date:20111202

[gmx-users] grompp error for CNT simulation

2011-12-02 Thread niaz poorgholami

 Dear gmx users,
I am using gromacs 4.5.3 to simulate CNT in water. up to now I have done
these things:
1. I used packmol to create my PDB file and the used editconf to change PDB
to gro file.
2. I copied oplsaa.ff folder in my working directory
3. I added following lines to atomname2type.n2t
Copls_9950  12.011  2C  0.142  C 0.142
Copls_9960  12.011  3C  0.142  C 0.142  C 0.142
Copls_9970  12.011  4C  0.142  C 0.142  C 0.142 C 0.142
Copls_9980  12.011  5C  0.142  C 0.142  C 0.142 C 0.142 C
0.142
4. I added these to atomtypes.atp
 opls_995   12.01100
 opls_996   12.01100
 opls_997   12.01100
 opls_998   12.01100

5. I added these to ffbonded.itp
[ bondtypes ]
 C   C  1   0.14210   478900

 [ angletypes ]
 C   C   C   1  120.000  397.480

[ dihedraltypes ]
 C   C   1   0.000 167.360  1
6. I used g_x2top to create topology for CNT.
Command line was:

g_x2top -f CNT.gro -o CNT.top -pbc -nopairs -name CNT -nexcl 5

7. I wrote a .top file given below,
; Include forcefield parameters
#include "./oplsaa.ff/forcefield.itp"
; Include topology for water
#include "oplsaa.ff/spc.itp"
; Include topology for CNT
#include "oplsaa.ff/CNT.itp"

[ system ]
; Name
SDS and CNT in water
[ molecules ]
; Compound#mols
water   9000
CNT 1
8. when I run grompp  for EM with this command line :grompp -f md.mdp -c
cnt_alone.gro -p topol.top -o em.tpr
it gave me the following error:Atomtype opls_995 not found.
 I would be pleased if anyone could help me how to fix this.
   niaz
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Re: [gmx-users] Check for bad contacts and/or reduce the timestep

2011-12-02 Thread Mark Abraham


On 3/12/2011 5:15 PM, pragna lakshmi wrote:
I understood that the system has large velocities. Since simulation 
has been stopped at Step 226040, time 452.08 (ps) can i conclude that 
error is because of any invalid parameters in topology file generated 
by server for ligand.


Such a conclusion would be premature, given your inappropriate use of 
thermostats and the information in the URL Justin provided...


Mark



On Sat, Dec 3, 2011 at 11:19 AM, Mark Abraham > wrote:


On 3/12/2011 4:42 PM, pragna lakshmi wrote:

Thank u for reply. I did energy minimization and equilibration
step. It converged in 696 steps which is shown below.

Step=  692, Dmax= 9.2e-03 nm, Epot= -7.12587e+05 Fmax=
7.62150e+03, atom= 2099
Step=  693, Dmax= 1.1e-02 nm, Epot= -7.12588e+05 Fmax=
9.72038e+03, atom= 2099
Step=  695, Dmax= 6.6e-03 nm, Epot= -7.12670e+05 Fmax=
9.39830e+02, atom= 2099

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 696 steps
Potential Energy  = -7.1266969e+05
Maximum force =  9.3982965e+02 on atom 2099
Norm of force =  2.1967674e+01



The atom that has the greatest force after EM is the same one for
which LINCS warnings arise later. That's worth paying attention
to. Read the advice about diagnosing unstable systems on the link
Justin gave you last time.



# md.mdp file

title = protein
cpp = /lib/cpp ; location of cpp on SGI
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 100 ; total 50 ps.
nstcomm = 1
nstxout = 500 ; output coordinates every 1.0 ps
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = berendsen
tau_t = 0.1 0.1 0.1 0.1 0.1
tc-grps = protein ZN IMP sol NA+
ref_t = 300 300 300 300 300


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



; Pressure coupling is on
Pcoupl = berendsen
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 = 300.0
gen_seed = 173529


It's probably not useful to re-generate velocities after the
position-restrained step.

Mark



# pr.mdp file

title = protein
cpp = /lib/cpp ; location of cpp on SGI
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 5 ; total 20.0 ps.
nstcomm = 1
nstxout = 250 ; output coordinates every 0.5 ps
nstvout = 1000 ; output velocities every 2.0 ps
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = V-rescale
tau_t = 0.1 0.1 0.1 0.1 0.1
tc_grps = protein ZN sol IMP NA+
ref_t = 300 300 300 300 300
; Pressure coupling is on
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 = 300.0
gen_seed = 173529

#em.mdp file

title = protein
cpp = /lib/cpp ; location of cpp on SGI
define = -DFLEX_SPC ; Use Ferguson's Flexible water model [4]
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 2000
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME ; Use particle-mesh ewald
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01

I need further help to trouble shoot this problem.




On Sat, Dec 3, 2011 at 10:46 AM, Justin A. Lemkul
mailto:jalem...@vt.edu>> wrote:



pragna lakshmi wrote:

Hi,
I am trying to run protein-ligand complex simulation.
At the final MD run step it is showing the following
error. Can anybody tell me the solution for this error?



http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

There are hundreds of threads in the archive with the same
issue and several possible solutions.  Please consult the
link above (and referenced pages), as well as other posts.

If you need further help diagnosing the problem, please post
a complete

Re: [gmx-users] Check for bad contacts and/or reduce the timestep

2011-12-02 Thread pragna lakshmi

I understood that the system has large velocities. Since simulation has
been stopped at Step 226040, time 452.08 (ps) can i conclude that error is
because of any invalid parameters in topology file generated by server for
ligand.

On Sat, Dec 3, 2011 at 11:19 AM, Mark Abraham wrote:

