Re: [gmx-users] (no subject)

2017-07-09 Thread Mark Abraham 
Hi,

You can't do that with normal gromacs. But googling may reveal options.

Mark

On Sat, 8 Jul 2017 14:07 Shivangi Agarwal 
wrote:

> hello to all
>
> How can i perform PBSA in gromacs
>
>
> Thanks in advance
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Re: [gmx-users] protein protein interaction: side chain contribution

2017-07-09 Thread Tushar Ranjan Moharana 
Hi Justin,
Thanks a lot for the valuable advice.






"A society with free knowledge is better than a society with free food"

On Fri, Jul 7, 2017 at 3:04 PM, Tushar Ranjan Moharana <
tusharranjanmohar...@gmail.com> wrote:

> Hi Justin,
> Thanks a lot for the advice. It looks like I had put one atom in the wrong
> index group. After correction my results looks as follows:
>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
> 
> ---
> Coul-SR:161TYR-161TYR_com   -75.05491.717.82618.26634
> (kJ/mol)
> LJ-SR:161TYR-161TYR_com-47.94641.510.25662.55572
> (kJ/mol)
> Coul-14:161TYR-161TYR_com  0  0  0  0
> (kJ/mol)
> LJ-14:161TYR-161TYR_com   0  0  0  0
> (kJ/mol)
>
> I think it should be fine as the result didn't change much (other than the
> LJ-14).
>
> As per your suggestion, calculation of kinetic energy by gmx traj or
> energy(after saving only desired atoms in the trajectory) are not
> meaningful. Is there any way to compute it?
>
> Thanks a lot for your time and effort.
>
>
> "A society with free knowledge is better than a society with free food"
> --
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
>



-- 
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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Re: [gmx-users] Fwd: Regarding getting the trajectories at certain time intervals

2017-07-09 Thread Mark Abraham 
Hi,

Look at "gmx help trjconv" ;-) The b and e options aren't measured in
frames, and another option is available for selecting frames at different
time intervals.

Mark

On Mon, 10 Jul 2017 06:06 Dilip H N  wrote:

> Hello,
> I have ran an md simulation  which has 6 frames (3000 / 500 ie.,
> nsteps / nstxout, nsteps = 0.001 * 3000 = 3 ps),  and now i need to
> get the trajectories, but this will be of very huge data (which gives
> trajectories of interval of every 0.5 ps)...So how can i get the
> trajectories from intial to final run but with interval of say 1000 ps , i
> tried with the following command as :-
>
> gmx trjconv -f md.trr -s md.tpr -o mdtrj.gro -b 0 -e 6
>
> but i am getting trajectories for every 0.5 ps interval, but i need it for
> say 1000 ps interval.
> How can i do this..??
>
> Thank you...
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
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[gmx-users] Fwd: Regarding getting the trajectories at certain time intervals

2017-07-09 Thread Dilip H N 
Hello,
I have ran an md simulation  which has 6 frames (3000 / 500 ie.,
nsteps / nstxout, nsteps = 0.001 * 3000 = 3 ps),  and now i need to
get the trajectories, but this will be of very huge data (which gives
trajectories of interval of every 0.5 ps)...So how can i get the
trajectories from intial to final run but with interval of say 1000 ps , i
tried with the following command as :-

gmx trjconv -f md.trr -s md.tpr -o mdtrj.gro -b 0 -e 6

but i am getting trajectories for every 0.5 ps interval, but i need it for
say 1000 ps interval.
How can i do this..??

Thank you...

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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[gmx-users] Regarding getting the trajectories at certain time intervals

2017-07-09 Thread Dilip H N 
Hello,
I have ran an md simulation  which has 6 frames (3000 / 500 ie.,
nsteps / nstxout, nsteps = 0.001 * 3000 = 3 ps),  and now i need to
get the trajectories, but this will be of very huge data (which gives
trajectories of interval of every 0.5 ps)...So how can i get the
trajectories from intial to final run but with interval of say 1000 ps , i
tried with the following command as :-

gmx trjconv -f md.trr -s md.tpr -o mdtrj.gro -b 0 -e 6

but i am getting trajectories for every 0.5 ps interval, but i need it for
say 1000 ps interval.
How can i do this..??

