[gmx-users] question in pulling in gromacs 4.0

[anirban polley]

Hi ,
  I want to pull a molecule from the membrane. My complete mdp file is
the following
;.
;   File 'mdout.mdp' was generated
;   By user: psn (17109)
;   On host: p690k
;   At date: Fri Jul 23 12:43:31 2004
;

; VARIOUS PREPROCESSING OPTIONS =
title= lipid bilayer in water
cpp  = /lib/cpp
include  =
define   =

; RUN CONTROL PARAMETERS =
integrator   = md
; start time and timestep in ps =
tinit= 500
dt   = 0.002
nsteps   = 175
; mode for center of mass motion removal =
comm-mode= Linear
; number of steps for center of mass motion removal =
nstcomm  = 1
; group(s) for center of mass motion removal =
comm-grps=

; LANGEVIN DYNAMICS OPTIONS =
; Temperature, friction coefficient (amu/ps) and random seed =
;bd-temp  = 300
;I have commute the above line as it has no exitance
bd-fric  = 0
ld-seed  = 1993

; ENERGY MINIMIZATION OPTIONS =
; Force tolerance and initial step-size =
emtol= 100
emstep   = 0.01
; Max number of iterations in relax_shells =
niter= 20
; Step size (1/ps^2) for minimization of flexible constraints =
fcstep   = 0
; Frequency of steepest descents steps when doing CG =
nstcgsteep   = 1000

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 5000
nstvout  = 5000
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 250
nstenergy= 250
; Output frequency and precision for xtc file =
nstxtcout= 0
xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps   =

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist  = 10
; ns algorithm (simple or grid) =
ns_type  = grid
; Periodic boundary conditions: xyz or no =
pbc  = xyz
; nblist cut-off =
rlist= 1.0
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype  = PME  ;Reaction-Field
rcoulomb-switch  = 0
rcoulomb = 1.0  ;2.0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r= 80.0
epsilon_rf   = 1
;I have done some thing new according to mannual and warnings and error
; Method for doing Van der Waals =
vdwtype  = Cut-off
; cut-off lengths=
rvdw-switch  = 0
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters =
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = yes

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
Tcoupl   = berendsen
; Groups to couple separately =
tc-grps  = DPP  SOL Na PIP
; Time constant (ps) and reference temperature (K) =
tau_t= 0.1   0.1   0.1   0.1
ref_t= 310   310   310   310
; Pressure coupling  =
Pcoupl   = berendsen
Pcoupltype   = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 1.01.0
compressibility  = 4.5e-5 4.5e-5
ref_p= 1.01.0

; SIMULATED ANNEALING CONTROL =
annealing= no
; Time at which temperature should be zero (ps) =
;zero-temp_time   = 0
;I have commute the above line as it has no exitance

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel  = yes
gen_temp = 310.0
gen_seed = 173529

; OPTIONS FOR BONDS =
constraints  = all-bonds
; Type of constraint algorithm =
constraint_algorithm = lincs
; Do not constrain the start configuration =
unconstrained-start  = no
; Use successive overrelaxation to reduce the number of shake iterations =
Shake-SOR= no
; Relative tolerance of shake =
shake-tol 

RE: [gmx-users] How to add another electrostatic summation method in Gromacs

[Berk Hess]

> Date: Fri, 27 Mar 2009 09:56:02 +1100
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] How to add another electrostatic summation method
> in  Gromacs
> 
> Shuangxing Dai wrote:
> > Thank you for your help. I attached the page of the form of potential. 
> > The equation (5.13) gives all the potential energy of neighbours of one 
> > ion in a truncation sphere.  Rc is cut-off. Since this potential depends 
> > on all the neighbours in a cut-off distance, I cannot give the pair 
> > interaction because in this method, only the total potential energy of 
> > one ion maks sense. In Ewald summation, both the real space and 
> > reciprocal space summation can be written as the summation of pair 
> > potential. But in wolf, I cannot do that.
> 
> It looks separable into a double sum over atom pairs from within a 
> cutoff, since the value of that limit is constant.
> 
> > Since I cannot use Ewald without peoriodical boundary conditions while 
> > this Wolf method can, so I cannot simply use Gromacs to do my 
> > simulation. The question is which files needed to be modified if I want 
> > to add a new one? Is there any direct way? Or I should read all the 
> > whole code?
> 
> You can start by reading the kernel code generated by mknb during the 
> make process and found in src/gmxlib/nonbonded/nb_kernel. If you play 
> with the flags to mknb you can get comments embedded in the C files. 
> Find the one that does Ewald without table lookups and consider how 
> you'd need to change it to suit your needs.
> 
> Mark