>  On 3/12/2011 4:42 PM, pragna lakshmi wrote:
>
> Thank u for reply. I did energy minimization and equilibration step. It
> converged in 696 steps which is shown below.
>
>  Step=  692, Dmax= 9.2e-03 nm, Epot= -7.12587e+05 Fmax= 7.62150e+03,
> atom= 2099
>  Step=  693, Dmax= 1.1e-02 nm, Epot= -7.12588e+05 Fmax= 9.72038e+03, atom=
> 2099
> Step=  695, Dmax= 6.6e-03 nm, Epot= -7.12670e+05 Fmax= 9.39830e+02, atom=
> 2099
>
>  writing lowest energy coordinates.
>
>  Steepest Descents converged to Fmax < 1000 in 696 steps
> Potential Energy  = -7.1266969e+05
> Maximum force =  9.3982965e+02 on atom 2099
> Norm of force =  2.1967674e+01
>
>
> The atom that has the greatest force after EM is the same one for which
> LINCS warnings arise later. That's worth paying attention to. Read the
> advice about diagnosing unstable systems on the link Justin gave you last
> time.
>
>
>  # md.mdp file
>
>  title = protein
> cpp = /lib/cpp ; location of cpp on SGI
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 100 ; total 50 ps.
> nstcomm = 1
> nstxout = 500 ; output coordinates every 1.0 ps
> nstvout = 0
> nstfout = 0
> nstlist = 10
> ns_type = grid
> rlist = 0.9
> coulombtype = PME
> rcoulomb = 0.9
> rvdw = 1.0
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 6
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on in four groups
> Tcoupl = berendsen
> tau_t = 0.1 0.1 0.1 0.1 0.1
> tc-grps = protein ZN IMP sol NA+
> ref_t = 300 300 300 300 300
>
>
> http://www.gromacs.org/Documentation/Terminology/Thermostats
>
>
>   ; Pressure coupling is on
> Pcoupl = berendsen
> 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 = 300.0
> gen_seed = 173529
>
>
> It's probably not useful to re-generate velocities after the
> position-restrained step.
>
> Mark
>
>
>  # pr.mdp file
>
>  title = protein
> cpp = /lib/cpp ; location of cpp on SGI
>  define = -DPOSRES
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 5 ; total 20.0 ps.
> nstcomm = 1
> nstxout = 250 ; output coordinates every 0.5 ps
> nstvout = 1000 ; output velocities every 2.0 ps
> nstfout = 0
> nstlog = 10
> nstenergy = 10
> nstlist = 10
> ns_type = grid
> rlist = 0.9
> coulombtype = PME
> rcoulomb = 0.9
> rvdw = 1.0
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 6
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on in four groups
> Tcoupl = V-rescale
> tau_t = 0.1 0.1 0.1 0.1 0.1
> tc_grps = protein ZN sol IMP NA+
> ref_t = 300 300 300 300 300
> ; Pressure coupling is on
> 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 = 300.0
> gen_seed = 173529
>
>  #em.mdp file
>
>  title = protein
> cpp = /lib/cpp ; location of cpp on SGI
> define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4]
> constraints = none
> integrator = steep
> dt = 0.002 ; ps !
> nsteps = 2000
> nstlist = 10
> ns_type = grid
> rlist = 0.9
> coulombtype = PME ; Use particle-mesh ewald
> rcoulomb = 0.9
> rvdw = 1.0
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ;
> ; Energy minimizing stuff
> ;
> emtol = 1000.0
> emstep = 0.01
>
>  I need further help to trouble shoot this problem.
>
>
>
>
> On Sat, Dec 3, 2011 at 10:46 AM, Justin A. Lemkul  wrote:
>
>>
>>
>> pragna lakshmi wrote:
>>
>>> Hi,
>>> I am trying to run protein-ligand complex simulation. At the final
>>> MD run step it is showing the following error. Can anybody tell me the
>>> solution for this error?
>>>
>>>
>>
>> http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
>>
>> There are hundreds of threads in the archive with the same issue and
>> several possible solutions.  Please consult the link above (and referenced
>> pages), as well as other posts.
>>
>> If you need further help diagnosing the problem, please post a complete
>> .mdp file, as well as a description of prior minimization and equilibration.
>>
>> -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.

Re: [gmx-users] Check for bad contacts and/or reduce the timestep

2011-12-02 Thread Mark Abraham


On 3/12/2011 4:42 PM, pragna lakshmi wrote:
Thank u for reply. I did energy minimization and equilibration step. 
It converged in 696 steps which is shown below.


Step=  692, Dmax= 9.2e-03 nm, Epot= -7.12587e+05 Fmax= 7.62150e+03, 
atom= 2099
Step=  693, Dmax= 1.1e-02 nm, Epot= -7.12588e+05 Fmax= 9.72038e+03, 
atom= 2099
Step=  695, Dmax= 6.6e-03 nm, Epot= -7.12670e+05 Fmax= 9.39830e+02, 
atom= 2099


writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 696 steps
Potential Energy  = -7.1266969e+05
Maximum force =  9.3982965e+02 on atom 2099
Norm of force =  2.1967674e+01



The atom that has the greatest force after EM is the same one for which 
LINCS warnings arise later. That's worth paying attention to. Read the 
advice about diagnosing unstable systems on the link Justin gave you 
last time.




# md.mdp file

title = protein
cpp = /lib/cpp ; location of cpp on SGI
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 100 ; total 50 ps.
nstcomm = 1
nstxout = 500 ; output coordinates every 1.0 ps
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = berendsen
tau_t = 0.1 0.1 0.1 0.1 0.1
tc-grps = protein ZN IMP sol NA+
ref_t = 300 300 300 300 300


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


; Pressure coupling is on
Pcoupl = berendsen
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 = 300.0
gen_seed = 173529


It's probably not useful to re-generate velocities after the 
position-restrained step.


Mark



# pr.mdp file

title = protein
cpp = /lib/cpp ; location of cpp on SGI
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 5 ; total 20.0 ps.
nstcomm = 1
nstxout = 250 ; output coordinates every 0.5 ps
nstvout = 1000 ; output velocities every 2.0 ps
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = V-rescale
tau_t = 0.1 0.1 0.1 0.1 0.1
tc_grps = protein ZN sol IMP NA+
ref_t = 300 300 300 300 300
; Pressure coupling is on
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 = 300.0
gen_seed = 173529

#em.mdp file

title = protein
cpp = /lib/cpp ; location of cpp on SGI
define = -DFLEX_SPC ; Use Ferguson's Flexible water model [4]
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 2000
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME ; Use particle-mesh ewald
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01

I need further help to trouble shoot this problem.




On Sat, Dec 3, 2011 at 10:46 AM, Justin A. Lemkul > wrote:




pragna lakshmi wrote:

Hi,
I am trying to run protein-ligand complex simulation. At
the final MD run step it is showing the following error. Can
anybody tell me the solution for this error?


http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

There are hundreds of threads in the archive with the same issue
and several possible solutions.  Please consult the link above
(and referenced pages), as well as other posts.

If you need further help diagnosing the problem, please post a
complete .mdp file, as well as a description of prior minimization
and equilibration.

-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 list gmx-users@gromacs.org


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Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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interface or send it to gmx-users-requ...@gromacs.org
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--
T.Pragna Lakshmi,
Junior Scientist,
Vision Research Center,
Sankara Netralaya,
Chennai,
India.
Pin:

Re: [gmx-users] Check for bad contacts and/or reduce the timestep

2011-12-02 Thread Mark Abraham


On 3/12/2011 4:42 PM, pragna lakshmi wrote:
Thank u for reply. I did energy minimization and equilibration step. 
It converged in 696 steps which is shown below.


Step=  692, Dmax= 9.2e-03 nm, Epot= -7.12587e+05 Fmax= 7.62150e+03, 
atom= 2099
Step=  693, Dmax= 1.1e-02 nm, Epot= -7.12588e+05 Fmax= 9.72038e+03, 
atom= 2099
Step=  695, Dmax= 6.6e-03 nm, Epot= -7.12670e+05 Fmax= 9.39830e+02, 
atom= 2099


writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 696 steps
Potential Energy  = -7.1266969e+05
Maximum force =  9.3982965e+02 on atom 2099
Norm of force =  2.1967674e+01



The atom that has the greatest force after EM is the same one for which 
LINCS warnings arise later. That's worth paying attention to. Read the 
advice about diagnosing unstable systems on the link Justin gave you 
last time.




# md.mdp file

title = protein
cpp = /lib/cpp ; location of cpp on SGI
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 100 ; total 50 ps.
nstcomm = 1
nstxout = 500 ; output coordinates every 1.0 ps
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = berendsen
tau_t = 0.1 0.1 0.1 0.1 0.1
tc-grps = protein ZN IMP sol NA+
ref_t = 300 300 300 300 300


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


; Pressure coupling is on
Pcoupl = berendsen
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 = 300.0
gen_seed = 173529


It's probably not useful to re-generate velocities after the 
position-restrained step.


Mark



# pr.mdp file

title = protein
cpp = /lib/cpp ; location of cpp on SGI
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 5 ; total 20.0 ps.
nstcomm = 1
nstxout = 250 ; output coordinates every 0.5 ps
nstvout = 1000 ; output velocities every 2.0 ps
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = V-rescale
tau_t = 0.1 0.1 0.1 0.1 0.1
tc_grps = protein ZN sol IMP NA+
ref_t = 300 300 300 300 300
; Pressure coupling is on
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 = 300.0
gen_seed = 173529

#em.mdp file

title = protein
cpp = /lib/cpp ; location of cpp on SGI
define = -DFLEX_SPC ; Use Ferguson's Flexible water model [4]
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 2000
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME ; Use particle-mesh ewald
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01

I need further help to trouble shoot this problem.