Thank you...

-- 
With Best Regards,

DILIP.H.N
Ph.D Student
-- 
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Re: [gmx-users] Can't locate state.cpt for gmx mdrun

2017-07-09 Thread Yonatan Zelnik 
Hello Justin,

I see now why there aren't checkpoint files being produced. I guess I
wanted to checkpoint files, in case the EM didn't converge in n steps, then
I could keep going from that point instead of starting over with >n steps.

Thanks for the response.

Yonatan

On Fri, Jul 7, 2017 at 8:14 PM, Justin Lemkul  wrote:

>
>
> On 7/7/17 8:00 PM, Yonatan Zelnik wrote:
>
>> Hello,
>>
>> I am running an energy minimization script that works quite well, except
>> that I can't find any of the checkpoint files that mdrun is supposed to
>> provide. I've been looking through the docs for a while, and I can't seem
>> to find a reason. I have tried the script on multiple systems, and
>> multiple
>> installations of gromacs (I am using 5.1.4 with MPI).
>>
>> Here is the mdrun command I am using:
>>
>> mdrun_sp -v -s em.tpr -o mintraj -g mdlog -c solvated.gro -x solvated_traj
>> -cpo state.cpt -cpt 1.
>>
>> The -cpt 1 should give mean that a .cpt file is recorded every minute, but
>> no file is found in the directory where I run the script from. mdrun works
>> well otherwise.
>>
>> I'd appreciate any help.
>>
>>
> Energy minimization doesn't produce checkpoint files.  There's no point -
> there are no velocities or state variables to save.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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-- 
Yonatan Zelnik
yonatanzel...@gmail.com
408.644.3931
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Re: [gmx-users] Check for bad contacts and/or reduce the timestep

2017-07-09 Thread Mark Abraham 
Hi,

Parrinello Rahman is not a great choice for the first stages of
equilbration, as suggested at e.g.
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation.
Your choice of temperature coupling groups is also an anti-pattern, e.g.
http://www.gromacs.org/Documentation/Terminology/Thermostats. These effects
are stronger when the temperature (ie KE) is increased despite a constant
time step.

Mark

On Sun, Jul 9, 2017 at 4:21 PM Md. Imrul Reza Shishir <
imrul.reza.shis...@gmail.com> wrote:

> Dear all
> I have simulated my system 7 different temperature from 300K~500K.Every
> time I simulated for 10ns. But when I run the simulation above 500K (I.e
> 530K/550K/560K) the simulation was crash in NPT equilibrium stage with
> following warning.
>
> *step XXX: Water molecule starting at atom  can not be settled. Check
> for bad contacts and/or reduce the timestep if appropriate.*
>
> ​What should be cause for that?
>
> my energy minimization  ​stage:
> *minim.mdp*
> title= OPLS Cellulose EM_steep simulation
> integrator= steep
> emtol= 1000.0 kJ/mol/nm
> emstep  = 0.0001
> nsteps= 5
> nstlist= 10
> cutoff-scheme= verlet
> ns-type= grid
> coulombtype= PME
> pme-order= 4
> fourierspacing= 0.12
> rlist  = 1.2
> rlistlong= 1.4
> rcoulomb= 1.2
> rvdw= 1.2
> pbc= xyz
> periodic-molecules  = yes
> constraints= none
> vdwtype   = Cut-off
>
> my npt equilibrium:
> *npt.mdp*
>
> title= Cellulose OPLS-AA NPT equilibration
> define= -DPOSRE
> integrator= md
> nsteps= 25
> dt= 0.002
> comm-mode= Linear
> comm-grps   = System
> nstcomm= 100
> pbc= xyz
> nstxout= 500
> nstvout= 500
> nstenergy= 500
> nstlog= 500
> nstxout-compressed  = 500
> compressed-x-grps   = System
> cutoff-scheme   = verlet
> ns-type= grid
> nstlist= 10
> rlist  = 1.2
> rlistlong= 1.4
> coulombtype= PME
> pme-order= 4
> rcoulomb= 1.2
> vdwtype   = Cut-off
> rvdw= 1.2
> fourierspacing= 0.12
> DispCorr= EnerPres
> continuation= yes
> constraint-algorithm= lincs
> constraints= all-bonds;
> lincs-iter= 1
> lincs-order= 4
> tcoupl= v-rescale
> tc-grps= OtherWaterIon
> tau_t= 0.10.10.1
> ref_t= 550 550550
> pcoupl= Parrinello-Rahman
> pcoupltype= isotropic
> tau-p= 1.0
> ref-p= 1.0
> compressibility = 4.5e-5
> refcoord_scaling= com;
>
> ; Velocity generation
> gen-vel= no
>
>
> ​Thank you in advance. ​
>
> --
> *Md Imrul Reza Shishir*
> Master Student
> ​
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[gmx-users] how to creat ligand topology to minimize in vacuo in the absence of the protein