Note that in 4.0 there are now also plain c loops:
src/gmxlib/nonbonded/nb_generic.c
which are easy to modify.
You will need to set the env var GMX_NB_GENERIC to use them.

Berk


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[gmx-users] how to deal with the hydrogen bonding interactions between bases

[He, Yang]

Hi all users,

I need to define the hydrogen bonding interactions between bases in the CG DNA 
model . Can anyone of you tell me how to do that in the gromacs force files?

Thank you very much in advance.

Yang
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Re:Re: [gmx-users] How to calculate PMF after AFM pulling

[huifang liu]

Hi Justin,

Thank you for your reply, but i am still a little confused. You said in
principal I should be able to extract a potential of mean force from an
AFM run by simply integrating the average force along the reaction
coordinate and if I have the average force as a function of position, I
could simply integrate that to get the PMF. However, actually, i don't know
how i can get the average force as a function of position and apply them in
the PMF calculation. Could you give me some suggestion?

Thanks a lot.

Huifang
-- 
Huifang Liu (Ph.D. Student)
School of Pharmacy
Fudan University

138 Yi Xue Yuan Rd.  Tel: (86-21)54237419 (O)
Shanghai, China, 200032 Cell phone: +86-13764669357
E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264
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Re: [gmx-users] How to add another electrostatic summation method in Gromacs

[Mark Abraham]

Shuangxing Dai wrote:
Thank you for your help. I attached the page of the form of potential. 
The equation (5.13) gives all the potential energy of neighbours of one 
ion in a truncation sphere.  Rc is cut-off. Since this potential depends 
on all the neighbours in a cut-off distance, I cannot give the pair 
interaction because in this method, only the total potential energy of 
one ion maks sense. In Ewald summation, both the real space and 
reciprocal space summation can be written as the summation of pair 
potential. But in wolf, I cannot do that.


It looks separable into a double sum over atom pairs from within a 
cutoff, since the value of that limit is constant.


Since I cannot use Ewald without peoriodical boundary conditions while 
this Wolf method can, so I cannot simply use Gromacs to do my 
simulation. The question is which files needed to be modified if I want 
to add a new one? Is there any direct way? Or I should read all the 
whole code?


You can start by reading the kernel code generated by mknb during the 
make process and found in src/gmxlib/nonbonded/nb_kernel. If you play 
with the flags to mknb you can get comments embedded in the C files. 
Find the one that does Ewald without table lookups and consider how 
you'd need to change it to suit your needs.


Mark
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Re: [gmx-users] Integrating with BOINC: failing at minimization

[Mark Abraham]

Jack Shultz wrote:

Hello,

I've tried a couple ways of running the workshop tutorial with a
different protein and amber03 force field. It works with a clean
install of gromacs, but I am trying to integrate it into a grid
computing project.
 https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf

I tried several approaches to running this app but encountered a
strange problem in both approaches to integrating. It always has
trouble minimizing. This indicates to me, there is something strange
with the environment that I created. If you have any hints for me that
would be great. The two approaches I tried were:
1) putting all the dependent files in the same directory as the binary
and executing it, this failed when I tested it stand alone and it
created this same error
2) I tried writing a bash script to mimics the GMXRC.bash except it
maps every directory relative to a temporary directory where
everything runs. (e.g. GMXBIN=../slot/0/bin/)
It seems to run fine through a workunit but then it does not minimize
properly causing additional problems downstream


Steepest Descents converged to machine precision in 54 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -8.35030867755191e+214
Maximum force = 7.83437759695905e+221 on atom 25439
Norm of force = 5.13628303396235e+219

http://www.hydrogenathome.org/result.php?resultid=1341858



grompp is giving a bunch of warnings about long bonds. If you really are 
doing the same calculation you did with a "clean install of GROMACS" 
then they were also given there. You should attend to them, since your 
output is consistent with http://wiki.gromacs.org/index.php/blowing_up. 
You need to fix that before you can isolate whether you have other problems.


