[gmx-users] Gromacs on GPU: GTX or Tesla?
Hi, We want to start using Gromacs on GPU and we are debating whether to purchase GeForce GTX card or Tesla platform. Looking at the published data it seems GTX580 has much impressive performance compared to Tesla C2050, and of course it is much cheaper. Is there a reason to prefer Tesla over GTX for running Gromacs in the short or long term? Thanks, Efrat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: Gromacs on GPU: GTX or Tesla?
Hi, In the long term the Tesla is much more preferable as the GTX would not support certain high end functions. Pls verify these before you purchase one. Also the Tesla C-2070 is the newer one available and with 6.0GB RAM it really gives out great performance. The price is the same. Rgds JSV From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Efrat Exlrod [efrat.exl...@biu.ac.il] Sent: Thursday, August 04, 2011 12:13 PM To: gmx-users@gromacs.org Subject: [gmx-users] Gromacs on GPU: GTX or Tesla? Hi, We want to start using Gromacs on GPU and we are debating whether to purchase GeForce GTX card or Tesla platform. Looking at the published data it seems GTX580 has much impressive performance compared to Tesla C2050, and of course it is much cheaper. Is there a reason to prefer Tesla over GTX for running Gromacs in the short or long term? Thanks, Efrat LEGAL DISCLAIMER Information contained and transmitted by this E-MAIL is proprietary to M/S. CONNOISEUR ELECTRONICS PVT. LTD., or M/S. CONNOISEUR INFOTECH LLC., or M/S. CONNOISEUR INFOTECH depending on the sender of the email. The transmitted E-MAIL is intended for exclusive use by the individual or entity to which it is addressed, and may contain information that is privileged, confidential or exempt from disclosure under applicable law and shall not attach any liability on the originator. If you have reason to belive that you are not the intended recipient of this E-MAIL,or,if you received this E-MAIL in error please inform the sender immediately by reply email destroy the E-MAIL. Any use, distribution, transmission, printing, copying or dissemination of this information in any way or in any manner is strictly prohibited unlawful. The sender belives that this email and its attachment(s) were free of any malicious code(s) when sent. However,infection may have occurred during transmission. By reading the message and opening any attachment, the recipient accepts full responsibility for taking protective and remedial action about viruses and other defects. M/S. CONNOISEUR ELECTRONICS PVT. LTD., or M/S CONNOISEUR INFOTECH LLC., or M/S CONNOISEUR INFOTECH is not liable for any loss or damage arising in any way from this message or its attachment(s). -- 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] Regarding Segmentation fault during mdrun_d
Dear All, I was trying to run NVT equilibration for cyclohexane. When I started running it shows following error Reading file nvt.tpr, VERSION 4.5.4 (double precision) Starting 2 threads Making 1D domain decomposition 2 x 1 x 1 starting mdrun 'Cyclohexane box' 5 steps,100.0 ps. Segmentation fault. Please suggest me something to overcome this. -- 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] Regarding Segmentation fault during mdrun_d
On Thu, Aug 4, 2011 at 3:03 PM, Ravi Kumar Venkatraman ravikumarvenkatra...@gmail.com wrote: Dear All, I was trying to run NVT equilibration for cyclohexane. When I started running it shows following error Reading file nvt.tpr, VERSION 4.5.4 (double precision) Starting 2 threads Making 1D domain decomposition 2 x 1 x 1 starting mdrun 'Cyclohexane box' 5 steps, 100.0 ps. Segmentation fault. Please suggest me something to overcome this. -- 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 try mdrun -pd -- Best Regards, lina -- 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] Regarding Segmentation fault during mdrun_d
On 4/08/2011 5:03 PM, Ravi Kumar Venkatraman wrote: Dear All, I was trying to run NVT equilibration for cyclohexane. When I started running it shows following error Reading file nvt.tpr, VERSION 4.5.4 (double precision) Starting 2 threads Making 1D domain decomposition 2 x 1 x 1 starting mdrun 'Cyclohexane box' 5 steps,100.0 ps. Segmentation fault. Please suggest me something to overcome this. Depends what is going wrong. Consult the .log file. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipoles - averaging
Hello, Is there any way to output the dipole moment averaged over all molecules or for each molecule separately (and not the total dipole moment of the simulation box) ? Apparently the dipole autocorrelation function can be obtained as an average over all molecules with the '-corr mol' option, but from the help info it is not clear, how and if the total dipole moment can be obtained in this way (and in which file Mtot.xvg or aver.xvg ?). Many thanks Andreas -- 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] the density does not stablize
Dear gmxers,
I try to perform NPT MD to obtain the density of system. But the value of
density does not stablize even after over 40 ns. The content of mdp file can be
seen below. How to deal with it? Please give me some hints. Thanks a lot for
any replies.
