[gmx-users] coordinated of center of mass
Hi all: I have a multiconponent system and for each component I wish to know the center of mass (COM) coordinates. I know that g_dist can give me the distances between the center of masses, but I do not want only the distances, I and interested in the x y and z coordinates as well. Could anyone please direct me to a gromacs utility or option that can help me achieve this? I looked in the manual but could not find my answer. Thanks, SN -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_wham issue
Hi all: I have been trying to figure out a problem in our umbrella sampling simulation. We are simulating a coarse grained protein passing through a coarse grained lipid bilayer. In the pull simulation, the protein was made to move from +z=6 nm of the box through the lipid layer at z=0 to z= -4 nm. For umbrella sampling 74 windows where chosen with a 0.2 nm. When we look at the histogram from the g_wham, we get good overlap before the protein touches the bilayer and after it has exited the bilayer. We also get the PMF curves for these regions. However, when the the protein is in contact, and barely touching the bilayer, the g_wham analysis gives 0.000E+0 for PMF and no histograms in the output. We have tried decreasing the window size from 0.2 to 0.1 nm but it does not help. I looked at the gmx-user list to find a possible solution to this issue but could not find any helpful clue. Could anyone point me to what should be done and what is possibly going wrong? Thanks, SNC -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Slicing .gro file geometry
Dear all: I would like to create a smaller simulation box (from a larger simulation box in .gro file) by removing atoms in the x, y and z-directions and saving the subset system into a new .gro file (smaller box and subset of molecules) For example: from original box 10x10x10 nm3 write coordinates of the atoms that form 5x5x 5 nm3 core of the larger cube. I tried editconf and trjconv but they both do not have any such option. Is there another utility in gromcas that can do this? Thanks, SN -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to get higher precision values for g_velacc
I want the velocity autocorrelation output in double precision. How can I get that? Thanks, SN --- On Thu, 4/28/11, Mark Abraham wrote: From: Mark Abraham Subject: Re: [gmx-users] how to get higher precision values for g_velacc To: "Discussion list for GROMACS users" Date: Thursday, April 28, 2011, 8:21 PM On 4/29/2011 4:48 AM, shivangi nangia wrote: > Dear gmx users, > > I am using g_velacc to calculate the velocity auto correlation. The output I > am getting in .xvg file is much lower precision than I require. > Is there a way to get the values in higher precision? Depends what you've done so far, but either you need to collect velocity data more often, or in double precision, or both. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Issues with NEMD simulations
Dear all, 1. I am performing MD simulation of a MARTINI coarse grained polymeric chains (named NGL in my mdp file below) in Coarse grained water (named W in mdp file below). 2. My equilibration and MD runs have been running perfectly until now. I have started doing NEMD simulations to get viscosity. The starting structure for NEMD came from an equilibrated system. 3. I am pretty sure that the error is in the mdp file. I am new to NEMD so it will be great if I can get some pointers of solving the issue. Is there a NEMD gromacs tutorial on the web? Here is the full mdp file for the NEMD run: title = Martini cpp = /usr/bin/cpp integrator = md tinit = 0.0 dt = 0.01 nsteps = 500 nstcomm = 1 comm-grps = system nstxout = 10 nstvout = 10 nstfout = 10 nstlog = 10 nstenergy = 10 nstxtcout = 2500 xtc_precision = 100 xtc-grps = energygrps = system nstlist = 1 ns_type = grid pbc = xyz rlist = 1.7 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r = 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = EnerPres tcoupl = V-rescale tc-grps = NGL W tau_t = 1.0 1.0 ref_t = 300. 300. Pcoupl = No Pcoupltype = Isotropic tau_p = 1.0 compressibility = 1e-5 ref_p = 1.0 gen_vel = Yes gen_temp = 300 gen_seed = 473529 constraints = None constraint_algorithm = Lincs unconstrained_start = no lincs_order = 1 lincs_warnangle = 30 ; Non-equilibrium MD stuff acc-grps = NGL W accelerate = 0.1 0 0 -0.1 0 0 freezegrps = freezedim = cos_acceleration = 0.1 deform = Best, SN Dr. Shikha Nangia 201D Chemistry Building Department of Chemistry The Pennsylvania State University University Park, PA 16802 Phone(o): 814-863-0289 Phone(cell): 612-599-9449 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Issues of NEMD + 1/viscosity from g_energy
Thanks again, Justin.