Mark
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Re: [gmx-users] about parallel run

[Justin A. Lemkul]

Mahnam wrote:



 
In God We Trust

Hello GMX users
I am trying to run one gromacs simulation in parallel. I have  
successfully compiled gromacs 4  with mpi support  on a cluster with 
x86_64 architecture with 4 cpus (intel core 2 Quad 6600).
when I run mdrun with single-processor  ,it works  fine and everything 
is ok, but when I run the same simulation  with 4 cpu,
it finishs again normally and I don't  get any error messages , but my 
protein breaks and box of sol becomes deformed.


Which (specific) version are you using?  Prior to 4.0.2 (I think), the final 
output was fragmented as a consequence of domain decomposition.  It can be 
"fixed" (i.e., molecules can be made whole again) with trjconv.


"Deformed" is a matter of perspective, and is typically an artifact of 
visualization.  You will have to describe your system in much greater detail to 
get any useful advice.



These are first few lines of my output (on screen)


These lines just indicate the run is being split between nodes; they are not 
indicative of a problem.


-Justin


NNODES=4, MYRANK=3, HOSTNAME=localhost.localdomain
NODEID=3 argc=16
NNODES=4, MYRANK=0, HOSTNAME=localhost.localdomain
NNODES=4, MYRANK=2, HOSTNAME=localhost.localdomain
NNODES=4, MYRANK=3, HOSTNAME=localhost.localdomain
NODEID=2 argc=15
NNODES=4, MYRANK=1, HOSTNAME=localhost.localdomain
NODEID=1 argc=15
NODEID=3 argc=15
NODEID=0 argc=15
 
here is my commands and mdp file  :

commands:
grompp -f sp.mdp -c fprmd.gro -r fprmd.gro -p n.top -o  sp.tpr  -n n.ndx 
-maxwarn  1000
mpirun -np 4 mdrun -s sp.tpr -o sp.trr -c fsp.gro -g sp.log -e sp.edr -n 
n.ndx -N 4
 
mdf file:
 
title   =  n.pdb

restraining
warnings=  10
cpp =  /lib/cpp
define  =  -DFLEXIBLE
constraints =  none
integrator  =  steep
nsteps  =  1
nstcomm =  1
comm_mode   =  Linear
comm_grps   =  protein
nstxout =  250
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  1.2
coulombtype =  PME
rcoulomb=  1.2
rvdw=  1.4
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  4
ewald_rtol  =  1e-5
optimize_fft=  yes
emtol   = 10.0
emstep  = 0.01

whould you please help me to overcome this problem. 
Many thanks in advance for your help and your reply.


Yours truly
Karim Mahnam
Institute of  Biochemistry  and  Biophysics (IBB)
Tehran University
P.O.box 13145-1384
Tehran
Iran
http://www.ibb.ut.ac.ir/




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--


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


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[gmx-users] Integrating with BOINC: failing at minimization

[Jack Shultz]

Hello,

I've tried a couple ways of running the workshop tutorial with a
different protein and amber03 force field. It works with a clean
install of gromacs, but I am trying to integrate it into a grid
computing project.
 https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf

I tried several approaches to running this app but encountered a
strange problem in both approaches to integrating. It always has
trouble minimizing. This indicates to me, there is something strange
with the environment that I created. If you have any hints for me that
would be great. The two approaches I tried were:
1) putting all the dependent files in the same directory as the binary
and executing it, this failed when I tested it stand alone and it
created this same error
2) I tried writing a bash script to mimics the GMXRC.bash except it
maps every directory relative to a temporary directory where
everything runs. (e.g. GMXBIN=../slot/0/bin/)
It seems to run fine through a workunit but then it does not minimize
properly causing additional problems downstream