.mdp file:
title=
cpp= /lib/cpp
include= -I../top
define= ;{-DFLEXIBLE,-DPOSRES}
integrator = md
dt= 0.001
comm_mode = Linear ;{Linear,Angular,No}
nstcomm = 10
nstcalcenergy = 1
nsttcouple = 1
nstpcouple = 1
comm_grps =
nsteps = 2500
nstxout= 1000
nstvout= 1000
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
nstlist= 10
ns_type= grid;{simple,grid}
rlist= 1.0
coulombtype = pme
fourierspacing = 0.12; [0.12 nm]
optimize_fft = yes;{no,yes}
rcoulomb = 1.0
rvdw= 1.0
DispCorr = EnerPres ;{no,EnerPres,Ener}
pbc= xyz; Periodic Boundary Conditions {xyz,no,xy}
tcoupl = berendsen ;no,berendsen,nose-hoover,v-rescale
tc-grps= Other
tau_t= 0.1
ref_t= 600
Pcoupl = berendsen ;{no,berendsen,Parrinello-Rahman}
Pcoupltype = isotropic ;{isotropic,semiisotropic;anisotropic;surface-tension}
tau_p= 0.1
compressibility = 4.5e-5
ref_p= 1.0;the unit is bar(1 bar =10^5 Pa)
gen_vel= no
gen_temp = 600
gen_seed = 173529
constraints = none;{none,hbonds,all-bonds,h-angles,all-angles}
constraint_algorithm = LINCS ;{LINCS,SHAKE}
periodic_molecules = no;{no,yes}
annealing = no ;{no,single,periodic}
annealing_npoints = 11
annealing_time = 0 100 200 300 400 500 600 700 800 900 1000
annealing_temp = 600 580 560 540 520 500 520 540 560 580 600
Best regards,
Dr. Chaofu Wu
--
Department of Chemistry and Materials Science
Hunan University of Humanities, Science and Technology,
Loudi 417000, the People's Republic of China (P.R. China)--
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] the density does not stablize
On 04/08/11, xiaowu759 xiaowu...@qq.com wrote:
Dear gmxers,
I try to perform NPT MD to obtain the density of system. But the value of
density does not stablize even after over 40 ns. The content of mdp file can
be seen below. How to deal with it? Please give me some hints. Thanks a lot
for any replies.
We have no idea whether your judgement that density is not stabilized after
40ns is sound, because you provided no data. Your temperature coupling is to
group Other, which may or may not be reasonable. Your integration time step
is possibly too large for a simulation using no bond constraints. Your initial
density could be so far from correct that reaching equilibrium is infeasible.
You'll need to provide a lot more information to get useful help.
Mark
.mdp file:
title =
cpp = /lib/cpp
include = -I../top
define = ;{-DFLEXIBLE,-DPOSRES}
integrator = md
dt = 0.001
comm_mode = Linear ;{Linear,Angular,No}
nstcomm = 10
nstcalcenergy = 1
nsttcouple = 1
nstpcouple = 1
comm_grps =
nsteps = 2500
nstxout = 1000
nstvout = 1000
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
nstlist = 10
ns_type = grid;{simple,grid}
rlist = 1.0
coulombtype = pme
fourierspacing = 0.12; [0.12 nm]
optimize_fft = yes;{no,yes}
rcoulomb = 1.0
rvdw = 1.0
DispCorr = EnerPres ;{no,EnerPres,Ener}
pbc = xyz; Periodic Boundary Conditions {xyz,no,xy}
tcoupl = berendsen ;no,berendsen,nose-hoover,v-rescale
tc-grps = Other
tau_t = 0.1
ref_t = 600
Pcoupl = berendsen ;{no,berendsen,Parrinello-Rahman}
Pcoupltype =
isotropic ;{isotropic,semiisotropic;anisotropic;surface-tension}
tau_p = 0.1
compressibility = 4.5e-5
ref_p = 1.0;the unit is bar(1 bar =10^5 Pa)
gen_vel = no
gen_temp = 600
gen_seed = 173529
constraints = none;{none,hbonds,all-bonds,h-angles,all-angles}
constraint_algorithm = LINCS ;{LINCS,SHAKE}
periodic_molecules = no;{no,yes}
annealing = no ;{no,single,periodic}
annealing_npoints = 11
annealing_time = 0 100 200 300 400 500 600 700 800 900 1000
annealing_temp = 600 580 560 540 520 500 520 540 560 580 600
Best regards,
Dr. Chaofu Wu
--
Department of Chemistry and Materials Science
Hunan University of Humanities, Science and Technology,
Loudi 417000, the People's Republic of China (P.R. China)
--
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] setting vdw cutoff with specific force-filed?