On Sat, Dec 3, 2011 at 10:46 AM, Justin A. Lemkul > wrote:




pragna lakshmi wrote:

Hi,
I am trying to run protein-ligand complex simulation. At
the final MD run step it is showing the following error. Can
anybody tell me the solution for this error?


http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

There are hundreds of threads in the archive with the same issue
and several possible solutions.  Please consult the link above
(and referenced pages), as well as other posts.

If you need further help diagnosing the problem, please post a
complete .mdp file, as well as a description of prior minimization
and equilibration.

-Justin

-- 



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


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--
T.Pragna Lakshmi,
Junior Scientist,
Vision Research Center,
Sankara Netralaya,
Chennai,
India.
Pin:

Re: [gmx-users] Check for bad contacts and/or reduce the timestep

2011-12-02 Thread pragna lakshmi

Thank u for reply. I did energy minimization and equilibration step. It
converged in 696 steps which is shown below.

Step=  692, Dmax= 9.2e-03 nm, Epot= -7.12587e+05 Fmax= 7.62150e+03, atom=
2099
Step=  693, Dmax= 1.1e-02 nm, Epot= -7.12588e+05 Fmax= 9.72038e+03, atom=
2099
Step=  695, Dmax= 6.6e-03 nm, Epot= -7.12670e+05 Fmax= 9.39830e+02, atom=
2099

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 696 steps
Potential Energy  = -7.1266969e+05
Maximum force =  9.3982965e+02 on atom 2099
Norm of force =  2.1967674e+01


# md.mdp file

title = protein
cpp = /lib/cpp ; location of cpp on SGI
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 100 ; total 50 ps.
nstcomm = 1
nstxout = 500 ; output coordinates every 1.0 ps
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = berendsen
tau_t = 0.1 0.1 0.1 0.1 0.1
tc-grps = protein ZN IMP sol NA+
ref_t = 300 300 300 300 300
; Pressure coupling is on
Pcoupl = berendsen
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 = 300.0
gen_seed = 173529

# pr.mdp file

title = protein
cpp = /lib/cpp ; location of cpp on SGI
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 5 ; total 20.0 ps.
nstcomm = 1
nstxout = 250 ; output coordinates every 0.5 ps
nstvout = 1000 ; output velocities every 2.0 ps
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = V-rescale
tau_t = 0.1 0.1 0.1 0.1 0.1
tc_grps = protein ZN sol IMP NA+
ref_t = 300 300 300 300 300
; Pressure coupling is on
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 = 300.0
gen_seed = 173529

#em.mdp file

title = protein
cpp = /lib/cpp ; location of cpp on SGI
define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4]
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 2000
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME ; Use particle-mesh ewald
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01

I need further help to trouble shoot this problem.




On Sat, Dec 3, 2011 at 10:46 AM, Justin A. Lemkul  wrote:

>
>
> pragna lakshmi wrote:
>
>> Hi,
>> I am trying to run protein-ligand complex simulation. At the final MD
>> run step it is showing the following error. Can anybody tell me the
>> solution for this error?
>>
>>
> http://www.gromacs.org/**Documentation/Errors#LINCS.**
> 2fSETTLE.2fSHAKE_warnings
>
> There are hundreds of threads in the archive with the same issue and
> several possible solutions.  Please consult the link above (and referenced
> pages), as well as other posts.
>
> If you need further help diagnosing the problem, please post a complete
> .mdp file, as well as a description of prior minimization and equilibration.
>
> -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
>



-- 
T.Pragna Lakshmi,
Junior Scientist,
Vision Research Center,
Sankara Netralaya,
Chennai,
India.
Pin: 66.
-- 
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Re: [gmx-users] Check for bad contacts and/or reduce the timestep

2011-12-02 Thread Justin A. Lemkul




pragna lakshmi wrote:

Hi,
 I am trying to run protein-ligand complex simulation. At the final 
MD run step it is showing the following error. Can anybody tell me the 
solution for this error?




http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

There are hundreds of threads in the archive with the same issue and several 
possible solutions.  Please consult the link above (and referenced pages), as 
well as other posts.


If you need further help diagnosing the problem, please post a complete .mdp 
file, as well as a description of prior minimization and equilibration.


-Justin

--


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


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[gmx-users] Check for bad contacts and/or reduce the timestep

2011-12-02 Thread pragna lakshmi

Hi,
 I am trying to run protein-ligand complex simulation. At the final MD
run step it is showing the following error. Can anybody tell me the
solution for this error?

Step 105692, time 211.384 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002880, max 0.071917 (between atoms 2097 and 2095)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2098   2099   38.60.1330   0.1371  0.1330
   2097   2098   45.20.1330   0.1370  0.1330
.
.
.
.
Step 226039, time 452.078 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 42.444550, max 1059.016235 (between atoms 2098 and 2099)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2095   2094   31.60.1441  10.5310  0.1250
   2113   2114   40.80.1471   0.1950  0.1470
   2117   2112   36.40.1521   0.1902  0.1520
   2111   2113   81.70.1535   0.2949  0.1520
   2111   2112   83.90.1534   0.2900  0.1520
   2111   2110  113.20.1833   0.8261  0.1780
   2109   2110   43.80.2063  11.5418  0.1750
   2107   2109   38.30.1516  11.2487  0.1390
   2107   2108  103.00.1581  11.5450  0.1530
   2106   2107   77.40.1333  30.0780  0.1530
   2104   2105  140.00.1080   2.2354  0.1000
   2102   2104   34.20.1426  16.8737  0.1430
   2102   2103   89.90.1637  15.4076  0.1530
   2101   2106  142.00.2077  63.6808  0.1530
   2101   2102  132.50.1659  62.8960  0.1530
   2101   2099  174.70.5646 127.3807  0.1390
   2099   2100  160.10.5219 101.4140  0.1230
   2106   2098  166.30.2022  76.2729  0.1480
   2098   2099  174.80.6156 140.9822  0.1330
   2097   2109  149.50.1057  36.9859  0.1330
   2097   2098  159.40.2818  84.7773  0.1330
   2097   2095  164.80.1042  37.0501  0.1330
   2095   2096   70.70.1482   9.8470  0.1250
Wrote pdb files with previous and current coordinates
There were 4 inconsistent shifts. Check your topology
Warning: 1-4 interaction between 2094 and 2098 at distance 44.117 which is
larger than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
.
.
.
.
   1416   1417   89.70.1530 705915256832.  0.1530
   1414   1416   90.40.1470 419510747136.  0.1470
   1414   1415   92.30.1000 45284384768.  0.1000
   1412   1414   89.50.1330 55051784192.  0.1330
   1412   1413  106.40.1230 13457604608.  0.1230
   1409   1411  119.20.1530 519590400.  0.1530
   1409   1410  107.40.1530 519590400.  0.1530
   1408   1412   99.10.1530 14933683200.  0.1530
   1408   1409   98.30.1530 4102264576.  0.1530
   1406   1408   98.50.1470 4076032256.  0.1470
   1406   1407  107.80.1000 606216384.  0.1000
   1404   1406  122.90.1330 606216384.  0.1330
   1404   1405   31.50.1230   0.1567  0.1230
   2120   2122  105.20.1473 84501076367114240.  0.1470
   2120   2121  105.80.1473 83934295302864896.  0.1470
   2118   2120   95.00.1349 219396825084329984.  0.1340
   2118   2119   96.00.1236 223179042004664320.  0.1230

t = 452.080 ps: Water molecule starting at atom 36608 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)


-- 
T.Pragna Lakshmi,
Junior Scientist,
Vision Research Center,
Sankara Netralaya,
Chennai,
India.
Pin: 66.
-- 
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Re: [gmx-users] A special case of cutoffs related to mdrun with -rerun option

2011-12-02 Thread Mark Abraham


On 3/12/2011 2:02 AM, Ioannis Beis wrote:

Dear GROMACS users,

I am interested in using mdrun of a special version of GROMACS 4.0.2 
made by Ollila et. al with -rerun option, made so that it can allow 
calculations of properties related to local pressure in lipid bilayer 
systems. I have used GROMOS54a7 with Poger parameters, but among other 
slight modifications I have used PME instead of reaction field with 
rcoulomb=0.9 and maintained the twin range cutoff used in the original 
study for van der Waals, using rlist=0.9 (instead of the original 0.8) 
and rvdw=1.4. The inner sphere neighborlist is updated every step, 
whereas the outer sector neighborlist every 5 steps.


