
amount of molecule overlap.

But as you said before, I now think that this should be also a
paralelization problem, not to mention the numerical instability
caused by this very low density.
And I think this is a paralelization problem associated with this
numerical instability judging from the system behavior.
In 4.5, using the option -nt in mdrun, I get some small droplets of
liquid chloroform, and in 4.0, using mpi, I get one large droplet of
chloroform. It looks like if 4.5 is treating the system like
independent small systems, while 4.0 is able to divide the system into
small, but interdependent systems.

On Wed, Oct 12, 2011 at 12:26 PM, Mark Abraham  wrote:
> On 12/10/2011 8:04 PM, Nuno Azoia wrote:
>>
>> Thank you Mark for your answer!
>>
>> I agree with you when you say that the high pressure is not itself a
>> problem. To avoid that problem I change my system from 1000 molecules
>> to 27000 molecules, and the pressure change from several thousands to
>> several hundreds bar.
>> What I found very strange was the increasing volume (and pressure). My
>> system is very unstable, I know, because the density is very low, and
>> not the opposite, so I was expecting to see the box getting smaller.
>> Looking to the trajectory I can see a box almost empty (with empty I
>> mean empty space, with chloroform molecules aggregating in small
>> droplets), and that's why I found the system behavior very strange.
>
> Sounds like your initial density might be far too low. grompp reports it, so
> do check.
>
> Mark
>>
>> I will follow your suggestion concerning nsttcouple and nstpcouple and
>> the other initial conditions.
>>
>> Nuno Azoia
>>
>>
>> On Wed, Oct 12, 2011 at 6:24 AM, Mark Abraham
>>  wrote:
>>>
>>> On 12/10/2011 2:22 AM, Nuno Azoia wrote:

 Hello!

 I found something very strange while making a CHCl3 box using
 gromacs-4.5.5.
 A look the mailing list, the manual and some release notes for
 gromacs-4.5 and I couldn't found the answer for my problem. It's
 possible that I'm doing something wrong, but I can not find what, so
 I'm describe my problem.

 I start a chloroform box from scratch, using genconf, and I get o
 chloroform box with 1000 molecules. I get energy minimization without
 problems.
 Then I've run some equilibration steps in a NVT ensemble and in the
 end I get pressure in the order of hundreds of bar.
>>>
>>> The high pressure is not itself a problem - small numbers of molecules
>>> and
>>> short simulation times lead to doubtful statistics for pressure.
>>>
  Then I change to
 NPT conditions and both the pressure and the volume keep increasing
 with time.
>>>
>>> Be sure to visualize your trajectory to confirm its behaviour matches
>>> what
>>> you expect from the trends in P and V.
>>>
 To discard the possibility of a size problem, I repeat everything with
 a box of 27000 molecules, with a volume of ~13800 nm^3. The problem
 was the same. Very high pressures (150-200 bar) and very low densities
 (<    200 g/L) after 750 ps simulation time. And both volume and
 pressure
 increasing with time.


 I'm doing now the same procedure, but using gromacs-4.0.7 and I'm
 getting very different (and better) results. After energy minimization
 I run 5 steps in a nvt ensemble and I got pressure around -30 bar
 (Ok for me). After that I start to run the simulations in npt ensemble
 and the pressure start to increase slowly, with negative values
 because the system have very low densities (~400 g/L), and the volume
 is decreasing. So I'm getting the normal reaction from the system.



 Where is the problem? There are some different parameters to set in
 the mdp file and I didn't realize that, or is this a problem in
 gromacs-4.5?
>>>
>>> It seems you are generating some numerical instability with your choice
>>> of
>>> initial and simulation conditions, and that gromacs-4.0 was luckier in
>>> avoiding the problem. If this is a parallel simulation, then the way
>>> communication is managed in order to organize T and P coupling changed
>>> going
>>> up to 4.5. For equilibration, I would encourage setting nsttcouple and
>>> nstpcouple to 1. Using a shorter time step can help with numerical
>>> instability. Berendsen T co

Re: [gmx-users] Gromacs: Cloud Vs. Boinc Server?

[Szilárd Páll]

Dear Stephan,

> Radeons work as well.  You can put a 3-4 GPU board together with the highest 
> end AMD or Intel chip for 3K, plus 16G RAM if you look around for a day or 
> two, but the cooling is the main problem (with 1/4 the price radeons Vs. GTI 
> cards), so one has to take cooling into account (h20 cost another 800$, or 
> investing in 4-6 good fans/cooling an additional 2-300$).  If you have a 
> slightly higher budget you can get multi CPU boards with 4 GPU slots, ie 4 or 
> 8 CPU's (direct via mail from Taiwan), but the CPU's and GPU's is where the 
> money is spent.

No, Radeons don't work and won't work in the near future - Gromacs
doesn't support OpenCL. Cooling needs attention, but in reality it's
nowhere near $2-300 extra - unless you want the fans with funky leds.

Btw, what software is the above hardware description targeting? To me
it sounds more like a gaming rig and not something specifically aiming
at maximum performance with Gromacs 4.5 (nor 4.6 which is yet to be
released).

> As far as I have seen GPU Gromacs runs at around 1 Teraflop per Radeon 5900 
> series (double percission, single is supposed to run around 4 tera flops per 
> GPU, so depends on your needs, desires as far as simulations), and the latest 
> Intel 970's are around 400-500 Gflops/chip.

Again, I might be missing something, but how exactly does Gromacs run
on Radeons? I assume when referring to the i7 970 (?) above you meant
40-50 GFlops/chip - the i7 970 should have 70 GFlops peak. Also note
that Flops are not every useful, what matters is time to solution for
the specific problem one wants to solve.

Cheers,
--
Szilárd

> --
> NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie!
> Jetzt informieren: http://www.gmx.net/de/go/freephone
> --
> 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
>
--
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

[gmx-users] Uniform Distribution of drug molecules inside water spc216

[meisam valizadeh kiamahalleh]

Dear GMX users
Good day to you
I have some drug molecules (cisplatin) added manually and randomly inside a
system which is going to be solvated in spc216 water.  I used genbox command
to add the correct number of water molecules needed to solvate the box. The
drug molecules are located very closed to each other. Kindly, would you
please let me know how I can distribute drug molecules uniformly among the
water molecoules to obtain a certain concentration of the drug? May I know
if there is any specific tool or script which can help me to do it?
Thank you very much
Kind regards
Meisam
-- 
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

[gmx-users] Potential Energy Landscape

[Natalie Stephenson]

I was recently told in passing that it would be possible to construct a 
'potential energy landscape' from the simulations I have performed.  This way I 
could remove any loading rate differences between simulations and experimental 
force experiments I've been performing ... however I cannot find anywhere in 
which this is mentioned.

The only thing close I could find that was close was the free energy landscape 
using g_anaeig under the Dihedral PCA 
(http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca)
 however, I'm not sure this is what I'm looking for.

Does anyone know where I would be able to find out / read more about how to 
create potential energy landscapes from my simulation outputs?

Thanks
Natalie


-- 
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

[gmx-users] Re: FEP

[Fabian Casteblanco]

Hello Michael or others,

It seems I'm still getting errors when doing a FEP on a molecule (a
-CH3 to a -H).  This below is for when I was charging things from a -H
uncharged to -H charged, although it also happens when I'm actually
converting the -CH3 to -H (at Lambdas greater than 85%).  I made sure
to keep the charges balanced at 0 while mutating and I did it at 3
steps like Michael Shirts suggested.

Set 1: turn R-CH3 charges off in a way that preserves the total charge.
Set 2: change CH3 LJ to H LJ
Set 3: Turn R-H charges on in a way that preserves the total charge.

In the portion of the error below atom 9 is -C9-(H67,H68,H66) which in
this specific case H67 is already a dummy molecule with no mass or
charge.  From what I can see, it seems that the atoms do not know how
to treat the dummy molecules in terms of angles.  How should I treat
the dummy molecules? Should I be treating them like hollow spheres
with no charge so I would assign them angle constraints?

I think it can also be that I'm peturbing the dihedral angles
incorrectly.  I received errors at first saying that dihedral
multiplicities can't be peturbed so I had to equal the multiplicities
just to get it to run.  Does anybody have any experience with this?

Thank you for your help.

-Fabian Casteblanco

Portion of Error Output:
-
Reading file nvt0.5.tpr, VERSION 4.5.3 (single precision)
starting mdrun 'SIMVASTATIN'
15 steps,300.0 ps.