Steepest Descents converged to machine precision in 54 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -8.35030867755191e+214
Maximum force = 7.83437759695905e+221 on atom 25439
Norm of force = 5.13628303396235e+219

http://www.hydrogenathome.org/result.php?resultid=1341858

-- 
Jack

http://www.facebook.com/home.php#/profile.php?id=832713248
http://hydrogenathome.org
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Re: [gmx-users] How to add another electrostatic summation method in Gromacs

[Shuangxing Dai]

Thank you for your help. I attached the page of the form of potential. The
equation (5.13) gives all the potential energy of neighbours of one ion in a
truncation sphere.  Rc is cut-off. Since this potential depends on all the
neighbours in a cut-off distance, I cannot give the pair interaction because
in this method, only the total potential energy of one ion maks sense. In
Ewald summation, both the real space and reciprocal space summation can be
written as the summation of pair potential. But in wolf, I cannot do that.
Since I cannot use Ewald without peoriodical boundary conditions while this
Wolf method can, so I cannot simply use Gromacs to do my simulation. The
question is which files needed to be modified if I want to add a new one? Is
there any direct way? Or I should read all the whole code?
Thank you very much.
Shuangxing Dai

On Mon, Mar 23, 2009 at 11:55 PM, Mark Abraham wrote:

> Shuangxing Dai wrote:
>
>> Hi, all,
>>I was wondering how to add another electrostatic summation method--Wolf
>> summation into Gromacs. Wolf summation is a treatment for summation of
>> Coulombic energy. Since the formula of total potential energy for each ion
>> is known, how to add this into Gromacs? According to Chapter 7, I should
>> give the f(x) and f'(x). The formula of f and f' depends on the neighbours
>> and varies from ion to ion, and I can not give f and f' without calculation.
>>
>
> If you have a functional form that depends only on pairwise distance and
> two atom types, then you can use the GROMACS table lookup machinery.
>
> Since Wolf method uses the same error function as Ewald summation, it might
>> be easier and possible to implement Wolf into Gromacs. If so, which files
>> need to be modified?
>> Hope I put my question clearly. Thank you in advance for suggestions and
>> help.
>>
>
> Evaluating erfc is not the core issue - but GROMACS does the evaluation of
> terms for the direct-space Ewald contribution via table-lookup. The big deal
> is whether you need a custom non-bonded kernel, and then whether you can
> make it run fast. You might need to post a link to some details of this
> summation method to get useful help.
>
> Mark
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-- 
Shuangxing Dai


Eqation.pdf
Description: Adobe PDF document
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[gmx-users] about parallel run

[Mahnam]

 
In God We Trust
Hello GMX users
I am trying to run one gromacs simulation in parallel. I have  successfully 
compiled gromacs 4  with mpi support  on a cluster with x86_64 architecture 
with 4 cpus (intel core 2 Quad 6600).
when I run mdrun with single-processor  ,it works  fine and everything is 
ok, but when I run the same simulation  with 4 cpu, 
it finishs again normally and I don't  get any error messages , but my 
protein breaks and box of sol becomes deformed.
These are first few lines of my output (on screen)
NNODES=4, MYRANK=3, HOSTNAME=localhost.localdomain
NODEID=3 argc=16
NNODES=4, MYRANK=0, HOSTNAME=localhost.localdomain
NNODES=4, MYRANK=2, HOSTNAME=localhost.localdomain
NNODES=4, MYRANK=3, HOSTNAME=localhost.localdomain
NODEID=2 argc=15
NNODES=4, MYRANK=1, HOSTNAME=localhost.localdomain
NODEID=1 argc=15
NODEID=3 argc=15
NODEID=0 argc=15
 
here is my commands and mdp file  :
commands:
grompp -f sp.mdp -c fprmd.gro -r fprmd.gro -p n.top -o  sp.tpr  -n n.ndx 
-maxwarn  1000
mpirun -np 4 mdrun -s sp.tpr -o sp.trr -c fsp.gro -g sp.log -e sp.edr -n 
n.ndx -N 4
 
mdf file:
 
title   =  n.pdb 
restraining
warnings=  10
cpp =  /lib/cpp
define  =  -DFLEXIBLE
constraints =  none
integrator  =  steep 
nsteps  =  1
nstcomm =  1
comm_mode   =  Linear
comm_grps   =  protein 
nstxout =  250
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  1.2
coulombtype =  PME
rcoulomb=  1.2
rvdw=  1.4
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  4
ewald_rtol  =  1e-5
optimize_fft=  yes
emtol   = 10.0
emstep  = 0.01

whould you please help me to overcome this problem. 
Many thanks in advance for your help and your reply.