The mdrun with -rerun flag of this package does not support PME, 
therefore the tpr file has to be reassembled without it. Instead, much 
larger plain cutoff than 1.8 alone has been shown by Sonne et al. to 
give close enough results to short cutoffs used together with PME, at 
least in a qualitative manner.


I can thereby use rcoulomb=2.0 for the purposes of the -rerun, but 
this no longer allows the twin range cutoff scheme. I tried to check 
if there could be some trick to be done with rlistlong (although I was 
almost sure there wouldn't be anything and that rlistlong just serves 
for switch/shift functions), but as far as my searching is concerned 
it didn't even exist as an option in GROMACS 4.0.2 (I assume that twin 
range cutoff was still supported but rlistlong would be automatically 
placed in the max(rcoulomb,rvdw).


Therefore my current problem is about the reliability of -rerun with 
plain vdw cutoff, while in the original simulation twin range cutoff 
was used. Is there any study comparing the results of the two 
different schemes mentioned above for GROMOS simulations? What would 
the consequenses in the physics be and how would the choice of the 
cutoff radius and number of steps affect the results? If someone 
really wants to obtain those calculations, what would be the best 
compromise?


VDW potentials are very close to zero by 0.9nm, so I'd expect you can do 
whatever you like here. Off the cuff, I'd be far more concerned about 
Coulomb cut-off force artefacts from plain (or RF) cut-offs, even out at 
2nm, but do graph the potentials and see.


Mark



If anyone has another recommendation about obtaining lateral presure 
profiles and associated properties by lipid bilayer simulations, such 
that would be compatible with my algorithm choices, please let me know.


I am grateful in advance.

Best regards,
Ioannis



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[gmx-users] Half double pair list method in GROMACS [update]

2011-12-02 Thread Chris Neale

What you have done seems alright. I didn't look closely enough to be 
sure though. One of the good things about this method is that you can 
easily test it yourself. To do this, create two different .gro files, 
one containing the atoms from one ff and the other containing the other 
atoms. For each, do separate zero-step mdrun evaluations of their 
energies under (a) their original ff, and (b) the combined HEDP ff that 
you have constructed. The energy evaluations should be the same once you 
account for rounding errors. Then all that is left is for you to be 
certain that you didn't cause any problems for nonbonded interactions. 
Note that you'll need to return to the original atomtypes for the first 
half of this test.

Note that the only thing that the HEDP method is intended to perturb is 
the 1-4 interactions (and by perturb I mean that they will now be correct).

Chris.

 -- original message --

Hi Stephane & Chris,
I followed all the threads posted by you two.
I have a protein using ff99SB and GLYCAM for sugars. I have a disaccharide
bound to protein. In xleap of AMBERTOOLS, I use the GLYCAM and ff99SB to
generate the topology and coordinate files. I did the tests as Chris'
original posts and by Stephane.
The 1-4 interaction terms match for sugar alone and protein alone with HEDP
method.
When I generate topology and coordinate files with xleap of AMBER, there
are three atom types that are common to protein and sugar. The atom types
for my case are H1, OH and HO.
Since for protein pairtypes using ff99SB, the epsilon has to be divided by
10 and pairs section be replicated five times and for sugar the epsilon in
the pairtypes be divided by six and replicated six times, I am a little
concerned about the three atomtypes that are common.
So what I did was to change the atomtypes of sugar as H1S, OHS HOS for
sugar and H1, OH and HO for protein and I made the changes accordingly in
the pairtypes section for protein and sugar.
Is this a valid approach?
Any suggestion will be helpful.

To make things little more clear:
H1H10.  0.  A   2.47135e-01  6.56888e-02
;originally obtained using amb2gmx.pl
H1S  H1S  0.  0.  A   2.47135e-01  6.56888e-02 ;Glycam
Hydrogen of Sugar ( I changed this so that the common atom types be
separated)

In the ffnonbonded_complex_mod.itp:
;;using combination rule of 2
[ pairtypes ]
;;for protein
H1  H1  1   0.247135000 0.006568880 ;the epsilon is divided
by 10

;;for sugar

 H1S   H1S 1   0.24713500  0.010948133 ;the epsilon is divided
by 6

Thanks for your time,

Regards
Sai

On Mon, Sep 5, 2011 at 11:33 AM, ABEL Stephane 175950
wrote:

> Dear All,
>
> Below a little update and results about the application of half double
> pair list method to scale properly the Coulombic 1-4 interactions in case
> of a system where the AMBER99SB (fudgeLJ=0.5 and fudgeLJ=0.8333) and
> GLYCAM06 (fudgeLJ=1.0 and fudgeLJ=1.0) force fields are combined.
>
> I have followed the 4 steps described in [1] and used the following 
values

> in my forcefield.itp file
>
> [ defaults ]
> ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
> 1   2   yes 1.0 0.16
> #include "ffnonbonded_mod.itp"
> ;#include "ffnonbonded.itp"
> #include "ffbonded.itp"
>
> I used two different topology files for the glycolipid (bDM) and the
> peptide. One with (*_mod.itp) with pair list parameters duplicated 6 
times

> (bDM) and 5 times (peptide) and with single pair list (*_no_mod.itp) as
> decribed in [1].
>
> TESTING:
>
> Three 3 different systems were examined:
>
> A. A first system containing 1 glycolipid (bDM)  in water cubic box
> B. A second system with 1 peptide in TIP3P water
> C. And a third system with 1 peptide and 1 glycolipid in water cubic box
>
> To obtain the glycolipid and peptide energy pairs, I did one step of 
MD in
> NVT ensemble with the *.mdp file given in [2] with different 
energygrps and

> tc_grps.
> For 1. energygrps and tc_grps = bDM SOL
> For 2. energygrps and tc_grps = Protein SOL
> For 3. energygrps and = Protein bDM SOL
>
> bDM/water system
>
> Test_A1
>
> ## Control with GLYCAM force field fudgeLJ fudgeQQ parameters and  the
> *_no_mod.itp file :
> ##; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
> ##  1   2   yes 1.0 1.0
> Epot (kJ/mol)Coul-SR  LJ-SRCoul-14  LJ-14
> bDM-bDM   -4.00855e+02   -3.71401e+012.03406e+032.79234e+02
>
> Test_A2
>
>  with the topology *_mod.itp file and the directive
> ##; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
> ##  1   2   yes 1.0
> 0.16
> Epot (kJ/mol)Coul-SR  LJ-SRCoul-14  LJ-14
> bDM-bDM   -4.00855e+02   -3.71401e+012.03406e+032.79234e+02
>
> Test_A3
>
>  with the topology *_no_mod.itp file and the directive
>

Re: [gmx-users] Half double pair list method in GROMACS [update]

2011-12-02 Thread Sai Kumar Ramadugu

Hi Stephane & Chris,
I followed all the threads posted by you two.
I have a protein using ff99SB and GLYCAM for sugars. I have a disaccharide
bound to protein. In xleap of AMBERTOOLS, I use the GLYCAM and ff99SB to
generate the topology and coordinate files. I did the tests as Chris'
original posts and by Stephane.
The 1-4 interaction terms match for sugar alone and protein alone with HEDP
method.
When I generate topology and coordinate files with xleap of AMBER, there
are three atom types that are common to protein and sugar. The atom types
for my case are H1, OH and HO.
Since for protein pairtypes using ff99SB, the epsilon has to be divided by
10 and pairs section be replicated five times and for sugar the epsilon in
the pairtypes be divided by six and replicated six times, I am a little
concerned about the three atomtypes that are common.
So what I did was to change the atomtypes of sugar as H1S, OHS HOS for
sugar and H1, OH and HO for protein and I made the changes accordingly in
the pairtypes section for protein and sugar.
Is this a valid approach?
Any suggestion will be helpful.