Yun Shi wrote: Hi all, I am working with GROMOS 53a6 ff in GROMACS 4.5, and I assume a Lennard-Jones interaction function was used for short-range vdw interactions. From the reference paper /A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6/, I found that for example, when rvdw = 1.5nm, the repulsion term of the interaction between two CH1 type atoms (C12ij = 9.85^2) can be calculated as 9.850*9.850 / (1.5^12) = 0.747786 kJ/mol. So I wonder if this value is considered to be small enough to be ignored. In addition, it seems not until 5 nm does the dispersion term become larger than the repulsion term in this case, so would turning on Dispersion Correction between, say 1.5 to 5 nm introduce more errors than turning it off? You should use the cutoff described the authors of the force field, in this case rvdw=1.4. Unless you can demonstrate that by using a different value you can achieve superior results, stick with the specifics of parameterization. I have never seen ill effects of setting rvdw=1.4 and using dispersion correction with this force field. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_membed stops after only one iteration
Hi I am trying to use g_membed to insert a protein into a bilayer. I made some changes to the sample.mdp file downloaded from the authors' homepage. The changes were: - reduced time step to 0.001 ps (instead of 0.002) - changed constraints to hbonds instead of all-bonds. g_membed runs fine, but stops only after one iteration after which the protein is of course shrunk. The command used is: echo 20 16 | g_membed -f membed.tpr -n membed.ndx -xyinit 0.1 -xyend 1.0 -nxy 1000 -maxwarn 10 I am wondering what is going on ? Also, is there a way to parallelize g_membed? -- Maria G. Technical University of Denmark Copenhagen -- 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] Fwd: Regarding segmentation fault
Please leave discussion on the mailing list so that the archives are available
for posterity and that you might get input from more than one person.
Apparently your .log file has been truncated abnormally, but the energy values
reported are clearly indicative of
http://www.gromacs.org/Documentation/Terminology/Blowing_Up See that link for
dealing with it.
Mark
---BeginMessage---
This is what I got from .log file please help me find the error.
---
Input Parameters:
integrator = md
nsteps = 5
init_step= 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 10
comm_mode= Linear
nstlog = 100
nstxout = 100
nstvout = 100
nstfout = 0
nstcalcenergy= 5
nstenergy= 100
nstxtcout= 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 21
nky = 21
nkz = 21
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = Berendsen
nsttcouple = 5
epc = No
epctype = Isotropic
nstpcouple = -1
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1.6
rlistlong= 1.6
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.6
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.6
epsilon_r= 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 1
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
sa_surface_tension = 2.05016
DispCorr = EnerPres
free_energy = no
init_lambda = 0
delta_lambda = 0
n_foreign_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
sc_sigma_min = 0.3
nstdhdl = 10
separate_dhdl_file = yes
dhdl_derivatives = yes
dh_hist_size = 1
dh_hist_spacing = 0.1
nwall= 0
wall_type= 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre= No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter= 20
fc_stepsize = 0
nstcgsteep = 1000
em_stepsize = 0.01
em_tol = 10
niter= 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Lincs
shake_tol= 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel= 0
deform (3x3):
deform[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1= 0
userreal2= 0
userreal3= 0
userreal4= 0
[gmx-users] Hydrogen atoms type
Hi Dear Users! I'm Using MMB to produce initial structures for my simulations. This program creating a .pdb file in output. The output file containing Hydrogen atoms that are not recognized by gromos53a5. I want to edit my pdb file but I can't find anything about hydrogen types in gromos! any suggestion? -- 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] Hydrogen atoms type
Amir Abbasi wrote: Hi Dear Users! I'm Using MMB to produce initial structures for my simulations. This program creating a .pdb file in output. The output file containing Hydrogen atoms that are not recognized by gromos53a5. I want to edit my pdb file but I can't find anything about hydrogen types in gromos! any suggestion? The Gromos force fields are united-atom, so most H atoms are not used. Aromatic hydrogens are type HC and polar hydrogens are type H. If you're trying to run your structure through pdb2gmx and it's complaining, use -ignh and only necessary hydrogens will be built back on. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] setting vdw cutoff with specific force-filed?
On 04/08/11, Justin A. Lemkul jalem...@vt.edu wrote: Yun Shi wrote: Hi all, I am working with GROMOS 53a6 ff in GROMACS 4.5, and I assume a Lennard-Jones interaction function was used for short-range vdw interactions. From the reference paper /A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6/, I found that for example, when rvdw = 1.5nm, the repulsion term of the interaction between two CH1 type atoms (C12ij = 9.85^2) can be calculated as 9.850*9.850 / (1.5^12) = 0.747786 kJ/mol. So I wonder if this value is considered to be small enough to be ignored. You should pay attention to the column headings in table 7 so that you can compute the contribution correctly. However, the magnitude of the energy of any particular interaction is not really of any concern. The evolution of the system depends on the *forces*, and it is likely that the sum of the forces on any atom from all its repulsion interactions from atoms that are (say) 1.4nm to 1.5nm away is very close to zero, except in highly non-homogeneous spatial distributions of particles. In any case, the sum of that contribution will be much smaller than the other contributions. Mark In addition, it seems not until 5 nm does the dispersion term become larger than the repulsion term in this case, so would turning on Dispersion Correction between, say 1.5 to 5 nm introduce more errors than turning it off? You should use the cutoff described the authors of the force field, in this case rvdw=1.4. Unless you can demonstrate that by using a different value you can achieve superior results, stick with the specifics of parameterization. I have never seen ill effects of setting rvdw=1.4 and using dispersion correction with this force field. -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 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] add Argon to a force field?