Dear all,
I figured out the problem. Error was in my mdp file options. I did not specify
the acc-groups correctly. I can get 1/viscosity using g_energy.
However, once the acc-groups are specified, now the NEW issue is not being able
to run my job correctly.
I get the following errors:
Step 376, time 7.52 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.006964, max 0.163855 (between atoms 861 and 859)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
---
---
Program mdrun, VERSION 4.5.4
Source code file: domdec.c, line: 4124
Fatal error:
A charge group moved too far between two domain decomposition steps
---
I did not have any problems in my equilibrium simulations...this is happening
in NEMD simulations.
Here is my .mdp file
title = Martini
cpp = /usr/bin/cpp
integrator = md
tinit = 0.0
dt = 0.01
nsteps = 500
nstcomm = 1
comm-grps = system
nstxout = 10
nstvout = 10
nstfout = 10
nstlog = 10
nstenergy = 10
nstxtcout = 2500
xtc_precision = 100
xtc-grps =
energygrps = system
nstlist = 1
ns_type = grid
pbc = xyz
rlist = 1.7
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = EnerPres
tcoupl = V-rescale
tc-grps = NGL W
tau_t = 1.0 1.0
ref_t = 300. 300.
Pcoupl = No
Pcoupltype = Isotropic
tau_p = 1.0
compressibility = 1e-5
ref_p = 1.0
gen_vel = Yes
gen_temp = 300
gen_seed = 473529
constraints = None
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 1
lincs_warnangle = 30
; Non-equilibrium MD stuff
acc-grps = NGL W
accelerate = 0.1 0 0 -0.1 0 0
freezegrps =
freezedim =
cos_acceleration = 0.1
deform =
Best,
SN
--- On Sat, 4/16/11, Justin A. Lemkul wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] 1/viscosity from g_energy
To: "Discussion list for GROMACS users"
Date: Saturday, April 16, 2011, 3:27 PM
shikha nangia wrote:
> Thanks for your instant reply, Justin.
>
> Dear all,
>
> Please correct me if I am woring herebut...reading through the user-list,
> I gathered that -vis option og g_energy oes not give good results and instead
> cos_accleration should be used from the following reference.
>
>> /@Article{Hess2002b,
> />/ author = {B. Hess},
> />/ title = {Determining the shear viscosity of model liquids from
> />/molecular simulation},
> />/ journal = {J. Chem. Phys.},
> />/ year = 2002,
> />/ volume = 116,
> />/ pages = {209-217}
> />/}
> /
>
> I am trying to get the results of viscosity through cos_acceleration that
> probably are formatted as below (taken from a user-list).
>
>> / Energy Average Err.Est. RMSD
> Tot-Drift
> />/
> ---
> />/ 1/Viscosity / (/ s/kg)
> /
>
>
If the proper output options are not there, then there may have been a problem
in the .mdp file that prevented the correct energy terms from being written.
If present in the .edr file, it should be shown in the list (sorry, I was
thinking of something else). Please post your .mdp file.
-Justin
> Thanks again,
>
> SN
>
> --- On *Sat, 4/16/11, Justin A. Lemkul //* wrote:
>
>
> From: Justin A. Lemkul
> Subject: Re: [gmx-users] 1/viscosity from g_energy
> To: "Discussion list for GROMACS users"
> Date: Saturday, April 16, 2011, 3:06 PM
>
>
>
> shikha nangia wrote:
> > Dear gmx-users,
> >
> > I am trying to obtain 1/viscosity values for my system after
> using the cos_acceleration option in the mdp file. My gromacs
> version is 4.5.4 released on March 21, 2011.
> > When I try using the g_energy option for my file
> >
> > g_energy -f ener.edr -o o
Re: [gmx-users] 1/viscosity from g_energy
Thanks for your instant reply, Justin.
Dear all,
Please correct me if I am woring herebut...reading through the user-list, I
gathered that -vis option og g_energy oes not give good results and instead
cos_accleration should be used from the following reference.