To make things little more clear:
H1H10.  0.  A   2.47135e-01  6.56888e-02
;originally obtained using amb2gmx.pl
H1S  H1S  0.  0.  A   2.47135e-01  6.56888e-02 ;Glycam
Hydrogen of Sugar ( I changed this so that the common atom types be
separated)

In the ffnonbonded_complex_mod.itp:
;;using combination rule of 2
[ pairtypes ]
;;for protein
H1  H1  1   0.247135000 0.006568880 ;the epsilon is divided
by 10

;;for sugar

 H1S   H1S 1   0.24713500  0.010948133 ;the epsilon is divided
by 6

Thanks for your time,

Regards
Sai

On Mon, Sep 5, 2011 at 11:33 AM, ABEL Stephane 175950
wrote:

> Dear All,
>
> Below a little update and results about the application of half double
> pair list method to scale properly the Coulombic 1-4 interactions in case
> of a system where the AMBER99SB (fudgeLJ=0.5 and fudgeLJ=0.8333) and
> GLYCAM06 (fudgeLJ=1.0 and fudgeLJ=1.0) force fields are combined.
>
> I have followed the 4 steps described in [1] and used the following values
> in my forcefield.itp file
>
> [ defaults ]
> ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
> 1   2   yes 1.0 0.16
> #include "ffnonbonded_mod.itp"
> ;#include "ffnonbonded.itp"
> #include "ffbonded.itp"
>
> I used two different topology files for the glycolipid (bDM) and the
> peptide. One with (*_mod.itp) with pair list parameters duplicated 6 times
> (bDM) and 5 times (peptide) and with single pair list (*_no_mod.itp) as
> decribed in [1].
>
> TESTING:
>
> Three 3 different systems were examined:
>
> A. A first system containing 1 glycolipid (bDM)  in water cubic box
> B. A second system with 1 peptide in TIP3P water
> C. And a third system with 1 peptide and 1 glycolipid in water cubic box
>
> To obtain the glycolipid and peptide energy pairs, I did one step of MD in
> NVT ensemble with the *.mdp file given in [2] with different energygrps and
> tc_grps.
> For 1. energygrps and tc_grps = bDM SOL
> For 2. energygrps and tc_grps = Protein SOL
> For 3. energygrps and = Protein bDM SOL
>
> bDM/water system
>
> Test_A1
>
> ## Control with GLYCAM force field fudgeLJ fudgeQQ parameters and  the
> *_no_mod.itp file :
> ##; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
> ##  1   2   yes 1.0 1.0
> Epot (kJ/mol)Coul-SR  LJ-SRCoul-14  LJ-14
> bDM-bDM   -4.00855e+02   -3.71401e+012.03406e+032.79234e+02
>
> Test_A2
>
>  with the topology *_mod.itp file and the directive
> ##; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
> ##  1   2   yes 1.0
> 0.16
> Epot (kJ/mol)Coul-SR  LJ-SRCoul-14  LJ-14
> bDM-bDM   -4.00855e+02   -3.71401e+012.03406e+032.79234e+02
>
> Test_A3
>
>  with the topology *_no_mod.itp file and the directive
> ##; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
> ##  1   2   yes 1.0
> 0.16
> Epot (kJ/mol)Coul-SR  LJ-SRCoul-14  LJ-14
> bDM-bDM   -4.00855e+02   -3.71401e+013.39010e+022.79234e+02
>
> Coul-14 energy for bDM-bDM in Test_A1 = Coul-14 energy in Test_A2 --> OK !
> Coul-14 energy for bDM-bDM Test_A3 is 6 smaller than Coul-14 energy in
> Test_A1 and Test 2 ---> OK !
>
> peptide/water system
>
> Test_B1
>
>  Control with AMBER force field fudgeLJ fudgeQQ parameters, the
> *_no_mod.itp file
> ##; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
> ##  1   2   yes 0.5  0.8333
> Epot (kJ/mol)Coul-SR  LJ-SRCoul-14  LJ-14
> Protein-Protein   -1.49026e+03   -4.12114e+023.80551e+036.55321e+02
>
> Test_B2
>
>  Control wit

Re: [gmx-users] QM calculation

2011-12-02 Thread Justin A. Lemkul




parto haghighi wrote:

Dear Justin,
Thank you for your response.
I have already read your paper and I have tried semi empirical methods ( 
Antechamber) and QM from Spartan 10 and I can reach results which have 
consistence with your paper.

But about large molecule like Lidocaine or Articaine I have some problems.
You said "QM calculations are the starting point, not the end" but 
becase my field is Chemical enginnering I do not have basic information 
of QM to continue my work.
So if it is possible for you please suggest me a book or any reference 
which can help me and introduce me methods of elementary quantum 
mechanics calculation. It will be really your kind.




You don't need more advanced QM to do the parameterization you're looking for. 
Refer to the primary literature for the Gromos96 force fields and you will find 
protocols for thermodynamic integration (free energy calculations, in general) 
that are required to validate parameters based on free energy of solvation.


If you're looking for more background in any of these topics, a simple Google 
search for "molecular modeling textbooks" turns up dozens of good ones that you 
should look into.


-Justin

--


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


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[gmx-users] QM calculation

2011-12-02 Thread parto haghighi

Dear Justin,
Thank you for your response.
I have already read your paper and I have tried semi empirical methods (
Antechamber) and QM from Spartan 10 and I can reach results which have
consistence with your paper.
But about large molecule like Lidocaine or Articaine I have some problems.
You said "QM calculations are the starting point, not the end" but becase
my field is Chemical enginnering I do not have basic information of QM to
continue my work.
So if it is possible for you please suggest me a book or any reference
which can help me and introduce me methods of elementary quantum mechanics
calculation. It will be really your kind.

Thanks a lot in advance.
Parto Haghighi
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Re: [gmx-users] can not restart a simulation from the checkpoint file

2011-12-02 Thread Justin A. Lemkul




Chen, Zhihong (chenz2) wrote:

Hi, I runed 2 ns membrane simulations. But I cann't restart these simulations
using the checkpoint file, The error message is   Warning: task died with
signal 11 (Segmentation fault). Since the trr file include the force,


What was your exact command?


velocity information of atoms, so I restarted the simulations from trr file
and it works. But when I tried to visionize the trr file in VMD, I saw weird
long lines between atoms across the cell box. I think that is because  atoms
are swithing from one periodic box to another. So the bond information are
messed up when shown in VMD.  What I am concerned is , is there a problem to
restart simulations from trrr file? And how to restart from cpt file, solving
that Segmentation Fault? Could someone give me help on this? Thanks chen



Without seeing the command you provided, there's no way to tell.  There is a 
how-to for doing restarts on the Gromacs website.  The weird bonds you're seeing 
are a normal consequence of PBC, nothing to worry about (again, see the website 
for more details).


-Justin

--


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


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Re: [gmx-users] Re: restraints between two molecules

2011-12-02 Thread Justin A. Lemkul




lq z wrote:
Thanks, Justin. How to use "index groups"? Do I do it in .mdp file or 
use some program in tools/?