Step 7, time 0.014 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.006111, max 0.139443 (between atoms 9 and 67)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 8, time 0.016 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.007341, max 0.167622 (between atoms 9 and 67)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 8, time 0.016 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.008771, max 0.201182 (between atoms 9 and 67)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length







On Mon, Oct 10, 2011 at 4:10 PM, Fabian Casteblanco
 wrote:
> Hi all,
>
> I have an additional question related to what Steven Neumann was
> mentioning.  I actually have to do a molecule mutation.  I'm trying to
> use Michael Shirts method  1) making small
> changes 'alchemical' changes in the molecules and computing the free
> energies by any method (BAR, TI, etc).  I'm specifically want to try
> to use BAR at the end once I collect all the data.  This helped a lot
> on clarification since it seemed that Justin's tutorial is essentially
> a FEP except its using the BAR mathematical method for computing the
> complete decoupling of the molecule rather than using the old FEP
> mathematics of the exponential averaging formula.  So BAR is only
> referring to the mathematical code used to calculate the overall free
> energy for the FEP, correct?
>
> My question is, for a mutation of a -CH3 group to a -H group, is it
> better to simply run:
> [+ from (Lambda=0 ,  R-CH3, full charges and interactions -STATE A)
> --> (Lambda=1, R-CH, full charges and interactions -STATE B)]
>
> OR
>
> [1) from (Lambda=0 ,  R-CH3, STATE A : Charges and LJ Interactions: ON)
> 2)  (Lambda=?, -CH3 Charges: OFF ,LJ Interactions: ON and unmutated)
> 3)  (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ Interactions: OFF)
> 4)  (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ interactions: ON and Mutated to 
> -H)
> 5)  (Lambda=1, R-CH3, -CH3  STATE B : Charges and LJ Interactions: ON)
>
> Reason I'm asking is because when I try the first choice to do it
> STATE A to STATE B in one step, when I reach Lambda=0.85 and above on
> the NVT equilibration right after EM, I receive errors saying that
> bonds are moving way to far off their constraints which leads me to
> believe that the system is moving too far from where it was energy
> minimized.  Errors such as:
>
> Step 188, time 0.376 (ps)
> LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.17, max 0.000636 (between atoms 9 and 68)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>      9     68   31.2    0.   0.1110      0.
>
> Step 188, time 0.376 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.15, max 0.000531 (between atoms 9 and 68)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>      9     68   31.0    0.   0.1110      0.
>
>
> **Please, if anybody can help, I would greatly appreciate it.  Thanks.
> --
> Best regards,
>
> Fabian F. Casteblanco
> Rutgers University --
> Chemical Engineering
> C: +908 917 0723
> E:  fabian.castebla...@gmail.com
>



-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 07

Re: [gmx-users] Uniform Distribution of drug molecules inside water spc216

[Justin A. Lemkul]

meisam valizadeh kiamahalleh wrote:

Dear GMX users
Good day to you
I have some drug molecules (cisplatin) added manually and 
randomly inside a system which is going to be solvated in spc216 water. 
 I used genbox command to add the correct number of water molecules 
needed to solvate the box. The drug molecules are located very closed to 
each other. Kindly, would you please let me know how I can distribute 
drug molecules uniformly among the water molecoules to obtain a 
certain concentration of the drug? May I know if there is any specific 
tool or script which can help me to do it?


I don't know how you did the initial insertion, but genbox -ci -nmol will add 
molecules randomly, after which you can solvate with water.  Don't combine these 
steps.  Do the insertion, then add the water.


-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


--
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

Re: [gmx-users] Gromacs: Cloud Vs. Boinc Server?

[Matt Larson]

>From the Gromacs on GPU page
(http://www.gromacs.org/Downloads/Installation_Instructions/GPUs)

These are the compatible GPU cards (Basically buy NVidia for now):

v2.0
Compatible NVIDIA CUDA versions (also see OpenMM version compatibility above):

v3.x
Compatible hardware (for details consult the NVIDIA CUDA GPUs list):

G92/G94:
GeForce 9800 GX2/GTX/GTX+/GT
GeForce 9800M GT
GeForce GTS 150, 250
GeForce GTX 280M, 285M
Quadro FX 4700
Quadro Plex 2100 D4
GT200:
GeForce GTX 260, 270, 280, 285, 295
Tesla C1060, S1070, M1060
Quadro FX 4800, 5800
Quadro CX
Quadro Plex 2200 D2, 2200 S4
GF1xx (Fermi)
GeForce GTX 460, 465, 470, 480, 570, 580
Tesla C2050, C2070, M2050, M2070

---

 I got an EVGA Geforce GTX 580, which is about $450 for trying out GPU
based MD, and has 512 GPU cores and a high clock rate, 1.5 gigs of
memory.  Having more cores and more memory are both important things
for the GPU side of molecular dynamics (cores = more parallel, memory
= more atoms and less memory transferring).  I think you have some
limitations with the GPU sims, like atoms < 100,000.  It is amazing
that with implicit solvent you can really see a huge benefit and
perhaps that might open some new doors.

-Matt Larson


On Wed, Oct 12, 2011 at 9:54 AM, Szilárd Páll  wrote:
> Dear Stephan,
>
>> Radeons work as well.  You can put a 3-4 GPU board together with the highest 
>> end AMD or Intel chip for 3K, plus 16G RAM if you look around for a day or 
>> two, but the cooling is the main problem (with 1/4 the price radeons Vs. GTI 
>> cards), so one has to take cooling into account (h20 cost another 800$, or 
>> investing in 4-6 good fans/cooling an additional 2-300$).  If you have a 
>> slightly higher budget you can get multi CPU boards with 4 GPU slots, ie 4 
>> or 8 CPU's (direct via mail from Taiwan), but the CPU's and GPU's is where 
>> the money is spent.
>
> No, Radeons don't work and won't work in the near future - Gromacs
> doesn't support OpenCL. Cooling needs attention, but in reality it's
> nowhere near $2-300 extra - unless you want the fans with funky leds.
>
> Btw, what software is the above hardware description targeting? To me
> it sounds more like a gaming rig and not something specifically aiming
> at maximum performance with Gromacs 4.5 (nor 4.6 which is yet to be
> released).
>
>> As far as I have seen GPU Gromacs runs at around 1 Teraflop per Radeon 5900 
>> series (double percission, single is supposed to run around 4 tera flops per 
>> GPU, so depends on your needs, desires as far as simulations), and the 
>> latest Intel 970's are around 400-500 Gflops/chip.
>
> Again, I might be missing something, but how exactly does Gromacs run
> on Radeons? I assume when referring to the i7 970 (?) above you meant
> 40-50 GFlops/chip - the i7 970 should have 70 GFlops peak. Also note
> that Flops are not every useful, what matters is time to solution for
> the specific problem one wants to solve.
>
> Cheers,
> --
> Szilárd
>
>> --
>> NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie!
>> Jetzt informieren: http://www.gmx.net/de/go/freephone
>> --
>> 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
>>
> --
> 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
>
--
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

[gmx-users] protein-water distance restraints

[Markus Weingarth]

Dear Gromacs-users,I would like to force an arbitrary water molcule from the box into an occluded cavity of a membrane-channel. It do not want this water molcule within the cavity at the beginning of the simulation.I though that I could implement intermolecular distance restraints between a water residue an the protein, but I did not manage that and all the suggestions I found here to implement intermolecular distance restraints seem not to work out for water - protein contacts. Does anybody has a suggestion how to implement such restraints ? Would the pull-code an option for my problem ?Thank you very muchMarkus  SMS schreiben mit WEB.DE FreeMail - einfach, schnell und   kostenguenstig. Jetzt gleich testen! http://f.web.de/?mc=021192

-- 
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

Re: [gmx-users] protein-water distance restraints

[Francesco Oteri]

Dear Markus,
If you know the residues composing the cavity (and I think you know it), 
you can simply change the coordinates

of the water molecule in the .gro file to move the water in the cavity.

Francesco


Il 12/10/2011 18:17, Markus Weingarth ha scritto:


Dear Gromacs-users,

I would like to force an arbitrary water molcule from the box into an 
occluded cavity of a membrane-channel. It do not want this water 
molcule within the cavity at the beginning of the simulation.


I though that I could implement intermolecular distance restraints 
between a water residue an the protein, but I did not manage that and 
all the suggestions I found here to implement intermolecular distance 
restraints seem not to work out for water - protein contacts. Does 
anybody has a suggestion how to implement such restraints ? Would the 
pull-code an option for my problem ?


Thank you very much
Markus





SMS schreiben mit WEB.DE FreeMail - einfach, schnell und
kostenguenstig. Jetzt gleich testen! *http://f.web.de/?mc=021192*





-- 
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

Re: [gmx-users] protein-water distance restraints

[Markus Weingarth]

Hi Francesco,Thanks for your answer, but that's not an option for me. I really would like to force the penetreation of a water-molecule into this cavity over the couse of the trajectory.CheersMarkusVon: "Francesco Oteri" Gesendet: Oct 12, 2011 6:41:05 PMAn: gmx-users@gromacs.orgBetreff: Re: [gmx-users] protein-water distance restraintsDear Markus,If you know the residues composing the cavity (and I think you know it), you can simply change the coordinatesof the water molecule in the .gro file to move the water in the cavity.FrancescoIl 12/10/2011 18:17, Markus Weingarth ha scritto:Dear Gromacs-users,I would like to force an arbitrary water molcule from the box into an occluded cavity of a membrane-channel. It do not want this water molcule within the cavity at the beginning of the simulation.I though that I could implement intermolecular distance restraints between a water residue an the protein, but I did not manage that and all the suggestions I found here to implement intermolecular distance restraints seem not to work out for water - protein contacts. Does anybody has a suggestion how to implement such restraints ? Would the pull-code an option for my problem ?Thank you very muchMarkus  SMS schreiben mit WEB.DE FreeMail - einfach, schnell und   kostenguenstig. Jetzt gleich testen! http://f.web.de/?mc=021192    SMS schreiben mit WEB.DE FreeMail - einfach, schnell und   kostenguenstig. Jetzt gleich testen! http://f.web.de/?mc=021192

-- 
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

Re: [gmx-users] protein-water distance restraints

[Justin A. Lemkul]

Markus Weingarth wrote:

Hi Francesco,

Thanks for your answer, but that's not an option for me. I really would 
like to force the penetreation of a water-molecule into this cavity over 
the couse of the trajectory.




Use the pull code.

-Justin


Cheers
Markus





*Von:* "Francesco Oteri" 
*Gesendet:* Oct 12, 2011 6:41:05 PM
*An:* gmx-users@gromacs.org
*Betreff:* Re: [gmx-users] protein-water distance restraints

Dear Markus,
If you know the residues composing the cavity (and I think you know
it), you can simply change the coordinates
of the water molecule in the .gro file to move the water in the cavity.