Hi! I want to simulate an RNA molecule. I have the .pdb file of that. I want to create an Argon wall and make a hole on it to pull my molecule through it. Argon defined in OPLS/AA force field. but it has not nucleic acids. how can i define the argon in other force fields? -- 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] add Argon to a force field?
Amir Abbasi wrote: Hi! I want to simulate an RNA molecule. I have the .pdb file of that. I want to create an Argon wall and make a hole on it to pull my molecule through it. Argon defined in OPLS/AA force field. but it has not nucleic acids. how can i define the argon in other force fields? http://www.gromacs.org/Documentation/How-tos/Parameterization http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field Simulations of argon have been done for many years. You may be able to find suitable parameters by doing a literature search. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] g_dipoles - averaging
Florian, I am not sure, which of the output files of g_current contains the dipole moment for each molecule. Applying g_current to a trajectory of four molecules of asparagin in water gives the following output: g_current -s tpr_200ps.tpr -f xtcIRWhole_100-200ps.xtc -eps 80 -o current.xvg (selecting 4 molecules of asparagin from the index group) md.xvg @title Averaged rotational part of M @xaxis label Time (ps) @yaxis label M\sD\N (enm) @TYPE xy # time x y z average of M_D^2std.dev 0.000 -0.10261 0.12324 0.27085 0.09908 0.31477 0.001 -0.10421 0.12287 0.27297 0.09977 0.31587 0.002 -0.09766 0.12637 0.27104 0.09951 0.31543 ... dsp.xvg @title MSD of the squared translational dipole moment M @xaxis label Time (ps) @yaxis label |M\sJ\N(t)-M\sJ\N(0)|\S2\N / 6.0*V*k\sB\N*T / Sm\S-1\Nps\S-1\N @TYPE xy #Prefactor fit E-H: 1 / 6.0*V*k_B*T: 3.15249e-11 0.0000 0.001 8.70985e-30 0.002 1.9936e-29 ... mj.xvg @title Averaged translational part of M @xaxis label Time (ps) @yaxis label M\sJ\N (enm) @TYPE xy # time x y z average of M_J^2std.dev 0.0000.1 0.0 0.0 0.0 0.1 0.0010.1 0.0 0.0 0.0 0.1 ... current.xvg was not produced due to: ... ... Average volume V=32.764893 nm^3 at T=300.00 K and corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 7.120911 Too less points for a fit.verage volume V=32.764893 nm^3 at T=300.00 K and corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 7.120911 Too less points for a fit. I am not sure, where to find the dipole moment for each of the four molecules. Many thanks Andreas -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Dommert Florian Sent: 04 August 2011 12:31 To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_dipoles - averaging On Thu, 2011-08-04 at 09:08 +0100, Kukol, Andreas wrote: Hello, Is there any way to output the dipole moment averaged over all molecules or for each molecule separately (and not the total dipole moment of the simulation box) ? Yes, the tool g_current decomposes the total dipole moment into a component in respect to the center of mass of the molecules and a translational term, which is present, if you are dealing with charged species. So, if you prepare a corresponding index file you can derive the average molecular dipole moment for every molecule and finally average the results. /Flo Apparently the dipole autocorrelation function can be obtained as an average over all molecules with the '-corr mol' option, but from the help info it is not clear, how and if the total dipole moment can be obtained in this way (and in which file Mtot.xvg or aver.xvg ?). Many thanks Andreas -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- 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] PRODRG topology
Dear Gromacs Users, I used PRODRG server in order to obtain the topology file for my molecule (52 atoms with all hydrogens). However, server generated Gromacs topology which involves 47 atoms (for PDB file with polar/aromatic hydrogens). Whether I will use the pdb file with missing 4 hydrogen that wont be a good apporximation. How to overcome this? Thank you in advance, Jan -- 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] PRODRG topology
Marzinek, Jan wrote: Dear Gromacs Users, I used PRODRG server in order to obtain the topology file for my molecule (52 atoms with all hydrogens). However, server generated Gromacs topology which involves 47 atoms (for PDB file with polar/aromatic hydrogens). Whether I will use the pdb file with missing 4 hydrogen that wont be a good apporximation. How to overcome this? The Gromos96 force fields are united-atom force fields and may not use all the H atoms your input coordinates did. If you suspect some issue with protonation state, PRODRG can be forced into certain protonation with the ADDHYD or DELHYD keywords. Be advised, of course, of the usual caveats regarding the quality of PRODRG topologies: http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] setting vdw cutoff with specific force-filed?