Any group can be specified by name in the .mdp file, which then must correspond 
to the desired group in an .ndx file (created by make_ndx).  There are more 
details in the manual and on the Gromacs website.


-Justin

--


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


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[gmx-users] Re: restraints between two molecules

2011-12-02 Thread lq z

Thanks, Justin. How to use "index groups"? Do I do it in .mdp file or use
some program in tools/?

Luke


*Justin A. Lemkul* jalemkul at vt.edu

*Fri Dec 2 18:04:37 CET 2011*

   - Previous message: [gmx-users] restraints between two molecules
   
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lq z wrote:
>* Dear GMXers,*>* *>* I can apply harmonic bond, angle, and dihedral 
>restraints between two *>* molecules (3 atoms on one, and one atom on the 
>other one). If yes, how *>* to set it up in the topology file?*>* *
They have to be in the same [moleculetype].

>* Question 2: Can I apply distance restraint between mass center of some *>* 
>atoms in one molecule and ONE ATOM in the other molecule?*>* *
Yes, with the pull code and suitable index groups.

>* Question 3: Can those restraints be lambda (in alchemical free energy *>* 
>simulation) dependent?*>* *
Yes, see the manual.

-Justin

>* You may have known what I'm trying to do: Change one molecule to dummy, *>* 
>so I need restrain it at dummy state while no restraint is wanted at *>* real 
>state.*>* *>* Thanks,*>* Luke*>* *
-- 


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





On Fri, Dec 2, 2011 at 11:59 AM, lq z  wrote:

> Dear GMXers,
>
> I can apply harmonic bond, angle, and dihedral restraints between two
> molecules (3 atoms on one, and one atom on the other one). If yes, how to
> set it up in the topology file?
>
> Question 2: Can I apply distance restraint between mass center of some
> atoms in one molecule and ONE ATOM in the other molecule?
>
> Question 3: Can those restraints be lambda (in alchemical free energy
> simulation) dependent?
>
> You may have known what I'm trying to do: Change one molecule to dummy, so
> I need restrain it at dummy state while no restraint is wanted at real
> state.
>
> Thanks,
> Luke
>
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[gmx-users] can not restart a simulation from the checkpoint file

2011-12-02 Thread Chen, Zhihong (chenz2)

Hi, 
  I runed 2 ns membrane simulations. But I cann't restart these simulations 
using the checkpoint file, The error message is   Warning: task died with 
signal 11 (Segmentation fault).
Since the trr file include the force, velocity information of atoms, so I 
restarted the simulations from trr file and it works. But when I tried to 
visionize the trr file in VMD, I saw weird long lines between atoms across the 
cell box. I think that is because  atoms are swithing from one periodic box to 
another. So the bond information are messed up when shown in VMD.  What I am 
concerned is , is there a problem to restart simulations from trrr file? And 
how to restart from cpt file, solving that Segmentation Fault? Could someone 
give me help on this? Thanks
chen  
   
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Re: [gmx-users] restraints between two molecules

2011-12-02 Thread Justin A. Lemkul




lq z wrote:

Dear GMXers,

I can apply harmonic bond, angle, and dihedral restraints between two 
molecules (3 atoms on one, and one atom on the other one). If yes, how 
to set it up in the topology file?




They have to be in the same [moleculetype].

Question 2: Can I apply distance restraint between mass center of some 
atoms in one molecule and ONE ATOM in the other molecule?




Yes, with the pull code and suitable index groups.

Question 3: Can those restraints be lambda (in alchemical free energy 
simulation) dependent?




Yes, see the manual.

-Justin

You may have known what I'm trying to do: Change one molecule to dummy, 
so I need restrain it at dummy state while no restraint is wanted at 
real state.


Thanks,
Luke



--


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


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[gmx-users] restraints between two molecules

2011-12-02 Thread lq z

Dear GMXers,

I can apply harmonic bond, angle, and dihedral restraints between two
molecules (3 atoms on one, and one atom on the other one). If yes, how to
set it up in the topology file?

Question 2: Can I apply distance restraint between mass center of some
atoms in one molecule and ONE ATOM in the other molecule?

Question 3: Can those restraints be lambda (in alchemical free energy
simulation) dependent?

You may have known what I'm trying to do: Change one molecule to dummy, so
I need restrain it at dummy state while no restraint is wanted at real
state.

Thanks,
Luke
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[gmx-users] Job announcement at University of Regensburg

2011-12-02 Thread Emanuel Peter

Dear Colleagues,

we are currently seeking a highly motivated candidate for a PhD-position in the

field of Computational Biophysical Chemistry. We would be very grateful if you 
could let us know or forward this e-mail to any suitable candidate in case if 
(and only if) he/she could not be funded in your group. The project will
involve 
the development and application of multiscale simulation techniques for
studying 
the interplay and signaling behavior of multi-protein complexes. The successful

candidate will be part of an interdisciplinary research consortium „Chemical
Photocatalysis 
- GRK 1626“ funded by Deutsche Forschungsgemeinschaft (DFG) (see for more
information 
http://www.chemie.uni-regensburg.de/fakultaet/forschung/grk1626/)

Candidates should have a Master degree in Chemistry, Computational Biophysics
or 
related fields, as well as expertise in Molecular Dynamics simulations,
Molecular 
Modeling and/or Monte Carlo techniques. Good programming skills in FORTRAN
and/or 
C++ as well as working knowledge of unix operating systems would be beneficial.

The research project will be carried out within the Theory & Computation of
Advanced 
Materials and Sensors group under guidance and supervision of PD Dr. Stephan A.
Baeurle, 
in collaboration with experimentalists from the IPTC. Main working location
will be the 
Department of Physical Chemistry at the Faculty of Chemistry and Pharmacy of
Regensburg 
University.

To apply, please send a short motivation letter, CV, list of publications, and
contact 
details of three references by 15 December 2011 to:

Stephan A. Baeurle
Priv.-Doz. Dr. rer. nat. habil.
Institut für Physikalische und Theoretische Chemie
Universität Regensburg
Universitätsstr. 31
D-93053 Regensburg
Telefon: +49 941 943 4470
E-mail: stephan.baeu...@chemie.uni-regensburg.de
Internet: 
www-dick.chemie.uni-regensburg.de/group/stephan_baeurle/9,0,group,index,0.html

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[gmx-users] QMMM Compilation

2011-12-02 Thread Ravi Kumar Venkatraman

Dear All,
  Is it possible to compile Gaussian 09 Linux with gromacs
4.5.4. If at all please help me in this regard.

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

+91-9686933963.*
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[gmx-users] A special case of cutoffs related to mdrun with -rerun option

2011-12-02 Thread Ioannis Beis


Dear GROMACS users,

I am interested in using mdrun of a special version of GROMACS 4.0.2  
made by Ollila et. al with -rerun option, made so that it can allow  
calculations of properties related to local pressure in lipid bilayer  
systems. I have used GROMOS54a7 with Poger parameters, but among other  
slight modifications I have used PME instead of reaction field with  
rcoulomb=0.9 and maintained the twin range cutoff used in the original  
study for van der Waals, using rlist=0.9 (instead of the original 0.8)  
and rvdw=1.4. The inner sphere neighborlist is updated every step,  
whereas the outer sector neighborlist every 5 steps.


The mdrun with -rerun flag of this package does not support PME,  
therefore the tpr file has to be reassembled without it. Instead, much  
larger plain cutoff than 1.8 alone has been shown by Sonne et al. to  
give close enough results to short cutoffs used together with PME, at  
least in a qualitative manner.


I can thereby use rcoulomb=2.0 for the purposes of the -rerun, but  
this no longer allows the twin range cutoff scheme. I tried to check  
if there could be some trick to be done with rlistlong (although I was  
almost sure there wouldn't be anything and that rlistlong just serves  
for switch/shift functions), but as far as my searching is concerned  
it didn't even exist as an option in GROMACS 4.0.2 (I assume that twin  
range cutoff was still supported but rlistlong would be automatically  
placed in the max(rcoulomb,rvdw).