Francesco


Il 12/10/2011 18:17, Markus Weingarth ha scritto:


Dear Gromacs-users,

I would like to force an arbitrary water molcule from the box
into an occluded cavity of a membrane-channel. It do not want
this water molcule within the cavity at the beginning of the
simulation.

I though that I could implement intermolecular distance
restraints between a water residue an the protein, but I did not
manage that and all the suggestions I found here to implement
intermolecular distance restraints seem not to work out for
water - protein contacts. Does anybody has a suggestion how to
implement such restraints ? Would the pull-code an option for my
problem ?

Thank you very much
Markus



  

SMS schreiben mit WEB.DE FreeMail - einfach, schnell und   
kostenguenstig. Jetzt gleich testen!

*http://f.web.de/?mc=021192*




 

  

SMS schreiben mit WEB.DE FreeMail - einfach, schnell und   
kostenguenstig. Jetzt gleich testen! *http://f.web.de/?mc=021192*




--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/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

Re: [gmx-users] Potential Energy Landscape

[Justin A. Lemkul]

Natalie Stephenson wrote:
I was recently told in passing that it would be possible to construct a 
'potential energy landscape' from the simulations I have performed.  
This way I could remove any loading rate differences between simulations 
and experimental force experiments I've been performing ... however I 
cannot find anywhere in which this is mentioned.


The only thing close I could find that was close was the free energy 
landscape using g_anaeig under the Dihedral PCA 
(http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca 
) 
however, I'm not sure this is what I'm looking for. 

Does anyone know where I would be able to find out / read more about how 
to create potential energy landscapes from my simulation outputs?




g_sham produces free energy landscapes for any variables plotted against one 
another.


-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


--
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

[gmx-users] mktop

[ram bio]

Dear Gromacs Users,

I am using opls FF for my protein-ligand simulations in lipid bilayer. I
have  generated the topologies for the ligand using MKtop. The output from
the MKTOP gives the top file, but not the coordinate/structure file. Please
let me know if any tutorial is available for merging the output of mktop
into gromacs MD simulation.



Thanks,

Pramod
-- 
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

Re: [gmx-users] mktop

[Justin A. Lemkul]

ram bio wrote:

Dear Gromacs Users,

I am using opls FF for my protein-ligand simulations in lipid bilayer. I 
have  generated the topologies for the ligand using MKtop. The output 
from the MKTOP gives the top file, but not the coordinate/structure 
file. Please let me know if any tutorial is available for merging the 
output of mktop into gromacs MD simulation.





You can #include any molecule topology in a system .top, provided you have the 
right format:


http://www.gromacs.org/Documentation/File_Formats/.itp_File

There is no tutorial for using mktop with a protein-ligand/membrane system, but 
there are tutorials for protein-ligand complexes:


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html

and membrane protein systems:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html

-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


--
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

Fwd: [gmx-users] mktop

[ram bio]

Dear Justin,

Thanks for the information.

Initially, i just wanted to run a simulation of protein-ligand in water
solvent . I renamed the topology.top generated from mktop to ligand.itp; and
included the ligand.itp line in the topol.top file generated from the
pdb2gmx. During the pdb2gmx command, i used opls FF.  The coordinates of
ligand used as input for mktop were added to the output of pdb2gmx
(process.pdb - only protein coordinates), so that the structure file along
with ligand coordinates (processlig.pdb) can be used for further steps.  I
doubt whether the procedure followed by me is correct, as when i execute
grompp command to add ions i am getting errors :


grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr


ERROR 1 [file ligand.itp, line 291]:
  No default Ryckaert-Bell. types

..

---
Program grompp, VERSION 4.5.4
Source code file: toppush.c, line: 1526

Fatal error:
[ file ligand.itp, line 397 ]:
Atom index (0) in dihedrals out of bounds (1-53).
This probably means that you have inserted topology section "dihedrals"
in a part belonging to a different molecule than you intended to.
In that case move the "dihedrals" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

The commands executed to reach the grompp step are as follows:


pdb2gmx -f jhcdyinteractionposea.pdb -ignh -o process.pdb
editconf -f processlig.pdb -o procent.pdb -princ
editconf -f procent.pdb -o procent.gro -c -d 1.0 -bt cubic
genbox -cp procent.gro -cs spc216.gro -o procentsolv.gro -p topol.top
grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr

I have attached the topol.top, ligand.itp  files for your information,
Please let me know your suggestions to fix this error.

Thanks,
Pramod





On Wed, Oct 12, 2011 at 12:38 PM, Justin A. Lemkul  wrote:

>
>
> ram bio wrote:
>
>> Dear Gromacs Users,
>>
>> I am using opls FF for my protein-ligand simulations in lipid bilayer. I
>> have  generated the topologies for the ligand using MKtop. The output from
>> the MKTOP gives the top file, but not the coordinate/structure file. Please
>> let me know if any tutorial is available for merging the output of mktop
>> into gromacs MD simulation.
>>
>>
>>
> You can #include any molecule topology in a system .top, provided you have
> the right format:
>
> http://www.gromacs.org/**Documentation/File_Formats/.**itp_File
>
> There is no tutorial for using mktop with a protein-ligand/membrane system,
> but there are tutorials for protein-ligand complexes:
>
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
> gmx-tutorials/complex/index.**html
>
> and membrane protein systems:
>
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
> gmx-tutorials/membrane_**protein/index.html
>
> -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
>
> ==**==
> --
> 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/Searchbefore
>  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
>


ligand.itp
Description: Binary data


topol.top
Description: Binary data
-- 
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

[gmx-users] Re: gmx-users Digest, Vol 90, Issue 48

[meisam valizadeh kiamahalleh]

Dear Justin
Thank you very much for your always prompt reply. Actually, I added many of
drug molecules by copying and pasting a single molecule in discovery studio
software. I could even move the drug molecules to any desired locations by
select and dragging them.  Finally I used the output pdb file from discovery
studio as initial structure in Gromacs, but I could not find any option for
the molecule uniform distribution.
1) May I know if I should use the drug resname or molecule name infront of
-nmol?
2) As you mention the method suggested by you would add the drug molecules
randomly. then, May I also Know if they can be uniformly distributed in the
water after solvation?
Thank you very much
Best regards
Meisam


> meisam valizadeh kiamahalleh wrote:
> > Dear GMX users
> > Good day to you
> > I have some drug molecules (cisplatin) added manually and
> > randomly inside a system which is going to be solvated in spc216 water.
> >  I used genbox command to add the correct number of water molecules
> > needed to solvate the box. The drug molecules are located very closed to
> > each other. Kindly, would you please let me know how I can distribute
> > drug molecules uniformly among the water molecoules to obtain a
> > certain concentration of the drug? May I know if there is any specific
> > tool or script which can help me to do it?
>
> I don't know how you did the initial insertion, but genbox -ci -nmol will
> add
> molecules randomly, after which you can solvate with water.  Don't combine
> these
> steps.  Do the insertion, then add the water.
>
> -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
>
> 
>
>
-- 
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

Re: [gmx-users] mktop

[Justin A. Lemkul]

ram bio wrote:

Dear Justin,

Thanks for the information.

Initially, i just wanted to run a simulation of protein-ligand in water 
solvent . I renamed the topology.top generated from mktop to ligand.itp; 
and included the ligand.itp line in the topol.top file generated from 
the pdb2gmx. During the pdb2gmx command, i used opls FF.  The 
coordinates of ligand used as input for mktop were added to the output 
of pdb2gmx (process.pdb - only protein coordinates), so that the 
structure file along with ligand coordinates (processlig.pdb) can be 
used for further steps.  I doubt whether the procedure followed by me is 
correct, as when i execute grompp command to add ions i am getting errors :



grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr


ERROR 1 [file ligand.itp, line 291]:
  No default Ryckaert-Bell. types

..

---
Program grompp, VERSION 4.5.4
Source code file: toppush.c, line: 1526

Fatal error:
[ file ligand.itp, line 397 ]:
Atom index (0) in dihedrals out of bounds (1-53).
This probably means that you have inserted topology section "dihedrals"
in a part belonging to a different molecule than you intended to.
In that case move the "dihedrals" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

The commands executed to reach the grompp step are as follows:


pdb2gmx -f jhcdyinteractionposea.pdb -ignh -o process.pdb
editconf -f processlig.pdb -o procent.pdb -princ
editconf -f procent.pdb -o procent.gro -c -d 1.0 -bt cubic
genbox -cp procent.gro -cs spc216.gro -o procentsolv.gro -p topol.top
grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr

I have attached the topol.top, ligand.itp and procentsolv.gro files for 
your information, Please let me know your suggestions to fix this error.




The ligand.itp file is trash.  Most of your atoms have zero charge (except for a 
few that have +/- 1...yikes!) and on line 397 (as cited in the error message) 
atom 0 is referenced, which of course does not exist, since numbering starts 
with 1.  You also have some exotic atom types present, and thus bonded 
parameters cannot be assigned, as grompp complained earlier.


You need a better quality topology, and perhaps a different force field that 
might be suited for doing these simulations.


-Justin


Thanks,
Pramod




On Wed, Oct 12, 2011 at 12:38 PM, Justin A. Lemkul > wrote:




ram bio wrote:

Dear Gromacs Users,

I am using opls FF for my protein-ligand simulations in lipid
bilayer. I have  generated the topologies for the ligand using
MKtop. The output from the MKTOP gives the top file, but not the
coordinate/structure file. Please let me know if any tutorial is
available for merging the output of mktop into gromacs MD
simulation.