2017-07-09 Thread ‪farial tavakoli‬ ‪ 
Dear gmx-usersI need to create a topology for my designed drug as a ligand to 
minimize it in the vacuo in the absence of the protein. But I dont know how can 
i convert the DRG.itp file which I obtained from PRODRG site to a .top file . I 
searched in the Google and found " Re: minimizing ligand only "but couldnt find 
a clear explanation for that.Could anyone advice me to fix this problem? sorry 
if the request seems to be trivial. but i really cant understand what to do.
Thanks in advance
Farial

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

2017-07-09 Thread Md. Imrul Reza Shishir 
Dear all
I have simulated my system 7 different temperature from 300K~500K.Every
time I simulated for 10ns. But when I run the simulation above 500K (I.e
530K/550K/560K) the simulation was crash in NPT equilibrium stage with
following warning.

*step XXX: Water molecule starting at atom  can not be settled. Check
for bad contacts and/or reduce the timestep if appropriate.*

​What should be cause for that?

my energy minimization  ​stage:
*minim.mdp*
title= OPLS Cellulose EM_steep simulation
integrator= steep
emtol= 1000.0 kJ/mol/nm
emstep  = 0.0001
nsteps= 5
nstlist= 10
cutoff-scheme= verlet
ns-type= grid
coulombtype= PME
pme-order= 4
fourierspacing= 0.12
rlist  = 1.2
rlistlong= 1.4
rcoulomb= 1.2
rvdw= 1.2
pbc= xyz
periodic-molecules  = yes
constraints= none
vdwtype   = Cut-off

my npt equilibrium:
*npt.mdp*

title= Cellulose OPLS-AA NPT equilibration
define= -DPOSRE
integrator= md
nsteps= 25
dt= 0.002
comm-mode= Linear
comm-grps   = System
nstcomm= 100
pbc= xyz
nstxout= 500
nstvout= 500
nstenergy= 500
nstlog= 500
nstxout-compressed  = 500
compressed-x-grps   = System
cutoff-scheme   = verlet
ns-type= grid
nstlist= 10
rlist  = 1.2
rlistlong= 1.4
coulombtype= PME
pme-order= 4
rcoulomb= 1.2
vdwtype   = Cut-off
rvdw= 1.2
fourierspacing= 0.12
DispCorr= EnerPres
continuation= yes
constraint-algorithm= lincs
constraints= all-bonds;
lincs-iter= 1
lincs-order= 4
tcoupl= v-rescale
tc-grps= OtherWaterIon
tau_t= 0.10.10.1
ref_t= 550 550550
pcoupl= Parrinello-Rahman
pcoupltype= isotropic
tau-p= 1.0
ref-p= 1.0
compressibility = 4.5e-5
refcoord_scaling= com;

; Velocity generation
gen-vel= no


​Thank you in advance. ​

-- 
*Md Imrul Reza Shishir*
Master Student
​
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