Therefore my current problem is about the reliability of -rerun with  
plain vdw cutoff, while in the original simulation twin range cutoff  
was used. Is there any study comparing the results of the two  
different schemes mentioned above for GROMOS simulations? What would  
the consequenses in the physics be and how would the choice of the  
cutoff radius and number of steps affect the results? If someone  
really wants to obtain those calculations, what would be the best  
compromise?


If anyone has another recommendation about obtaining lateral presure  
profiles and associated properties by lipid bilayer simulations, such  
that would be compatible with my algorithm choices, please let me know.


I am grateful in advance.

Best regards,
Ioannis

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Re: [gmx-users] Pdb2gmx with Amber99SB-ILDN

2011-12-02 Thread Justin A. Lemkul




Alberto Arrigoni wrote:

Dear gmx-users,
I encountered a problem using pdb2gmx with Amber99SB-ILDN when I tried 
to use the -ter flag in order to select "none" as termini state.
Pdb2gmx simply ignores -ter, and doesn't prompt the list of entries for 
termini selection.


Has anyone else had this kind of problem?



This is the way the AMBER force fields work; they are different from all the 
others.  All potential terminal residues and caps are listed in the 
aminoacids.rtp file.


-Justin

--


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


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Re: [gmx-users] Re: Re: couple-moltype of FEP (Justin A. Lemkul)

2011-12-02 Thread Justin A. Lemkul




Chunxia Gao wrote:

Dear Justin:

What I mean is can I calculate the free energy of restraining the ligand in the 
binding site, since I put on distance restraint to the ligand and the protein?



Ah, now I see.  I'm not sure, but I know the answer is out in the literature 
somewhere; various types of restraints are implemented in free energy 
calculations fairly routinely.


-Justin


Regards
Chunxia

Chunxia Gao wrote:

Dear Justin,

If I apply the pull code to the distance restraints, can I calculate the free 
energy of those restraints through g_bar? In what way?



The pull code and free energy code are independent.  I see no reason why you
could not proceed in the same manner as the free energy tutorial describes, but
with the addition of your restraint.


and the pull code can only be applied to distance restraints, right? not angle 
or dihedral restraints?



Correct.

-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


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[gmx-users] Harmonic potentials -- Lagrangian multipliers

2011-12-02 Thread Emanuel Peter

Dear Gromacs Users,

Following question -
Are bonded intramolecular interactions also solved
by Lagrangian multipliers, in case of harmonic
potentials in Gromacs ?
Could you please give me some reference or hint.

Thanks for your kind advice.

Emanuel Peter



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Re: [gmx-users] compiling with the pathscale compiler hangs on gmx_rms.c.o

2011-12-02 Thread Szilárd Páll

Hi,

I tried a Pathscale 4.0.12 nightly and except a few warnings
compilation went fine. I don't have 4.0.11 around, though.

However, mdrun segfaults at the very end of the run while generating
the cycle and time counter table. I don't have time to look into this,
but I'll get back to the issue when I'll have a bit of time to spare.

Cheers,
--
Szilárd



On Wed, Nov 30, 2011 at 9:44 PM, Chris Neale  wrote:
> Dear users:
>
> My compilation with the pathscale compiler hangs for over an hour on the
> gmx_rms.c.o file (or perhaps the one that comes next).
>
> [ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_principal.c.o
> [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_polystat.c.o
> [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_potential.c.o
> [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rama.c.o
> [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rdf.c.o
> [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rms.c.o
> [hangs here]
>
> I compiled like this:
>
> module purge
> module load pathscale/4.0.11
> module load openmpi_pathscale64/1.4.3_ofed
> module load cmake/2.8.5
> export CCDIR=/opt/ekopath/4.0.11/bin
>
> ## set the location of the single precision FFTW isntallation
> export FFTW_LOCATION=/home/nealechr/exe/pathscale/fftw-3.1.2/exec
>
> # Nothing below this line usually needs to be changed
>
> export CXX=pathCC
> export CC=pathcc
>
> cmake ../source/ \
>      -DFFTW3F_INCLUDE_DIR=$FFTW_LOCATION/include \
>      -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f.a \
>      -DCMAKE_INSTALL_PREFIX=$(pwd) \
>      -DGMX_X11=OFF \
>      -DCMAKE_CXX_COMPILER=${CCDIR}/pathCC \
>      -DCMAKE_C_COMPILER=${CCDIR}/pathcc \
>      -DGMX_PREFER_STATIC_LIBS=ON \
>      -DGMX_MPI=OFF
>
>
> make
>
> make install
>
> #
>
> If anybody has successfully compiled with the pathscale compiler, I would
> love to hear any suggestions that you can offer.
>
> I have tried 3 fresh installations, and I have also tried cntrl^C and then
> run make again without a clean. It's always the same.
>
> Thank you,
> Chris.
>
> --
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[gmx-users] PhD position

2011-12-02 Thread Kukol, Andreas

This a PhD position suitable for EU or UK permanent residents only:

Part-time PhD combined with Technical Officer at the University of 
Hertfordshire, United Kingdom, closing date 3rd of January 2012

In the area of bioinformatics/computational biochemistry/computational biology
£8112 - £9910 per annum salary for the 50% part-time technical officer

We are looking for a molecular/computational biologist/biochemist or 
bioinformatician who will provide specialist technical support for our teaching 
and research in computational biology/bioinformatics. This post is combined 
with a research studentship that according to the candidate's interests may 
focus on 1) the analyis of the evolutionary conservation of influenza virus 
proteins aiming at the discovery of novel antiviral drugs, or 2) the 
investigation of structure and dynamics of the cardiac 
sodium-pump/phospholemman complex. Both projects may involve comparative/ 
homology modelling, molecular dynamics simulations and molecular docking 
techniques. LINUX workstations and a high-performance computer cluster provide 
an excellent research environment (further details and how to apply: 
https://sites.google.com/site/bioherts/home/jobs). 

For informal enquiries please contact Dr. Andreas Kukol (a.ku...@herts.ac.uk).
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Re: [gmx-users] compiling with the PGI compiler

2011-12-02 Thread Szilárd Páll

Hi,

Pathscale seems to be as fast as gcc 4.5 on AMD Barcelona and the
-march=barcelona option unfortunately doesn't seem to help much.
However, I didn't try any other compiler optimization options.

We do have several Magny-Cours machines around we can benchmark on,
but thanks for the offer!