You can #include any molecule topology in a system .top, provided
you have the right format:

http://www.gromacs.org/__Documentation/File_Formats/.__itp_File


There is no tutorial for using mktop with a protein-ligand/membrane
system, but there are tutorials for protein-ligand complexes:


http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/complex/index.__html



and membrane protein systems:


http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/index.html



-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


==__==
-- 
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





--
===

Re: [gmx-users] Uniform Distribution of drug molecules inside water spc216

[Justin A. Lemkul]

meisam valizadeh kiamahalleh wrote:

Dear Justin
Thank you very much for your always prompt reply. Actually, I added many 
of drug molecules by copying and pasting a single molecule in discovery 
studio software. I could even move the drug molecules to any desired 
locations by select and dragging them.  Finally I used the output pdb 
file from discovery studio as initial structure in Gromacs, but I could 
not find any option for the molecule uniform distribution.
1) May I know if I should use the drug resname or molecule name infront 
of -nmol?


The -nmol option takes an integer argument.  Please see genbox -h.

2) As you mention the method suggested by you would add the drug 
molecules randomly. then, May I also Know if they can 
be uniformly distributed in the water after solvation?


You can only build a random configuration with genbox -ci -nmol.  If you want an 
artificially crystalline system, use genconf -nbox to replicate your existing 
drug molecule as many times as you'd like in whatever dimensions you want. 
Either way, you'll have to do sufficient equilibration to get a homogeneous 
system, if it's even possible.  I'd think the latter approach would be worse 
since you're starting from a very highly ordered system.


-Justin


Thank you very much
Best regards
Meisam
 


meisam valizadeh kiamahalleh wrote:
 > Dear GMX users
 > Good day to you
 > I have some drug molecules (cisplatin) added manually and
 > randomly inside a system which is going to be solvated in spc216
water.
 >  I used genbox command to add the correct number of water molecules
 > needed to solvate the box. The drug molecules are located very
closed to
 > each other. Kindly, would you please let me know how I can distribute
 > drug molecules uniformly among the water molecoules to obtain a
 > certain concentration of the drug? May I know if there is any
specific
 > tool or script which can help me to do it?

I don't know how you did the initial insertion, but genbox -ci -nmol
will add
molecules randomly, after which you can solvate with water.  Don't
combine these
steps.  Do the insertion, then add the water.

-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





--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/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

Re: [gmx-users] mktop

[ram bio]

Dear Justin,

As i generated the protein-ligand docked complex using opls FF, for the
consistency, i am trying to use opls ff generated ligand parameters during
md simulations in lipid bi layer. I found that MKTOP can generate topology
files using opls ff for small molecules.

 I have also tried  swiss param to generate the ligand parameters to be used
in protein ligand simulation using gromacs. The force field i am using for
simulations is OPLS. My ligand contains an azido group and a tropane ring
with protonated nitrogen. SwissParam force field has been designed to be
compatible with the Charmm force field, but they are not tested on
opls.Using the ligand topologies from  swissparam, i was able to run the MD
simulations using gromacs with opls without errors (swissparam - gromacs
tutorial), only issues being the charges on the ligand, so i generated
various input files (mol2 files) for swissparam with charges generated
using ambcc1, gastergier and MMFF. But the itp files obtained from
swissparam had same charges for the ligand atoms irrespective of the input
provided i.e. charged or uncharged mol2 files, and

As per Gromacs website:

"Note that an .itp
filewill
be specific to a given force field, and will only function when
included by a .top
filethat
has previously included the .itp
files  for that
force field. Appropriate use of the #define and #ifdef mechanisms can permit
the same .itp 
fileto
work with multiple force fields, e.g.
share/top/water.itp."

so, i think even though the swissparam generated topologies based on MMFF
fit to charmm (based on testing), they could also be used with opls. It was
informed by swiss param team  that the ligand parameters generated by
swissparam could also be used with opls FF in principle as they are based on
MMFF
So, in order to cross check or validate my results i was trying to use mktop
to generate the ligand topologies for MD simulations.

Please let me know your comments and suggestions on the procedure ,
regarding the compatibility of MMFF generated topologies to be used by OPLS
and other methods to validate my results.

Thanks,

Pramod

On Wed, Oct 12, 2011 at 1:28 PM, Justin A. Lemkul  wrote:

>
>
> ram bio wrote:
>
>> Dear Justin,
>>
>> Thanks for the information.
>>
>> Initially, i just wanted to run a simulation of protein-ligand in water
>> solvent . I renamed the topology.top generated from mktop to ligand.itp; and
>> included the ligand.itp line in the topol.top file generated from the
>> pdb2gmx. During the pdb2gmx command, i used opls FF.  The coordinates of
>> ligand used as input for mktop were added to the output of pdb2gmx
>> (process.pdb - only protein coordinates), so that the structure file along
>> with ligand coordinates (processlig.pdb) can be used for further steps.  I
>> doubt whether the procedure followed by me is correct, as when i execute
>> grompp command to add ions i am getting errors :
>>
>>
>> grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr
>>
>>
>> ERROR 1 [file ligand.itp, line 291]:
>>  No default Ryckaert-Bell. types
>>
>> ..
>>
>> --**-
>> Program grompp, VERSION 4.5.4
>> Source code file: toppush.c, line: 1526
>>
>> Fatal error:
>> [ file ligand.itp, line 397 ]:
>> Atom index (0) in dihedrals out of bounds (1-53).
>> This probably means that you have inserted topology section "dihedrals"
>> in a part belonging to a different molecule than you intended to.
>> In that case move the "dihedrals" section to the right molecule.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at 
>> http://www.gromacs.org/**Documentation/Errors
>> --**-
>>
>> The commands executed to reach the grompp step are as follows:
>>
>>
>> pdb2gmx -f jhcdyinteractionposea.pdb -ignh -o process.pdb
>> editconf -f processlig.pdb -o procent.pdb -princ
>> editconf -f procent.pdb -o procent.gro -c -d 1.0 -bt cubic
>> genbox -cp procent.gro -cs spc216.gro -o procentsolv.gro -p topol.top
>> grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr
>>
>> I have attached the topol.top, ligand.itp and procentsolv.gro files for
>> your information, Please let me know your suggestions to fix this error.
>>
>>
> The ligand.itp file is trash.  Most of your atoms have zero charge (except
> for a few that have +/- 1...yikes!) and on line 397 (as cited in the error
> message) atom 0 is referenced, which of course does not exist, since
> numbering starts with 1.  You also have some exotic atom types present, and
> thus bonded parameters cannot be assigned, as grompp complained earlier.
>
> You need a better quality top

Re: [gmx-users] mktop

[Justin A. Lemkul]

ram bio wrote:

Dear Justin,

As i generated the protein-ligand docked complex using opls FF, for the 
consistency, i am trying to use opls ff generated ligand parameters 
during md simulations in lipid bi layer. I found that MKTOP can generate 
topology files using opls ff for small molecules.




I understand that.  The program did a poor job, per the reasons I cited before. 
 I do not know anything about mktop (other than what it does), so I cannot 
analyze its suitability here, but due to missing parameters and bogus charges, 
you should not use that topology for anything.


 I have also tried  swiss param to generate the ligand parameters to be 
used in protein ligand simulation using gromacs. The force field i am 
using for simulations is OPLS. My ligand contains an azido group and a 
tropane ring with protonated nitrogen. SwissParam force field has been 
designed to be compatible with the Charmm force field, but they are not 
tested on opls.Using the ligand topologies from  swissparam, i was able 
to run the MD simulations using gromacs with opls without errors 
(swissparam - gromacs tutorial), only issues being the charges on the 
ligand, so i generated various input files (mol2 files) for swissparam 
with charges generated  using ambcc1, gastergier and MMFF. But the itp 
files obtained from swissparam had same charges for the ligand atoms 
irrespective of the input provided i.e. charged or uncharged mol2 files, and




If SwissParam was designed to be used with CHARMM, the most intuitive next step 
is to use CHARMM for the MD, is it not?  I understand the point about trying to 
keep the force fields consistent between docking and MD, but it may not be 
feasible (i.e., there may not be suitable parameters in OPLS for the bizarre 
functional groups you're dealing with).



As per Gromacs website:

"Note that an .itp file 
 will be 
specific to a given force field, and will only function when included by 
a .top file 
 that has 
previously included the .itp files 
 for that 
force field. Appropriate use of the |#define| and |#ifdef| mechanisms 
can permit the same .itp file 
 to work 
with multiple force fields, e.g. |share/top/water.itp|."




Note the key caveat here - through the use of #define and #ifdef you can make 
use of different force fields.  That means you can control which parameters are 
applied based on different conditions.  I could write an .itp file for any 
molecule that has force field parameters for any force field, and all I'd have 
to do is enclose all relevant directives within #ifdef blocks and it would work. 
 This note does *not* indicate that you can mix and match force fields.  Doing 
so is generally a very bad idea, if it even works syntactically.


so, i think even though the swissparam generated topologies based on 
MMFF fit to charmm (based on testing), they could also be used with 
opls. It was informed by swiss param team  that the ligand parameters 
generated by swissparam could also be used with opls FF in principle as 
they are based on MMFF
So, in order to cross check or validate my results i was trying to use 
mktop to generate the ligand topologies for MD simulations.