Hi Justin and Mark, Thank you very much for the reply. I was using table 7 (Normal van der Waals Parameters) to calculate non-bonded vdw interactions that are not between third neighbors, such as CH1 carbons between different chains in a biomolecular system. Anything wrong here? I understand that it is the force that dictates the MD evolution, and I calculated in this case as F = 12 * 9.85^2 / 1.5^13 = 5.98 kJ/mol/nm for the repulsion term. The force from different directions on a atom in a homogeneous system would cancel each other to some extend, but what about the energy arises from this interaction? Would this considerably affect the calculation of, say, binding energy of a ligand to a receptor from thermodynamic integration or pulling simulation? Besides, the GROMOS 53a6 paper used triple range scheme for calculations of nonbonded interactions, and I guess it was rlist = 0.8 nm while rvdw = rcoulomb = 1.4 nm. So is this considered to be accurate enough in calculating free enthalpies of solvation since we know the interactions between 0.8 and 1.4 nm were calculated every 5 steps? The paper also used reaction-field instead PME to account for long-range electrostatic interactions. I heard some people argue that PME would be more accurate and it seemed to be utilized more often even in gromacs tutorials. So does this mean certain accuracy could be achieved by using triple range scheme and reaction-field together because the errors they incur respectively somehow cancel out each other? Thanks a lot, Yun Shi On 04/08/11, Justin A. Lemkul jalem...@vt.edu wrote: Yun Shi wrote: Hi all, I am working with GROMOS 53a6 ff in GROMACS 4.5, and I assume a Lennard-Jones interaction function was used for short-range vdw interactions. From the reference paper /A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6/, I found that for example, when rvdw = 1.5nm, the repulsion term of the interaction between two CH1 type atoms (C12ij = 9.85^2) can be calculated as 9.850*9.850 / (1.5^12) = 0.747786 kJ/mol. So I wonder if this value is considered to be small enough to be ignored. You should pay attention to the column headings in table 7 so that you can compute the contribution correctly. However, the magnitude of the energy of any particular interaction is not really of any concern. The evolution of the system depends on the *forces*, and it is likely that the sum of the forces on any atom from all its repulsion interactions from atoms that are (say) 1.4nm to 1.5nm away is very close to zero, except in highly non-homogeneous spatial distributions of particles. In any case, the sum of that contribution will be much smaller than the other contributions. Mark In addition, it seems not until 5 nm does the dispersion term become larger than the repulsion term in this case, so would turning on Dispersion Correction between, say 1.5 to 5 nm introduce more errors than turning it off? You should use the cutoff described the authors of the force field, in this case rvdw=1.4. Unless you can demonstrate that by using a different value you can achieve superior results, stick with the specifics of parameterization. I have never seen ill effects of setting rvdw=1.4 and using dispersion correction with this force field. -Justin -- == == Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] setting vdw cutoff with specific force-filed?
Yun Shi wrote: Hi Justin and Mark, Thank you very much for the reply. I was using table 7 (Normal van der Waals Parameters) to calculate non-bonded vdw interactions that are not between third neighbors, such as CH1 carbons between different chains in a biomolecular system. Anything wrong here? I understand that it is the force that dictates the MD evolution, and I calculated in this case as F = 12 * 9.85^2 / 1.5^13 = 5.98 kJ/mol/nm for the repulsion term. The force from different directions on a atom in a homogeneous system would cancel each other to some extend, but what about the energy arises from this interaction? Would this considerably affect the calculation of, say, binding energy of a ligand to a receptor from thermodynamic integration or pulling simulation? Check your units and the column headings of Table 7. Plugging in 9.85 as the energy will give you a wildly inflated result. The C12 parameters listed are actually square roots and listed as 10^-3. I think you will find the resulting energies and forces are vastly smaller for a simple interaction between two atoms. Besides, the GROMOS 53a6 paper used triple range scheme for calculations of nonbonded interactions, and I guess it was rlist = 0.8 nm while rvdw = rcoulomb = 1.4 nm. So is this considered to be accurate enough in calculating free enthalpies of solvation since we know the interactions between 0.8 and 1.4 nm were calculated every 5 steps? There is no need to update the neighbor list every single step. Typically, water is the fastest-diffusing molecule in the system, but it will generally not have a dramatic displacement on the scale of 10 fs or so. The paper also used reaction-field instead PME to account for long-range electrostatic interactions. I heard some people argue that PME would be more accurate and it seemed to be utilized more often even in gromacs tutorials. So does this mean certain accuracy could be achieved by using triple range scheme and reaction-field together because the errors they