Cheers,
--
Szilárd



On Fri, Dec 2, 2011 at 2:24 AM,   wrote:
> Dear Szilárd:
>
> Thank you for the advice. I made a mistake when I said that I was using new
> Xeons. The new cluster is actually composed of AMD Opteron Magny-cours 6172
> (12-cores at 2.1 or 2.2 GHz grouped as 24-cores per node). It was because of
> the AMD architecture that I was trying with the pathscale and PGI compilers
> in addition to Intel. For the one system that I have checked, the intel
> compilation is 20% faster than the pathscale compilation, although I didn't
> provide any special compilation options to either. I will continue to look
> into using pathscale optimizations for gromacs on AMDs.
>
> If you are still interested in benchmark speeds on the opterons, then please
> point me to system and mdp files that people are using nowadays for
> comparisons and I will reply back with the benchmark information.
>
> Thank you,
> Chris.
>
> -- original message --
>
> Hi,
>
> I've personally never heard of anybody using gromacs compiled with PGI.
>
>> I am using a new cluster of Xeons and, to get the most efficient
>> compilation, I have compiled gromacs-4.5.4 separately with the intel,
>> pathscale, and pgi compilers.
>
>
> I did try Pathscale a few months ago and AFAIR it wasn't very
> difficult to get it working - although I do remember getting some
> segfaults from time to time. The Intel Compiler support in CMake is
> kind of broken in 4.5, you need to fiddle with the flags a bit, but it
> should be quite straightforward.
>
>> With the pgi compiler, I am most concerned about this floating point
>> overflow warning:
>>
>> ...
>> [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o
>> [ 19%] Building C object
>> src/gmxlib/CMakeFiles/gmx.dir/trajana/centerofmass.c.o
>> [ 19%] Building C object
>> src/gmxlib/CMakeFiles/gmx.dir/trajana/nbsearch.c.o
>> PGC-W-0129-Floating point overflow. Check constants and constant
>> expressions
>>
>> (/home/nealechr/exe/pgi/gromacs-4.5.4/source/src/gmxlib/trajana/nbsearch.c:
>> 166)
>
>
> That looks like a bug, in case of real==float HUGE_VALF should be used
> instead of HUGE_VAL.
>
>> PGC/x86-64 Linux 11.8-0: compilation completed with warnings
>> [ 19%] Building C object
>> src/gmxlib/CMakeFiles/gmx.dir/trajana/displacement.c.o
>> [ 19%] Building C object
>> src/gmxlib/CMakeFiles/gmx.dir/trajana/position.c.o
>> ...
>>
>>
>> There are also a lot of warnings about a type cast, which seems less like
>> a
>> real problem:
>
>
> Looks like all of them are enum to string-related stuff, they are harmless.
>
>> I compiled like this:
>>
>> module purge
>> module load pgi64/11.8 openmpi_pgi64/1.4.3_ofed
>> module load cmake/2.8.5
>> export CCDIR=/opt/pgi/linux86-64/11.8/bin
>>
>> ## set the location of the single precision FFTW isntallation
>> export FFTW_LOCATION=/home/nealechr/exe/pgi/fftw-3.1.2/exec
>>
>> # Nothing below this line usually needs to be changed
>>
>> export CXX=pgCC
>> export CC=pgcc
>>
>> cmake ../source/ \
>>     -DFFTW3F_INCLUDE_DIR=$FFTW_LOCATION/include \
>>     -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f.a \
>>     -DCMAKE_INSTALL_PREFIX=$(pwd) \
>>     -DGMX_X11=OFF \
>>     -DCMAKE_CXX_COMPILER=${CCDIR}/pgCC \
>>     -DCMAKE_C_COMPILER=${CCDIR}/pgcc \
>>     -DGMX_PREFER_STATIC_LIBS=ON \
>>     -DGMX_MPI=OFF
>>
>>
>> make
>>
>> make install
>
>
> That looks fine, if you're benchmarking you might want to try the arch
> specific flags - I assume PGI does have something, even if not
> specific for Xeon E5.
>
>> ##
>>
>> I don't get any similar errors with the intel or pathscale compilers
>> (although intel gives me "icc: command line warning #10159: invalid
>> argument
>> for option '-m'" a lot) and the pathscale compilation appears to be hung
>> on
>
>
> Yeah, as I sad that's kind of broken.
>
>> If anybody has run into this warning, or knows enough to be sure that I
>> don't need to worry about it during mdrun (it seems to be in an analysis
>> file, but I'm not entirely sure), then I would be happy to hear about it.
>> A
>> gmx-users search for PGI returned zero results. I saw something here, but
>> it
>> was not very specific about the problem with pgi (
>> http://www.levlafayette.com/node/175 ).
>
>
> The overflow error is in the trajectory analysis tool's source files
> and doesn't concern mdrun (btw, you can do make mdrun and even make
> install-mdrun ;).
>
> Would it be possible for you to share some performance numbers you're
> getting on the E5?
>
> Cheers,
> --
> Szilárd
>
>> Thank you,
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromac

[gmx-users] postdoctoral vacancy in computational biochemistry/biophysics

2011-12-02 Thread David van der Spoel


On behalf of my colleague:

This is to announce a postdoctoral vacancy in computational 
biochemistry/biophysics in the Kamerlin lab at Uppsala University. The 
focus of our research is on evolutionary based protein redesign, using 
in silico approaches to navigate sequence space. The position is 
available from early January (or as soon as possible thereafter), and we 
are looking for exceptionally driven and talented researchers to join us 
to work in this highly competitive research area.


Further information about the vacancy can be found here:

http://xray.bmc.uu.se/kamerlin/?page=Vacancies

To apply, send a CV, publications list, brief overview of research 
interests and contact details of three people who can provide letters of 
recommendation directly to Lynn Kamerlin at kamerlin[at]icm.uu.se



--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] Pdb2gmx with Amber99SB-ILDN

2011-12-02 Thread Alberto Arrigoni

Dear gmx-users,
I encountered a problem using pdb2gmx with Amber99SB-ILDN when I tried to
use the -ter flag in order to select "none" as termini state.
Pdb2gmx simply ignores -ter, and doesn't prompt the list of entries for
termini selection.

Has anyone else had this kind of problem?

Alberto
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[gmx-users] Re: Re: couple-moltype of FEP (Justin A. Lemkul)

2011-12-02 Thread Chunxia Gao

Dear Justin:

What I mean is can I calculate the free energy of restraining the ligand in the 
binding site, since I put on distance restraint to the ligand and the protein?

Regards
Chunxia

Chunxia Gao wrote:
> Dear Justin,
>
> If I apply the pull code to the distance restraints, can I calculate the free 
> energy of those restraints through g_bar? In what way?
>

The pull code and free energy code are independent.  I see no reason why you
could not proceed in the same manner as the free energy tutorial describes, but
with the addition of your restraint.

> and the pull code can only be applied to distance restraints, right? not 
> angle or dihedral restraints?
>

Correct.

-Justin

--

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

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[gmx-users] grompp error for CNT simulation

Re: [gmx-users] Check for bad contacts and/or reduce the timestep

Re: [gmx-users] Check for bad contacts and/or reduce the timestep

Re: [gmx-users] Check for bad contacts and/or reduce the timestep

Re: [gmx-users] Check for bad contacts and/or reduce the timestep

Re: [gmx-users] Check for bad contacts and/or reduce the timestep

Re: [gmx-users] Check for bad contacts and/or reduce the timestep

[gmx-users] Check for bad contacts and/or reduce the timestep

Re: [gmx-users] A special case of cutoffs related to mdrun with -rerun option

[gmx-users] Half double pair list method in GROMACS [update]

Re: [gmx-users] Half double pair list method in GROMACS [update]

Re: [gmx-users] QM calculation

[gmx-users] QM calculation

Re: [gmx-users] can not restart a simulation from the checkpoint file

Re: [gmx-users] Re: restraints between two molecules

[gmx-users] Re: restraints between two molecules

[gmx-users] can not restart a simulation from the checkpoint file

Re: [gmx-users] restraints between two molecules

[gmx-users] restraints between two molecules

[gmx-users] Job announcement at University of Regensburg

[gmx-users] QMMM Compilation

[gmx-users] A special case of cutoffs related to mdrun with -rerun option

Re: [gmx-users] Pdb2gmx with Amber99SB-ILDN

Re: [gmx-users] Re: Re: couple-moltype of FEP (Justin A. Lemkul)

[gmx-users] Harmonic potentials -- Lagrangian multipliers

Re: [gmx-users] compiling with the pathscale compiler hangs on gmx_rms.c.o

[gmx-users] PhD position

Re: [gmx-users] compiling with the PGI compiler

[gmx-users] postdoctoral vacancy in computational biochemistry/biophysics

[gmx-users] Pdb2gmx with Amber99SB-ILDN

[gmx-users] Re: Re: couple-moltype of FEP (Justin A. Lemkul)

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