Maybe the SwissParam-generated topology will work.  There are commonalities 
underlying these force fields, to be sure.  Still, the methodology for properly 
deriving OPLS parameters is quite well described in the literature, right down 
to the QM basis sets required to run the geometry optimizations and charge 
calculations.


-Justin

Please let me know your comments and suggestions on the procedure , 
regarding the compatibility of MMFF generated topologies to be used by 
OPLS and other methods to validate my results.


Thanks,

Pramod

On Wed, Oct 12, 2011 at 1:28 PM, Justin A. Lemkul > wrote:




ram bio wrote:

Dear Justin,

Thanks for the information.

Initially, i just wanted to run a simulation of protein-ligand
in water solvent . I renamed the topology.top generated from
mktop to ligand.itp; and included the ligand.itp line in the
topol.top file generated from the pdb2gmx. During the pdb2gmx
command, i used opls FF.  The coordinates of ligand used as
input for mktop were added to the output of pdb2gmx (process.pdb
- only protein coordinates), so that the structure file along
with ligand coordinates (processlig.pdb) can be used for further
steps.  I doubt whether the procedure followed by me is correct,
as when i execute grompp command to add ions i am getting errors :


grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr


ERROR 1 [file ligand.itp, line 291]:
 No default Ryckaert-Bell

[gmx-users] Peturbing a Dihedral for FEP

[Fabian Casteblanco]

Hello all,

 It seems I'm still getting errors when doing a FEP on a molecule (a
 -CH3 to a -H).  This below is for when I was charging things from a -H
 uncharged to -H charged, although it also happens when I'm actually
 converting the -CH3 to -H (at Lambdas greater than 85%).  I made sure
 to keep the charges balanced at 0 while mutating and I did it at 3
 steps like Michael Shirts suggested.

 Set 1: turn R-CH3 charges off in a way that preserves the total charge.
 Set 2: change CH3 LJ to H LJ
 Set 3: Turn R-H charges on in a way that preserves the total charge.

 In the portion of the error below atom 9 is -C9-(H67,H68,H66) which in
 this specific case H67 is already a dummy molecule with no mass or
 charge.  From what I can see, it seems that the atoms do not know how
 to treat the dummy molecules in terms of angles.  How should I treat
 the dummy molecules? Should I be treating them like hollow spheres
 with no charge so I would assign them angle constraints?

 I think it can also be that I'm peturbing the dihedral angles
 incorrectly.  I received errors at first saying that dihedral
 multiplicities can't be peturbed so I had to equal the multiplicities
 just to get it to run.  Does anybody have any experience with this?

 Thank you for your help.

 -Fabian Casteblanco

 Portion of Error Output:
 -
 Reading file nvt0.5.tpr, VERSION 4.5.3 (single precision)
 starting mdrun 'SIMVASTATIN'
 15 steps,    300.0 ps.

 Step 7, time 0.014 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.006111, max 0.139443 (between atoms 9 and 67)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length

 Step 8, time 0.016 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.007341, max 0.167622 (between atoms 9 and 67)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length

 Step 8, time 0.016 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.008771, max 0.201182 (between atoms 9 and 67)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length







> On Mon, Oct 10, 2011 at 4:10 PM, Fabian Casteblanco
>  wrote:
>> Hi all,
>>
>> I have an additional question related to what Steven Neumann was
>> mentioning.  I actually have to do a molecule mutation.  I'm trying to
>> use Michael Shirts method  1) making small
>> changes 'alchemical' changes in the molecules and computing the free
>> energies by any method (BAR, TI, etc).  I'm specifically want to try
>> to use BAR at the end once I collect all the data.  This helped a lot
>> on clarification since it seemed that Justin's tutorial is essentially
>> a FEP except its using the BAR mathematical method for computing the
>> complete decoupling of the molecule rather than using the old FEP
>> mathematics of the exponential averaging formula.  So BAR is only
>> referring to the mathematical code used to calculate the overall free
>> energy for the FEP, correct?
>>
>> My question is, for a mutation of a -CH3 group to a -H group, is it
>> better to simply run:
>> [+ from (Lambda=0 ,  R-CH3, full charges and interactions -STATE A)
>> --> (Lambda=1, R-CH, full charges and interactions -STATE B)]
>>
>> OR
>>
>> [1) from (Lambda=0 ,  R-CH3, STATE A : Charges and LJ Interactions: ON)
>> 2)  (Lambda=?, -CH3 Charges: OFF ,LJ Interactions: ON and unmutated)
>> 3)  (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ Interactions: OFF)
>> 4)  (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ interactions: ON and Mutated to 
>> -H)
>> 5)  (Lambda=1, R-CH3, -CH3  STATE B : Charges and LJ Interactions: ON)
>>
>> Reason I'm asking is because when I try the first choice to do it
>> STATE A to STATE B in one step, when I reach Lambda=0.85 and above on
>> the NVT equilibration right after EM, I receive errors saying that
>> bonds are moving way to far off their constraints which leads me to
>> believe that the system is moving too far from where it was energy
>> minimized.  Errors such as:
>>
>> Step 188, time 0.376 (ps)
>> LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.17, max 0.000636 (between atoms 9 and 68)
>> bonds that rotated more than 30 degrees:
>>  atom 1 atom 2  angle  previous, current, constraint length
>>      9     68   31.2    0.   0.1110      0.
>>
>> Step 188, time 0.376 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.15, max 0.000531 (between atoms 9 and 68)
>> bonds that rotated more than 30 degrees:
>>  atom 1 atom 2  angle  previous, current, constraint length
>>      9     68   31.0    0.   0.1110      0.
>>
>>
>> **Please, if anybody can help, I would greatly appreciate it.  Thanks.
>> --
>> Best regards,
>>
>> Fabian F. Casteblanco
>> Rutgers University --
>> Chemical Engineering
>> C: +908 917 0723
>> E:  fabian.castebla...@gmail.com
>>
>
>
>
> --
> Best re

Re: [gmx-users] mktop

[ram bio]

Dear Justin,

Thanks, and I accept your suggestions;

If SwissParam was designed to be used with CHARMM, the most intuitive next
step is to use CHARMM for the MD, is it not?I understand the point about
trying to keep the force fields consistent between docking and MD, but it
may not be feasible (i.e., there may not be suitable parameters in OPLS for
the bizarre functional groups you're dealing with).

Yes, I also tried CHARMM FF to generate the topology file of the protein
using pdb2gmx (without ligand), and as per the swissparam and gromacs
tutorial i could build the protein-ligand-lipid bilayer and minimize it
using mdrun and and i am at the NPT equilibration step, everything is ok
with this procedure and without errors, but my lipid bilayer is made up of
POPC and the POPC itp file has OPLS FF topologies. So, i was wondering
whether the POPC itp file i am using for MD simulations can be used with the
protein and ligand topology file generated by CHARMM.

and as per the swissparam tutorial the command to generate topology file for
protein is:

 pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp



in the gromacs 4.5.4 version the option to select Charmm FF from the pdb2gmx
command is available, but i could not understand the usage of -nochargegp
flag as per the tutorial, is this flag still valid while generating
toplogies.

Please let me  know your comments and suggestions regarding the procedure
followed and the itp files usage for gromacs MD simulations.

Thanks in advance,

Pramod


On Wed, Oct 12, 2011 at 3:10 PM, Justin A. Lemkul  wrote:

>
>
> ram bio wrote:
>
>> Dear Justin,
>>
>> As i generated the protein-ligand docked complex using opls FF, for the
>> consistency, i am trying to use opls ff generated ligand parameters during
>> md simulations in lipid bi layer. I found that MKTOP can generate topology
>> files using opls ff for small molecules.
>>
>>
> I understand that.  The program did a poor job, per the reasons I cited
> before.  I do not know anything about mktop (other than what it does), so I
> cannot analyze its suitability here, but due to missing parameters and bogus
> charges, you should not use that topology for anything.
>
>
>   I have also tried  swiss param to generate the ligand parameters to be
>> used in protein ligand simulation using gromacs. The force field i am using
>> for simulations is OPLS. My ligand contains an azido group and a tropane
>> ring with protonated nitrogen. SwissParam force field has been designed to
>> be compatible with the Charmm force field, but they are not tested on
>> opls.Using the ligand topologies from  swissparam, i was able to run the MD
>> simulations using gromacs with opls without errors (swissparam - gromacs
>> tutorial), only issues being the charges on the ligand, so i generated
>> various input files (mol2 files) for swissparam with charges generated
>>  using ambcc1, gastergier and MMFF. But the itp files obtained from
>> swissparam had same charges for the ligand atoms irrespective of the input
>> provided i.e. charged or uncharged mol2 files, and
>>
>>
> If SwissParam was designed to be used with CHARMM, the most intuitive next
> step is to use CHARMM for the MD, is it not?  I understand the point about
> trying to keep the force fields consistent between docking and MD, but it
> may not be feasible (i.e., there may not be suitable parameters in OPLS for
> the bizarre functional groups you're dealing with).
>
>  As per Gromacs website:
>>
>> "Note that an .itp file > Documentation/File_Formats/.**itp_File>
>> will be specific to a given force field, and will only function when
>> included by a .top file > Documentation/File_Formats/.**top_File>
>> that has previously included the .itp files > Documentation/File_Formats/.**itp_File>
>> for that force field. Appropriate use of the |#define| and |#ifdef|
>> mechanisms can permit the same .itp file > Documentation/File_Formats/.**itp_File>
>> to work with multiple force fields, e.g. |share/top/water.itp|."
>>
>>
> Note the key caveat here - through the use of #define and #ifdef you can
> make use of different force fields.  That means you can control which
> parameters are applied based on different conditions.  I could write an .itp
> file for any molecule that has force field parameters for any force field,
> and all I'd have to do is enclose all relevant directives within #ifdef
> blocks and it would work.  This note does *not* indicate that you can mix
> and match force fields.  Doing so is generally a very bad idea, if it even
> works syntactically.
>
>
>  so, i think even though the swissparam generated t