incur respectively somehow cancel out each other? PME is substantially more accurate. Using it also requires rlist=rcoulomb, so the exact details of the Gromos96 derivation may be somewhat outdated. Typical settings for Gromos96 would be something like: rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 nstlist = 5 coulombtype = PME Note that the value of rcoulomb and rlist can vary a bit as a consequence of PME. -Justin Thanks a lot, Yun Shi On 04/08/11, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Yun Shi wrote: Hi all, I am working with GROMOS 53a6 ff in GROMACS 4.5, and I assume a Lennard-Jones interaction function was used for short-range vdw interactions. From the reference paper /A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6/, I found that for example, when rvdw = 1.5nm, the repulsion term of the interaction between two CH1 type atoms (C12ij = 9.85^2) can be calculated as 9.850*9.850 / (1.5^12) = 0.747786 kJ/mol. So I wonder if this value is considered to be small enough to be ignored. You should pay attention to the column headings in table 7 so that you can compute the contribution correctly. However, the magnitude of the energy of any particular interaction is not really of any concern. The evolution of the system depends on the *forces*, and it is likely that the sum of the forces on any atom from all its repulsion interactions from atoms that are (say) 1.4nm to 1.5nm away is very close to zero, except in highly non-homogeneous spatial distributions of particles. In any case, the sum of that contribution will be much smaller than the other contributions. Mark In addition, it seems not until 5 nm does the dispersion term become larger than the repulsion term in this case, so would turning on Dispersion Correction between, say 1.5 to 5 nm introduce more errors than turning it off? You should use the cutoff described the authors of the force field, in this case rvdw=1.4. Unless you can demonstrate that by using a different value you can achieve superior results, stick with the specifics of parameterization. I have never seen ill effects of setting rvdw=1.4 and using dispersion correction with this force field. -Justin -- == == Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
RE: [gmx-users] g_dipoles - averaging
On Thu, 2011-08-04 at 15:49 +0100, Kukol, Andreas wrote: Florian, I am not sure, which of the output files of g_current contains the dipole moment for each molecule. Applying g_current to a trajectory of four molecules of asparagin in water gives the following output: To obtain the dipole moment for every single molecule you have to create index groups for every single molecule, and the output you are looking for is the rotational part of M contained in md.xvg the -eps flag is also not necessary and only required for the calculation of the dielectric constant. /Flo g_current -s tpr_200ps.tpr -f xtcIRWhole_100-200ps.xtc -eps 80 -o current.xvg (selecting 4 molecules of asparagin from the index group) md.xvg @title Averaged rotational part of M @xaxis label Time (ps) @yaxis label M\sD\N (enm) @TYPE xy # time x y z average of M_D^2std.dev 0.000 -0.10261 0.12324 0.27085 0.09908 0.31477 0.001 -0.10421 0.12287 0.27297 0.09977 0.31587 0.002 -0.09766 0.12637 0.27104 0.09951 0.31543 ... dsp.xvg @title MSD of the squared translational dipole moment M @xaxis label Time (ps) @yaxis label |M\sJ\N(t)-M\sJ\N(0)|\S2\N / 6.0*V*k\sB\N*T / Sm\S-1\Nps\S-1\N @TYPE xy #Prefactor fit E-H: 1 / 6.0*V*k_B*T: 3.15249e-11 0.000 0 0.001 8.70985e-30 0.002 1.9936e-29 ... mj.xvg @title Averaged translational part of M @xaxis label Time (ps) @yaxis label M\sJ\N (enm) @TYPE xy # time x y z average of M_J^2std.dev 0.000 0.1 0.0 0.0 0.0 0.1 0.001 0.1 0.0 0.0 0.0 0.1 ... current.xvg was not produced due to: ... ... Average volume V=32.764893 nm^3 at T=300.00 K and corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 7.120911 Too less points for a fit.verage volume V=32.764893 nm^3 at T=300.00 K and corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 7.120911 Too less points for a fit. I am not sure, where to find the dipole moment for each of the four molecules. Many thanks Andreas -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Dommert Florian Sent: 04 August 2011 12:31 To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_dipoles - averaging On Thu, 2011-08-04 at 09:08 +0100, Kukol, Andreas wrote: Hello, Is there any way to output the dipole moment averaged over all molecules or for each molecule separately (and not the total dipole moment of the simulation box) ? Yes, the tool g_current decomposes the total dipole moment into a component in respect to the center of mass of the molecules and a translational term, which is present, if you are dealing with charged species. So, if you prepare a corresponding index file you can derive the average molecular dipole moment for every molecule and finally average the results. /Flo Apparently the dipole autocorrelation function can be obtained as an average over all molecules with the '-corr mol' option, but from the help info it is not clear, how and if the total dipole moment can be obtained in this way (and in which file Mtot.xvg or aver.xvg ?). Many thanks Andreas -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- 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] RE: Gromacs on GPU: GTX or Tesla?