Yours truly 
Karim Mahnam
Institute of  Biochemistry  and  Biophysics (IBB)
Tehran University 
P.O.box 13145-1384
Tehran 
Iran 
http://www.ibb.ut.ac.ir/
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Re: [gmx-users] How to calculate PMF after AFM pulling

[Justin A. Lemkul]

huifang liu wrote:


Hello, Justin
 
As the mannul said,  it is intended to analyze .pdo files generated by 
mdrun using
umbrella sampling tocreate a potential of mean force (PMF). But i were 
using AFM method not umbrella sampling. How can i do that? Thanks.
 


http://www.gromacs.org/pipermail/gmx-users/2003-May/005606.html

-Justin


Huifang
--
Huifang Liu (Ph.D. Student)
School of Pharmacy
Fudan University

138 Yi Xue Yuan Rd.  Tel: (86-21)54237419 (O)
Shanghai, China, 200032 Cell phone: +86-13764669357
E-mail: huifangliu1...@gmail.com  Fax: 
(86-21)54237264


--


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


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Re: [gmx-users] How to calculate PMF after AFM pulling

[huifang liu]

Hello, Justin

As the mannul said,  it is intended to analyze .pdo files generated by mdrun
using
umbrella sampling tocreate a potential of mean force (PMF). But i were using
AFM method not umbrella sampling. How can i do that? Thanks.

Huifang

-- 
Huifang Liu (Ph.D. Student)
School of Pharmacy
Fudan University

138 Yi Xue Yuan Rd.  Tel: (86-21)54237419 (O)
Shanghai, China, 200032 Cell phone: +86-13764669357
E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264
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Re: [gmx-users] How to calculate PMF after AFM pulling

[Justin A. Lemkul]

huifang liu wrote:

Hello everybody,
 
I have recently run a SMD with AFM method, and i got the .pdo file. But 
i don't know how to use the .pdo file to calculate the PMF profile. 
Could someone give me some suggestion? Thanks a lot.
 


g_wham -h

-Justin


Huifang

--
Huifang Liu (Ph.D. Student)
School of Pharmacy
Fudan University

138 Yi Xue Yuan Rd.  Tel: (86-21)54237419 (O)
Shanghai, China, 200032 Cell phone: +86-13764669357
E-mail: huifangliu1...@gmail.com  Fax: 
(86-21)54237264





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--


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


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Re: [gmx-users] Re: g_covar

[Tsjerk Wassenaar]

Hi,

The covariances are defined as the second central moment, i.e. the
mean square displacement about the mean. Thus to make the PCA
interpretable straightforwardly, you'll need to calculate the
fluctuations with respect to the average structure.

This stands apart from fitting. The fit is performed to define the
conformational space, by removing translational and rotational degrees
of freedom. There you'll have freedom to choose the reference and the
fitting group, which will both have an influence on the results.
Especially when using different groups for fitting and for performing
the analysis, you'll have to make sure you know what you're doing, as
this can have an enormous impact on the results. The influence of the
reference used for fitting, assuming the same group is used for both
the fit and the analysis, shouldn't be too big.