Re: [gmx-users] mktop/swissparam

[ram bio]

> Thanks, and I accept your suggestions;
>
> If SwissParam was designed to be used with CHARMM, the most intuitive next
> step is to use CHARMM for the MD, is it not?I understand the point about
> trying to keep the force fields consistent between docking and MD, but it
> may not be feasible (i.e., there may not be suitable parameters in OPLS for
> the bizarre functional groups you're dealing with).
>
> Yes, I also tried CHARMM FF to generate the topology file of the protein
> using pdb2gmx (without ligand), and as per the swissparam and gromacs
> tutorial i could build the protein-ligand-lipid bilayer and minimize it
> using mdrun and and i am at the NPT equilibration step, everything is ok
> with this procedure and without errors, but my lipid bilayer is made up of
> POPC and the POPC itp file has OPLS FF topologies. So, i was wondering
> whether the POPC itp file i am using for MD simulations can be used with the
> protein and ligand topology file generated by CHARMM.
>
> and as per the swissparam tutorial the command to generate topology file
> for protein is:
>
>  pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb 
> -nochargegrp
>
>
>
> in the gromacs 4.5.4 version the option to select Charmm FF from the
> pdb2gmx command is available, but i could not understand the usage of
> -nochargegp flag as per the tutorial, is this flag still valid while
> generating toplogies.
>
> Please let me  know your comments and suggestions regarding the procedure
> followed and the itp files usage for gromacs MD simulations.
>
> Thanks in advance,
>
> Pramod
>
>
>
> On Wed, Oct 12, 2011 at 3:10 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> ram bio wrote:
>>
>>> Dear Justin,
>>>
>>> As i generated the protein-ligand docked complex using opls FF, for the
>>> consistency, i am trying to use opls ff generated ligand parameters during
>>> md simulations in lipid bi layer. I found that MKTOP can generate topology
>>> files using opls ff for small molecules.
>>>
>>>
>> I understand that.  The program did a poor job, per the reasons I cited
>> before.  I do not know anything about mktop (other than what it does), so I
>> cannot analyze its suitability here, but due to missing parameters and bogus
>> charges, you should not use that topology for anything.
>>
>>
>>   I have also tried  swiss param to generate the ligand parameters to be
>>> used in protein ligand simulation using gromacs. The force field i am using
>>> for simulations is OPLS. My ligand contains an azido group and a tropane
>>> ring with protonated nitrogen. SwissParam force field has been designed to
>>> be compatible with the Charmm force field, but they are not tested on
>>> opls.Using the ligand topologies from  swissparam, i was able to run the MD
>>> simulations using gromacs with opls without errors (swissparam - gromacs
>>> tutorial), only issues being the charges on the ligand, so i generated
>>> various input files (mol2 files) for swissparam with charges generated
>>>  using ambcc1, gastergier and MMFF. But the itp files obtained from
>>> swissparam had same charges for the ligand atoms irrespective of the input
>>> provided i.e. charged or uncharged mol2 files, and
>>>
>>>
>> If SwissParam was designed to be used with CHARMM, the most intuitive next
>> step is to use CHARMM for the MD, is it not?  I understand the point about
>> trying to keep the force fields consistent between docking and MD, but it
>> may not be feasible (i.e., there may not be suitable parameters in OPLS for
>> the bizarre functional groups you're dealing with).
>>
>>  As per Gromacs website:
>>>
>>> "Note that an .itp file >> Documentation/File_Formats/.**itp_File>
>>> will be specific to a given force field, and will only function when
>>> included by a .top file >> Documentation/File_Formats/.**top_File>
>>> that has previously included the .itp files >> Documentation/File_Formats/.**itp_File>
>>> for that force field. Appropriate use of the |#define| and |#ifdef|
>>> mechanisms can permit the same .itp file >> Documentation/File_Formats/.**itp_File>
>>> to work with multiple force fields, e.g. |share/top/water.itp|."
>>>
>>>
>> Note the key caveat here - through the use of #define and #ifdef you can
>> make use of different force fields.  That means you can control which
>> parameters are applied based on different conditions.  I could write an .itp
>> file for any molecule that has force field parameters for any force field,
>> and all I'd have to do is enclose all relevant directives within #ifdef
>> blocks and it would work.  This note does *not* indicate that you can mix
>> and match force fields.  Doing so is ge

RE: [gmx-users] Implicit solvent problems

[Dallas Warren]

Did you look at atom 2073?

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 liaoxyi
Sent: Wednesday, 12 October 2011 3:59 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Implicit solvent problems

Hi, dear all,
I'm doing the simulation involved in protein and some surface.
I encounter this problem when trying to use implicit solvent model with 
GMX4.5.3.

First, minimize. When doing this I got the result as below:
Step=0, Dmax= 1.0e-02 nm, Epot= -1.91727e+06 Fmax= 6.19542e+06, atom= 2073
Step=1, Dmax= 1.0e-02 nm, Epot= -1.99260e+06 Fmax= 1.05712e+06, atom= 2073
Step=2, Dmax= 1.2e-02 nm, Epot= -2.09734e+06 Fmax= 1.79058e+05, atom= 2073
Step=4, Dmax= 7.2e-03 nm, Epot= -2.17474e+06 Fmax= 7.22113e+04, atom= 2073
Step=6, Dmax= 4.3e-03 nm, Epot= -2.17724e+06 Fmax= 4.33926e+04, atom= 2073
Step=8, Dmax= 2.6e-03 nm, Epot= -2.18069e+06 Fmax= 3.24778e+04, atom= 2073
Step=   10, Dmax= 1.6e-03 nm, Epot= -2.18404e+06 Fmax= 2.76114e+04, atom= 2073
Step=   13, Dmax= 4.7e-04 nm, Epot= -2.18500e+06 Fmax= 2.63803e+04, atom= 2073
Step=   17, Dmax= 7.0e-05 nm, Epot= -2.18514e+06 Fmax= 2.62045e+04, atom= 2073
Step=   19, Dmax= 4.2e-05 nm, Epot= -2.18522e+06 Fmax= 2.61000e+04, atom= 2073
Step=   22, Dmax= 1.3e-05 nm, Epot= -2.18524e+06 Fmax= 2.60689e+04, atom= 2073
Step=   23, Dmax= 1.5e-05 nm, Epot= -2.18527e+06 Fmax= 2.60315e+04, atom= 2073
Step=   27, Dmax= 2.3e-06 nm, Epot= -2.18527e+06 Fmax= 2.60258e+04, atom= 2073
Step=   29, Dmax= 1.4e-06 nm, Epot= -2.18488e+06 Fmax= 2.60222e+04, atom= 2073
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.
writing lowest energy coordinates.

Steepest Descents converged to machine precision in 30 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -2.1852700e+06
Maximum force =  2.6025840e+04 on atom 2073
Norm of force =  2.2667976e+03
---
>From above, the force is extremely large. And I don't know why.

the minim.mdp is as below:
; 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 = 1000.0  ; 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  = Cut-off ; for Implicit solvent long-range electrostatics
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)
; implicit_solvent
implicit_solvent = GBSA
gb_algorithm   = OBC
nstgbradii   = 1
rgbradii = 1.0
gb_epsilon_solvent   = 78.3
gb_obc_alpha = 1  ; OBC(II)
gb_obc_beta  = 0.8 ; OBC(II)
gb_obc_gamma = 4.85 ; OBC(II)
gb_dielectric_offset = 0.09
-
Is there any item that's not proper or needed to add?

Is the minimization necessary for implicit solvent?
Thank you again for your reading.

Kiara


-- 
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

Re: [gmx-users] Pressure very high with chloroform and gromacs-4.5.5

[Mark Abraham]

On 13/10/2011 12:35 AM, Nuno Azoia wrote:

I know that from the beginning. That's why I found very strange the
increasing on the system volume. My initial setup have a density of
~400g/L, and for liquid chloroform is ~1400g/L.
Using gromacs-4.5 I get densities of about 200 after 750ps simulation
time, and using 4.0 I get almost 500 after 1ns.


Your chloroform parameters are probably only valid for a condensed 
phase, and your initial density is nowhere near that. Please follow the 
approach here 
http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation.




And I was using such low densities because I build the box using
genconf with the options -nbox and -dist, starting with one molecule
of chloroform. If I used small distance values I get LINCS warnings in
the energy minimization step. Using genbox to solvate one empty box
with chloroform, I get very strange behaviors, with a very large
amount of molecule overlap.


Shrug. Without command lines and descriptions of what is in your input, 
we are helpless. Please follow the above advice.




But as you said before, I now think that this should be also a
paralelization problem, not to mention the numerical instability
caused by this very low density.
And I think this is a paralelization problem associated with this
numerical instability judging from the system behavior.
In 4.5, using the option -nt in mdrun, I get some small droplets of
liquid chloroform, and in 4.0, using mpi, I get one large droplet of
chloroform. It looks like if 4.5 is treating the system like
independent small systems, while 4.0 is able to divide the system into
small, but interdependent systems.


No, the implementation of parallelization might have an effect here if 
you were starting from a reasonable approximation of a condensed phase. 
These two observations are just two of the possible things that could 
happen to a liquid at extremely low density.