>@Article{Hess2002b,
> author = {B. Hess},
> title = {Determining the shear viscosity of model liquids from
>molecular simulation},
> journal ={J. Chem. Phys.},
> year = 2002,
> volume = 116,
> pages = {209-217}
>}
I am trying to get the results of viscosity through cos_acceleration that
probably are formatted as below (taken from a user-list).
> Energy Average Err.Est. RMSD Tot-Drift
> ---
> 1/Viscosity ( s/kg)
Thanks again,
SN
--- On Sat, 4/16/11, Justin A. Lemkul wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] 1/viscosity from g_energy
To: "Discussion list for GROMACS users"
Date: Saturday, April 16, 2011, 3:06 PM
shikha nangia wrote:
> Dear gmx-users,
>
> I am trying to obtain 1/viscosity values for my system after using the
> cos_acceleration option in the mdp file. My gromacs version is 4.5.4 released
> on March 21, 2011.
> When I try using the g_energy option for my file
>
> g_energy -f ener.edr -o outfile.xvg
>
> I get the following options
>
> End your selection with an empty line or a zero.
> ---
> 1 Bond 2 Angle 3 Improper-Dih. 4 LJ-(SR)
> 5 Disper.-corr. 6 Coulomb-(SR) 7 Potential 8 Kinetic-En.
> 9 Total-Energy 10 Conserved-En. 11 Temperature 12 Pres.-DC
>13 Pressure 14 Box-XX 15 Box-YY 16 Box-ZZ
>17 Box-YX 18 Box-ZX 19 Box-ZY 20 Volume
>21 Density 22 pV 23 Enthalpy 24 Vir-XX
>25 Vir-XY 26 Vir-XZ 27 Vir-YX 28 Vir-YY
>29 Vir-YZ 30 Vir-ZX 31 Vir-ZY 32 Vir-ZZ
>33 Pres-XX 34 Pres-XY 35 Pres-XZ 36 Pres-YX
>37 Pres-YY 38 Pres-YZ 39
Pres-ZX 40 Pres-ZY 41 Pres-ZZ 42 #Surf*SurfTen 43
Mu-X 44 Mu-Y 45 Mu-Z 46 T-System 47
Lamb-System
>
> I am not sure which option (1 to 47) gives 1/viscosity. I tried looking
> through the manual and searching the user list but could not resolve the
> issue.
>
> Please let me know what am I missing here.
>
Use -vis rather than -o.
-Justin
> Thanks,
> SN
>
>
--
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] 1/viscosity from g_energy
Dear gmx-users, I am trying to obtain 1/viscosity values for my system after using the cos_acceleration option in the mdp file. My gromacs version is 4.5.4 released on March 21, 2011. When I try using the g_energy option for my file g_energy -f ener.edr -o outfile.xvg I get the following options End your selection with an empty line or a zero. --- 1 Bond 2 Angle 3 Improper-Dih. 4 LJ-(SR) 5 Disper.-corr. 6 Coulomb-(SR) 7 Potential 8 Kinetic-En. 9 Total-Energy 10 Conserved-En. 11 Temperature 12 Pres.-DC 13 Pressure 14 Box-XX 15 Box-YY 16 Box-ZZ 17 Box-YX 18 Box-ZX 19 Box-ZY 20 Volume 21 Density 22 pV 23 Enthalpy 24 Vir-XX 25 Vir-XY 26 Vir-XZ 27 Vir-YX 28 Vir-YY 29 Vir-YZ 30 Vir-ZX 31 Vir-ZY 32 Vir-ZZ 33 Pres-XX 34 Pres-XY 35 Pres-XZ 36 Pres-YX 37 Pres-YY 38 Pres-YZ 39 Pres-ZX 40 Pres-ZY 41 Pres-ZZ 42 #Surf*SurfTen 43 Mu-X 44 Mu-Y 45 Mu-Z 46 T-System 47 Lamb-System I am not sure which option (1 to 47) gives 1/viscosity. I tried looking through the manual and searching the user list but could not resolve the issue. Please let me know what am I missing here. Thanks, SN -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] stress autocorrelation function
Hello all: I need to calculate stress autocorrelation function for my polymeric system. Is there a way to calculate this using gromacs tools? Thanks, SN -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