Hi, Tesla cards won't give you much benefit when it comes to running the current Gromacs. Additionally, I can tell you so much that this won't change in the future either. The only advantage of the C20x0-s is ECC and double precision - which is ATM anyway not supported in Gromacs on GPUs. Gromacs in general doesn't use much memory so unless you will want to run gigantic systems with a single card, C2070 will not give you any added benefit at all, in fact 1-1.5GB/card should be more than enough. What kind of machine are you planning to buy/how many GPUs? -- Szilárd On Thu, Aug 4, 2011 at 8:59 AM, Jagdish S. Varma jsva...@connoiseur.com wrote: Hi, In the long term the Tesla is much more preferable as the GTX would not support certain high end functions. Pls verify these before you purchase one. Also the Tesla C-2070 is the newer one available and with 6.0GB RAM it really gives out great performance. The price is the same. Rgds JSV From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Efrat Exlrod [efrat.exl...@biu.ac.il] Sent: Thursday, August 04, 2011 12:13 PM To: gmx-users@gromacs.org Subject: [gmx-users] Gromacs on GPU: GTX or Tesla? Hi, We want to start using Gromacs on GPU and we are debating whether to purchase GeForce GTX card or Tesla platform. Looking at the published data it seems GTX580 has much impressive performance compared to Tesla C2050, and of course it is much cheaper. Is there a reason to prefer Tesla over GTX for running Gromacs in the short or long term? Thanks, Efrat LEGAL DISCLAIMER Information contained and transmitted by this E-MAIL is proprietary to M/S. CONNOISEUR ELECTRONICS PVT. LTD., or M/S. CONNOISEUR INFOTECH LLC., or M/S. CONNOISEUR INFOTECH depending on the sender of the email. The transmitted E-MAIL is intended for exclusive use by the individual or entity to which it is addressed, and may contain information that is privileged, confidential or exempt from disclosure under applicable law and shall not attach any liability on the originator. If you have reason to belive that you are not the intended recipient of this E-MAIL,or,if you received this E-MAIL in error please inform the sender immediately by reply email destroy the E-MAIL. Any use, distribution, transmission, printing, copying or dissemination of this information in any way or in any manner is strictly prohibited unlawful. The sender belives that this email and its attachment(s) were free of any malicious code(s) when sent. However,infection may have occurred during transmission. By reading the message and opening any attachment, the recipient accepts full responsibility for taking protective and remedial action about viruses and other defects. M/S. CONNOISEUR ELECTRONICS PVT. LTD., or M/S CONNOISEUR INFOTECH LLC., or M/S CONNOISEUR INFOTECH is not liable for any loss or damage arising in any way from this message or its attachment(s). -- 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] angular velocities in gromacs?
Dear Gromacs User, Gromacs *trr file has the velocities. They are for translational motions. But how can we get the angular velocities? Thanks for the information! Tom -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: setting vdw cutoff with specific force-filed?
Hi Justin, I got it now. During the 10fs, even water molecules with a speed of 500 m/s only have a 0.005 nm displacement, which is far less than than 0.9 nm or 1.4 nm. Thanks again! Yun Yun Shi wrote: Hi Justin and Mark, Thank you very much for the reply. I was using table 7 (Normal van der Waals Parameters) to calculate non-bonded vdw interactions that are not between third neighbors, such as CH1 carbons between different chains in a biomolecular system. Anything wrong here? I understand that it is the force that dictates the MD evolution, and I calculated in this case as F = 12 * 9.85^2 / 1.5^13 = 5.98 kJ/mol/nm for the repulsion term. The force from different directions on a atom in a homogeneous system would cancel each other to some extend, but what about the energy arises from this interaction? Would this considerably affect the calculation of, say, binding energy of a ligand to a receptor from thermodynamic integration or pulling simulation? Check your units and the column headings of Table 7. Plugging in 9.85 as the energy will give you a wildly inflated result. The C12 parameters listed are actually square roots and listed as 10^-3. I think you will find the resulting energies and forces are vastly smaller for a simple interaction between two atoms. Besides, the GROMOS 53a6 paper used triple range scheme for calculations of nonbonded interactions, and I guess it was rlist = 0.8 nm while rvdw = rcoulomb = 1.4 nm. So is this considered to be accurate enough in calculating free enthalpies of solvation since we know the interactions between 0.8 and 1.4 nm were calculated every 5 steps? There is no need to update the neighbor list every single step. Typically, water is the fastest-diffusing molecule in the system, but it will generally not have a dramatic displacement on the scale of 10 fs or so. The paper also used reaction-field instead PME to account for long-range electrostatic interactions. I heard some people argue that PME would be more accurate and it seemed to be utilized more often even in gromacs tutorials. So does this mean certain accuracy could be achieved by using triple