Mark



On Wed, Oct 12, 2011 at 12:26 PM, Mark Abraham  wrote:

On 12/10/2011 8:04 PM, Nuno Azoia wrote:

Thank you Mark for your answer!

I agree with you when you say that the high pressure is not itself a
problem. To avoid that problem I change my system from 1000 molecules
to 27000 molecules, and the pressure change from several thousands to
several hundreds bar.
What I found very strange was the increasing volume (and pressure). My
system is very unstable, I know, because the density is very low, and
not the opposite, so I was expecting to see the box getting smaller.
Looking to the trajectory I can see a box almost empty (with empty I
mean empty space, with chloroform molecules aggregating in small
droplets), and that's why I found the system behavior very strange.

Sounds like your initial density might be far too low. grompp reports it, so
do check.

Mark

I will follow your suggestion concerning nsttcouple and nstpcouple and
the other initial conditions.

Nuno Azoia


On Wed, Oct 12, 2011 at 6:24 AM, Mark Abraham
  wrote:

On 12/10/2011 2:22 AM, Nuno Azoia wrote:

Hello!

I found something very strange while making a CHCl3 box using
gromacs-4.5.5.
A look the mailing list, the manual and some release notes for
gromacs-4.5 and I couldn't found the answer for my problem. It's
possible that I'm doing something wrong, but I can not find what, so
I'm describe my problem.

I start a chloroform box from scratch, using genconf, and I get o
chloroform box with 1000 molecules. I get energy minimization without
problems.
Then I've run some equilibration steps in a NVT ensemble and in the
end I get pressure in the order of hundreds of bar.

The high pressure is not itself a problem - small numbers of molecules
and
short simulation times lead to doubtful statistics for pressure.


  Then I change to
NPT conditions and both the pressure and the volume keep increasing
with time.

Be sure to visualize your trajectory to confirm its behaviour matches
what
you expect from the trends in P and V.


To discard the possibility of a size problem, I repeat everything with
a box of 27000 molecules, with a volume of ~13800 nm^3. The problem
was the same. Very high pressures (150-200 bar) and very low densities
(<  200 g/L) after 750 ps simulation time. And both volume and
pressure
increasing with time.


I'm doing now the same procedure, but using gromacs-4.0.7 and I'm
getting very different (and better) results. After energy minimization
I run 5 steps in a nvt ensemble and I got pressure around -30 bar
(Ok for me). After that I start to run the simulations in npt ensemble
and the pressure start to increase slowly, with negative values
because the system have very low densities (~400 g/L), and the volume
is decreasing. So I'm getting the normal reaction from the system.



Where is the problem? There are some different parameters to set in
the mdp file and I didn't realize that, or is this a problem in
gromacs-4.5?

It seems you are generating some numerical instability with your choice
of
initial and simulation conditions, and that 

Re: [gmx-users] Uniform Distribution of drug molecules inside water spc216

[Mark Abraham]

On 13/10/2011 2:13 AM, meisam valizadeh kiamahalleh wrote:

Dear GMX users
Good day to you
I have some drug molecules (cisplatin) added manually and 
randomly inside a system which is going to be solvated in spc216 
water.  I used genbox command to add the correct number of water 
molecules needed to solvate the box. The drug molecules are located 
very closed to each other. Kindly, would you please let me know how I 
can distribute drug molecules uniformly among the water molecoules to 
obtain a certain concentration of the drug? May I know if there is any 
specific tool or script which can help me to do it?




Decide how many drug molecules you want in a box of a given size, and 
place one in a much smaller box. Then use genconf to replicate that 
small box up to the proper size. Use the genconf option to randomize the 
orientation, solvate with genbox, then equilibrate for a long time.


Mark
--
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

Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff

[César Ávila]

Done

2011/10/10 Mark Abraham 

>  On 11/10/2011 4:51 AM, César Ávila wrote:
>
> v4.5.4
> As I commented above, I had to manually add an entrance for the cmap terms
> in the topology file as pdb2gmx would not generate them for the alanine
> dipeptide. There seems to be no problem for larger peptides.
> Cheers
> Cesar
>
>
> That sounds like a bug. Please describe your symptoms in a new issue here -
> http://redmine.gromacs.org
>
> Mark
>
>
>  2011/10/10 Jianguo Li 
>
>>  which gromacs version are you using? cMAP is implemented in v4.5  or
>> later
>>  Jianguo
>>
>>   --
>> *From:* César Ávila 
>> *To:* Discussion list for GROMACS users 
>> *Sent:* Sunday, 9 October 2011 12:07 AM
>> *Subject:* [gmx-users] CMAP for alanine dipeptide in Charmm27 ff
>>
>> I would like to run REMD simulations on the alanine dipeptide using the
>> Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do not
>> see any entrance referring to the cmap term in the topology file. Does this
>> mean that Cmap won't be calculated?
>>
>>
>>  --
>> 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
>>
>>
>> --
>> 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
>>
>
>
>
>
>
> --
> 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
>
-- 
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

Re: [gmx-users] mktop

[Justin A. Lemkul]

ram bio wrote:

Dear Justin,

Thanks, and I accept your suggestions;

If SwissParam was designed to be used with CHARMM, the most intuitive 
next step is to use CHARMM for the MD, is it not?I understand the point 
about trying to keep the force fields consistent between docking and MD, 
but it may not be feasible (i.e., there may not be suitable parameters 
in OPLS for the bizarre functional groups you're dealing with).


Yes, I also tried CHARMM FF to generate the topology file of the protein 
using pdb2gmx (without ligand), and as per the swissparam and gromacs 
tutorial i could build the protein-ligand-lipid bilayer and minimize it 
using mdrun and and i am at the NPT equilibration step, everything is ok 
with this procedure and without errors, but my lipid bilayer is made up 
of POPC and the POPC itp file has OPLS FF topologies. So, i was 
wondering whether the POPC itp file i am using for MD simulations can be 
used with the protein and ligand topology file generated by CHARMM.




You shouldn't mix and match force fields.  Suitable CHARMM lipid parameters are 
widely available.


and as per the swissparam tutorial the command to generate topology file 
for protein is:


 pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp



in the gromacs 4.5.4 version the option to select Charmm FF from the 
pdb2gmx command is available, but i could not understand the usage of 
-nochargegp flag as per the tutorial, is this flag still valid while 
generating toplogies.




CHARMM does not use charge groups.  Therefore, each atom should be its own 
"group" in the topology.  Using -nochargegrp overrides the default behavior of 
the .rtp files (which has multi-atom charge groups, although I think this was 
changed somewhere along the way, but I don't remember if it was before or after 
4.5.4).


-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


--
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

Re: [gmx-users] Gromacs: Cloud Vs. Boinc Server?

[Szilárd Páll]

> G92/G94:
> GeForce 9800 GX2/GTX/GTX+/GT
> GeForce 9800M GT
> GeForce GTS 150, 250
> GeForce GTX 280M, 285M
> Quadro FX 4700
> Quadro Plex 2100 D4
> GT200:
> GeForce GTX 260, 270, 280, 285, 295
> Tesla C1060, S1070, M1060
> Quadro FX 4800, 5800
> Quadro CX
> Quadro Plex 2200 D2, 2200 S4
> GF1xx (Fermi)
> GeForce GTX 460, 465, 470, 480, 570, 580
> Tesla C2050, C2070, M2050, M2070

Ummm, that compatibility table is a little outdated. I've just added a
few more cards (GTX 5xx, some 4xx, and Tesla 2090s, 2075s).

>  I got an EVGA Geforce GTX 580, which is about $450 for trying out GPU
> based MD, and has 512 GPU cores and a high clock rate, 1.5 gigs of
> memory.  Having more cores and more memory are both important things
> for the GPU side of molecular dynamics (cores = more parallel, memory
> = more atoms and less memory transferring).  I think you have some
> limitations with the GPU sims, like atoms < 100,000.  It is amazing
> that with implicit solvent you can really see a huge benefit and
> perhaps that might open some new doors.

Right, the GTX 580 is as fast as it gets. However, from a
price/performance point of view the 570 way better and depending on
the use case even a 560 can be a decent and cheap option.

--
Szilárd



> On Wed, Oct 12, 2011 at 9:54 AM, Szilárd Páll  wrote:
>> Dear Stephan,
>>
>>> Radeons work as well.  You can put a 3-4 GPU board together with the 
>>> highest end AMD or Intel chip for 3K, plus 16G RAM if you look around for a 
>>> day or two, but the cooling is the main problem (with 1/4 the price radeons 
>>> Vs. GTI cards), so one has to take cooling into account (h20 cost another 
>>> 800$, or investing in 4-6 good fans/cooling an additional 2-300$).  If you 
>>> have a slightly higher budget you can get multi CPU boards with 4 GPU 
>>> slots, ie 4 or 8 CPU's (direct via mail from Taiwan), but the CPU's and 
>>> GPU's is where the money is spent.
>>
>> No, Radeons don't work and won't work in the near future - Gromacs
>> doesn't support OpenCL. Cooling needs attention, but in reality it's
>> nowhere near $2-300 extra - unless you want the fans with funky leds.
>>
>> Btw, what software is the above hardware description targeting? To me
>> it sounds more like a gaming rig and not something specifically aiming
>> at maximum performance with Gromacs 4.5 (nor 4.6 which is yet to be
>> released).
>>
>>> As far as I have seen GPU Gromacs runs at around 1 Teraflop per Radeon 5900 
>>> series (double percission, single is supposed to run around 4 tera flops 
>>> per GPU, so depends on your needs, desires as far as simulations), and the 
>>> latest Intel 970's are around 400-500 Gflops/chip.
>>
>> Again, I might be missing something, but how exactly does Gromacs run
>> on Radeons? I assume when referring to the i7 970 (?) above you meant
>> 40-50 GFlops/chip - the i7 970 should have 70 GFlops peak. Also note
>> that Flops are not every useful, what matters is time to solution for
>> the specific problem one wants to solve.
>>
>> Cheers,
>> --
>> Szilárd
>>
>>> --
>>> NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie!
>>> Jetzt informieren: http://www.gmx.net/de/go/freephone
>>> --
>>> 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
>>>
>> --
>> 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
>>
> --
> 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
>
--
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

Re: [gmx-users] mktop

[ram bio]

Dear Justin,


Thanks.