Hope it helps,

Tsjerk

On Thu, Mar 26, 2009 at 9:33 AM, Ran Friedman  wrote:
> Dear Dagoberto,
>
> Choosing the right protein structure (and also which part of the protein
> to align) depends a lot of your system. I wouldn't use an average
> structure for a system that's changing a lot, because it may not be
> representative. It's hard to provide a more elaborate answer without
> many details about your system and what you're trying to simulate. It
> can be helpful to read both on the methods of covariance analysis and on
> some implementation - i.e., papers in which it has been used to
> calculate correlated motion.
>
> As to modification of the code, I found it easiest to compile the source
> code for various tools within GMX. It's not necessary, but it makes your
> life easier.
>
> Since your question doesn't refer to the modified g_covar code directly,
> I'm ccing the gromacs mailing list. Please keep future correspondence there.
>
> Good luck,
> Ran
>
> darme...@ibt.unam.mx wrote:
>> Dear Ran friedman
>>
>> I'm actually biochemistry student and I'm using your uploaded version of 
>> g_covar
>> in order to calculate correlated motion. I have c-alpha trajectory of 50 ns
>> simulation that describe the functional movement of my protein, but the
>> trajectory are not in the equilibrium. My questions are,  what reference
>> structure I must use in order to calculate correlated motion?, could I use 
>> the
>> average structure as reference?
>>
>> In the other hand, Im doing some modifications to the g_covar program and I 
>> want
>> to know the way to compile it. Is necessary to compile within gromacs?   
>> What is
>> the easiest way?
>>
>> I would appreciate any help in this matter.
>>
>> Dagoberto Armenta Medina
>>
>>
>>
>> 
>> Este mensaje fue enviado desde el servidor Webmail del Instituto de 
>> Biotecnologia.
>>
>>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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[gmx-users] Re: g_covar

[Ran Friedman]

Dear Dagoberto,

Choosing the right protein structure (and also which part of the protein
to align) depends a lot of your system. I wouldn't use an average
structure for a system that's changing a lot, because it may not be
representative. It's hard to provide a more elaborate answer without
many details about your system and what you're trying to simulate. It
can be helpful to read both on the methods of covariance analysis and on
some implementation - i.e., papers in which it has been used to
calculate correlated motion.

As to modification of the code, I found it easiest to compile the source
code for various tools within GMX. It's not necessary, but it makes your
life easier.

Since your question doesn't refer to the modified g_covar code directly,
I'm ccing the gromacs mailing list. Please keep future correspondence there.

Good luck,
Ran

darme...@ibt.unam.mx wrote:
> Dear Ran friedman
>
> I'm actually biochemistry student and I'm using your uploaded version of 
> g_covar
> in order to calculate correlated motion. I have c-alpha trajectory of 50 ns
> simulation that describe the functional movement of my protein, but the
> trajectory are not in the equilibrium. My questions are,  what reference
> structure I must use in order to calculate correlated motion?, could I use the
> average structure as reference?
>
> In the other hand, Im doing some modifications to the g_covar program and I 
> want
> to know the way to compile it. Is necessary to compile within gromacs?   What 
> is
> the easiest way?
>
> I would appreciate any help in this matter.
>
> Dagoberto Armenta Medina
>
>
>
> 
> Este mensaje fue enviado desde el servidor Webmail del Instituto de 
> Biotecnologia.
>
>   

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Re: [gmx-users] Using R.E.D. charges with OPLS AA

[Ran Friedman]

Hi,

HF with 6-31G usually provide a good start for getting OPLS charges:
@article{Jorgensen1996,
   Author = {Jorgensen, W. L.  and Maxwell, D. S. and Tirado-Rives, J.},
   Title = {Development and Testing of the {O}{P}{L}{S} All-Atom Force
Field on
Conformational Energetics and Properties of Organic Liquids.},
   Journal = {J Am Chem Soc},
   Volume = {118},
   Pages = {11225-11236},
 Year = {1996} }

How you assign your charges to the molecule is another issue. I normally
fit the partial charges to the electrostatic potential around the
molecule. RESP was indeed developed with AMBER, but I don't know if the
charges are so different.

Good luck,
Ran

DimitryASuplatov wrote:
> Hello,
>
> I need to simulate a protein with deprotonated Tyr (HH hydrogen should
> be off). I used R.E.D. approach with PCGAMESS and RESP to calculate the
> charges. 
>
> 1/ The problem is that to my understanding RESP charges apply to AMBER
> only. Am I correct?
>
> 2/ Can I use R.E.D. charges with OPLS AA?
>
> 3/ If not how can I recalculate them to fit the OPLS AA?
>
> 4/ Any Tyr-Deprot topology already available??? 
>
> Thanks, I appreciate your time.
> SDA
>
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>   


-- 
--
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.fried...@bioc.unizh.ch
Skype: ran.friedman
--

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