range scheme and reaction-field together because the errors they incur respectively somehow cancel out each other? PME is substantially more accurate. Using it also requires rlist=rcoulomb, so the exact details of the Gromos96 derivation may be somewhat outdated. Typical settings for Gromos96 would be something like: rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 nstlist = 5 coulombtype = PME Note that the value of rcoulomb and rlist can vary a bit as a consequence of PME. -Justin Thanks a lot, Yun Shi On 04/08/11, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Yun Shi wrote: Hi all, I am working with GROMOS 53a6 ff in GROMACS 4.5, and I assume a Lennard-Jones interaction function was used for short-range vdw interactions. From the reference paper /A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6/, I found that for example, when rvdw = 1.5nm, the repulsion term of the interaction between two CH1 type atoms (C12ij = 9.85^2) can be calculated as 9.850*9.850 / (1.5^12) = 0.747786 kJ/mol. So I wonder if this value is considered to be small enough to be ignored. You should pay attention to the column headings in table 7 so that you can compute the contribution correctly. However, the magnitude of the energy of any particular interaction is not really of any concern. The evolution of the system depends on the *forces*, and it is likely that the sum of the forces on any atom from all its repulsion interactions from atoms that are (say) 1.4nm to 1.5nm away is very close to zero, except in highly non-homogeneous spatial distributions of particles. In any case, the sum of that contribution will be much smaller than the other contributions. Mark In addition, it seems not until 5 nm does the dispersion term become larger than the repulsion term in this case, so would turning on Dispersion Correction between, say 1.5 to 5 nm introduce more errors than turning it off? You should use the cutoff described the authors of the force field, in this case rvdw=1.4. Unless you can demonstrate that by using a different value you can achieve superior results, stick with the specifics of parameterization. I have never seen ill effects of setting rvdw=1.4 and using dispersion correction with this force field. -Justin -- == == Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin == ==
Re: [gmx-users] Problem of Kinetic Energy
On 4/08/2011 7:17 AM, Size Zheng wrote: Hi Mark, When I used the g_traj with options of -ekt and -ekr, i made a selection as follow Group 0 ( System) has 6400 elements Group 1 (TP4) has 6400 elements Select a group: 1 Selected 1: 'TP4' So according to you that g_traj uses the whole 1600-molecules' COM to report the value of translational and rotational kinetics energy, rather than the sum of all 1600 rigid molecules? That is my understanding, based purely on reading g_traj -h. Is there any other command or options can operate ekrot and ektrans on atoms or molecules? I don't know, but I would start by looking in Chapter 8 of the manual. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] angular velocities in gromacs?
On 5/08/2011 6:08 AM, Tom wrote: Dear Gromacs User, Gromacs *trr file has the velocities. They are for translational motions. But how can we get the angular velocities? Angular velocities with respect to what? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to exclude the interactions between molecule A and B in Gromacs?
Dear all, I want to use Gromacs to run an enhanced sampling molecular dynamics (ESMD) proposed by Karplus’s group (J. Am. Chem. Soc. (1990) 112, 9161-9175. J. Mol. Biol. (1999) 291, 101-115). In the ESMD simulation, we need to exclude the interactions (especially the Coulomb interactions) between some small molecules (e.g. ligand A and its replica). How can Gromacs to do this? Any suggestion will be very appreciated. Best regards, = Dechang Li, Ph.D Biomechanics and Biomaterials Laboratory Department of Applied Mechanics School of Aerospace Engineering Beijing Institute of Technology Beijing 100081, P. R. China = -- 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] angular velocities in gromacs?
Hi Tom, TRR files contain velocities for individual atoms as a function of time, which is all the velocity information there is in an MD simulation. You can reduce that information to rotation about a principle molecular axis, or rotation with respect to the simulation box, or whatever you need. MZ On Thu, Aug 4, 2011 at 4:08 PM, Tom dna...@gmail.com wrote: Dear Gromacs User, Gromacs *trr file has the velocities. They are for translational motions. But how can we get the angular velocities? Thanks for the information! Tom -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to exclude the interactions between molecule A and B in Gromacs?
On 5/08/2011 1:17 PM, DeChang Li wrote: Dear all, I want to use Gromacs to run an enhanced sampling molecular dynamics (ESMD) proposed by Karplus's group (J. Am. Chem. Soc. (1990) 112, 9161-9175. J. Mol. Biol. (1999) 291, 101-115). In the ESMD simulation, we need to exclude the interactions (especially the Coulomb interactions) between some small molecules (e.g. ligand A and its replica). How can Gromacs to do this? Any suggestion will be very appreciated. See energy groups and energy group exclusions in 3.3 and 7.3.19 of the manual. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