The POPC bilayer i am using is with berger lipids, corrected for dihedrals
so as to be compatible with the OPLS FF for aminoacids.

While searching for the literature on compatibility of lipid FF and protein
FF, I found few references where similar modification was done for DOPC
lipid bilayer  and were suitable with various FF for proteins and also with
CHARMM FF:

1. Membrane protein simulations with a united-atom lipid and all-atom
protein model: lipid–protein interactions, side chain transfer free energies
and model proteins.J. Phys.: Condens. Matter 18 (2006) S1221–S1234

2. Combination of the CHARMM27 Force Field with United-Atom Lipid Force
Fields.J Comput Chem 32: 1400–1410, 2011.

I don't have the lipid bilayer with their  itp files with CHARMM FF
parameterization. Please could you inform me where to obtain them, so that i
can use the lipid bilayer structure for embedding the protein and use the
related CHARMM FF parameterised itp in the topology file in gromacs for MD
simulation.

Thanks in advance,

Pramod


On Wed, Oct 12, 2011 at 7:51 PM, Justin A. Lemkul  wrote:

>
>
> ram bio wrote:
>
>> Dear Justin,
>>
>> Thanks, and I accept your suggestions;
>>
>> If SwissParam was designed to be used with CHARMM, the most intuitive next
>> step is to use CHARMM for the MD, is it not?I understand the point about
>> trying to keep the force fields consistent between docking and MD, but it
>> may not be feasible (i.e., there may not be suitable parameters in OPLS for
>> the bizarre functional groups you're dealing with).
>>
>> Yes, I also tried CHARMM FF to generate the topology file of the protein
>> using pdb2gmx (without ligand), and as per the swissparam and gromacs
>> tutorial i could build the protein-ligand-lipid bilayer and minimize it
>> using mdrun and and i am at the NPT equilibration step, everything is ok
>> with this procedure and without errors, but my lipid bilayer is made up of
>> POPC and the POPC itp file has OPLS FF topologies. So, i was wondering
>> whether the POPC itp file i am using for MD simulations can be used with the
>> protein and ligand topology file generated by CHARMM.
>>
>>
> You shouldn't mix and match force fields.  Suitable CHARMM lipid parameters
> are widely available.
>
>
>  and as per the swissparam tutorial the command to generate topology file
>> for protein is:
>>
>>  pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb
>> -nochargegrp
>>
>>
>>
>> in the gromacs 4.5.4 version the option to select Charmm FF from the
>> pdb2gmx command is available, but i could not understand the usage of
>> -nochargegp flag as per the tutorial, is this flag still valid while
>> generating toplogies.
>>
>>
> CHARMM does not use charge groups.  Therefore, each atom should be its own
> "group" in the topology.  Using -nochargegrp overrides the default behavior
> of the .rtp files (which has multi-atom charge groups, although I think this
> was changed somewhere along the way, but I don't remember if it was before
> or after 4.5.4).
>
> -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
>
> ==**==
> --
> 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/Searchbefore
>  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
>
-- 
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

Re: [gmx-users] mktop

[Justin A. Lemkul]

ram bio wrote:

Dear Justin,
 


Thanks.

The POPC bilayer i am using is with berger lipids, corrected for 
dihedrals so as to be compatible with the OPLS FF for aminoacids.




I think significantly more parameters than just dihedrals need to be altered to 
make the Berger united-atom force field compatible with OPLS.


While searching for the literature on compatibility of lipid FF and 
protein FF, I found few references where similar modification was done 
for DOPC lipid bilayer  and were suitable with various FF for proteins 
and also with CHARMM FF:


1. Membrane protein simulations with a united-atom lipid and all-atom 
protein model: lipid–protein interactions, side chain transfer free 
energies and model proteins.J. Phys.: Condens. Matter 18 (2006) S1221–S1234


2. Combination of the CHARMM27 Force Field with United-Atom Lipid Force 
Fields.J Comput Chem 32: 1400–1410, 2011.


I don't have the lipid bilayer with their  itp files with CHARMM FF 
parameterization. Please could you inform me where to obtain them, so 
that i can use the lipid bilayer structure for embedding the protein and 
use the related CHARMM FF parameterised itp in the topology file in 
gromacs for MD simulation.




The lipids are built into the CHARMM27 implementation in Gromacs.  You can 
generate their topology with pdb2gmx.  Run pdb2gmx on a single lipid, convert it 
to an .itp file, and #include it in the topology.  The CHARMM36 force field is 
also available in the User Contributions section of the Gromacs website.


-Justin


Thanks in advance,

Pramod


On Wed, Oct 12, 2011 at 7:51 PM, Justin A. Lemkul > wrote:




ram bio wrote:

Dear Justin,

Thanks, and I accept your suggestions;

If SwissParam was designed to be used with CHARMM, the most
intuitive next step is to use CHARMM for the MD, is it not?I
understand the point about trying to keep the force fields
consistent between docking and MD, but it may not be feasible
(i.e., there may not be suitable parameters in OPLS for the
bizarre functional groups you're dealing with).

Yes, I also tried CHARMM FF to generate the topology file of the
protein using pdb2gmx (without ligand), and as per the
swissparam and gromacs tutorial i could build the
protein-ligand-lipid bilayer and minimize it using mdrun and and
i am at the NPT equilibration step, everything is ok with this
procedure and without errors, but my lipid bilayer is made up of
POPC and the POPC itp file has OPLS FF topologies. So, i was
wondering whether the POPC itp file i am using for MD
simulations can be used with the protein and ligand topology
file generated by CHARMM.


You shouldn't mix and match force fields.  Suitable CHARMM lipid
parameters are widely available.


and as per the swissparam tutorial the command to generate
topology file for protein is:

 pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o
conf.pdb -nochargegrp



in the gromacs 4.5.4 version the option to select Charmm FF from
the pdb2gmx command is available, but i could not understand the
usage of -nochargegp flag as per the tutorial, is this flag
still valid while generating toplogies.


CHARMM does not use charge groups.  Therefore, each atom should be
its own "group" in the topology.  Using -nochargegrp overrides the
default behavior of the .rtp files (which has multi-atom charge
groups, although I think this was changed somewhere along the way,
but I don't remember if it was before or after 4.5.4).

-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


==__==
-- 
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





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virg

Re: [gmx-users] using gromacs with an specific GCC

[Szilárd Páll]

Hi Nathalia,

Right, gcc 4.1 is quite controversial as these is bug in it which is
though to be causing mdrun crashes. So you better stay away from 4.1
as well as from other old gcc versions. I'd recommend 4.5 or 4.6 as
these have gotten really good, even compared to icc - at least when it
comes to Gromacs performance. I'd especially recommend 4.6 if you're
using Nehalem CPUs (with the -mtune/-march=corei7 flag).

Compiling gcc is rather straightforward and there are plenty of guide online.

When it comes to running binaries, depending on where you install the
new gcc you might have to set the LD_LIBRARY_PATH to contain the
custom gcc installation's lib directory before the standard lib path.
This is of course unless you link statically against standard
libraries.

Cheers,
--
Szilárd



On Mon, Oct 10, 2011 at 6:51 PM, Nathalia Garces  wrote:
> Good morning,
>
> I'm trying to use Scientific Linux 5.5 to run Gromacs 4.5.4. The problem is
> that the default version of gcc in this distribution is 4.1, which is broken
> for Gromacs!!
> I can install a newer version of gcc in compatible mode with gcc 4.1, but
> the last one will still be the default.
> Now, my problem is that I don't know how to specify to Gromacs to use the
> newer version. I've seen that you can specify which gcc to use while you
> configure the program, but I found no information of how to specify which
> compiler to use while running a MD simulation??.. I mean when using mdrun
> command or even while using every command in Gromacs.
>
> Thank you for four answer
>
> Nathalia
> --
> 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
>
--
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

[gmx-users] Error while running methane in water simulation

[vivek sharma]

Hi there,
I am trying to run the free energy tutorial by David mobley mentioned at *h
ttp://
www.dillgroup.ucsf.edu/group/wiki/index.php?title=Free_Energy:_Tutorial*
While running a test run for lambda value of 0, I found that there is some
problem with the generated trajectory, I observed the distorted (straight
lines running between box edges) methane structure in the water box while
viewing the co-ordinate movie.
Thinking that, this scenario relates to the periodic boundary conditions. I
checked the parameter file where *pbc = xyz.

*Please suggest what may be the reason for the distortion in methane during
simulation.*
*
Thanks and regards,
*Vivek Sharma*
-- 
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

[gmx-users] Unable to download gromacs-4.5.5.tar.gz

[Rasale, Anupama]

All,
When I try to download Gromacs-XXX from 
ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz, I am getting following 
error:
ISA Server: extended error message :
200 Switching to Binary mode.
200 PORT command successful. Consider using PASV.
425 Failed to establish connection.

Can you please restore the server connection?

Thanks
Anupama


-- 
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