[gmx-users] epsilon_r vs. gb_epsilon_solvent
Hi, all, I have a question regarding epsilon_r value. Do I have to specify the value in .mdp file? What is the default value if I do not specify it? If I use implicit solvent, there is one parameter: gb_epsilon_solvent, which is recommended to be 80 in the manual. What is the difference between gb_epsilon_solvent and epsilon_r? Thank you! Bo -- 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] hydrogen hydrogen interaction
Hi, all, Does hydrogen hydrogen non-bond interactions be calculated in the simulation? It looks to me this kind of non-bond interaction is ignored. If not, is there a way to let it count h-h interaction? Thank you! Bo -- 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: Re: hydrophobic and hydrophilic in implicit solvent
Hi, Thank you for your answer. May I ask where I can find the right parameter in gbsa.itp for ions? These should be very basic things in simulation, but I cannot find their parameters anywhere. How do you guys use implicit solvent if you want to have ions inside? Thank you! Bo bo.shuang wrote: For example, if I want to simulate how Membrane phospholipid bilayer form its configuration in water, and want to use CG model and implicit solvent, then I need the heads of these phospholipid molecules to be hydrophilic and their tail to be hydrophobic. How can I specify parameter of these particles to make them have these different properties in implicit solvent? It just an example. Hydrophobic also play important role in protein and DNA folding. That's why I want to make hydrophobic work in implicit solvent. Thank you very much for your help! Hydrophobicity and hydrophilicity are functions of the nonbonded parameters (charges and van der Waals parameters) of the individual atom types, which are essential components of a force field. There's nothing extra you need to do beyond defining these parameters (or using those that already exist). -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] hydrophobic and hydrophilic in implicit solvent
Hi, all, Is that possible to define hydrophobic or hydrophilic properties in implicit solvent? Which parameter control these properties of particles? Thank you! Bo -- 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: Re: [gmx-users] hydrophobic and hydrophilic in implicit solvent
For example, if I want to simulate how Membrane phospholipid bilayer form its configuration in water, and want to use CG model and implicit solvent, then I need the heads of these phospholipid molecules to be hydrophilic and their tail to be hydrophobic. How can I specify parameter of these particles to make them have these different properties in implicit solvent? It just an example. Hydrophobic also play important role in protein and DNA folding. That's why I want to make hydrophobic work in implicit solvent. Thank you very much for your help! Bo On 8/03/2012 2:59 AM, bo.shuang wrote: Hi, all, Is that possible to define hydrophobic or hydrophilic properties in implicit solvent? Which parameter control these properties of particles? Thank you! For what purpose? Simulations don't care about such labels. 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] Re: Re: mdrun -multi flag (Mark Abraham)
Hi, Mark, Thank you for help. It works. But now I have new fatal error: Fatal error: The number of nodes (1) is not a multiple of the number of simulations (2) MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. What does it mean about nodes? Thank you! Bo On Thu, Mar 1, 2012 at 7:42 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: mdrun -multi flag (Mark Abraham) 2. Re: dihedral distributions (Juliette N.) -- Message: 1 Date: Fri, 02 Mar 2012 10:17:12 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] mdrun -multi flag To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4f500378.7030...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2/03/2012 10:15 AM, bo.shuang wrote: Hello, all, I am trying to do REMD simulation. So I used command: mdrun -s t2T.tpr -multi 2 -replex 1000 And gromacs gives error report: Fatal error: mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Then I tried re-install mdrun: ./configure --enable-mpi --program-suffix=_mpiq make mdrun make install-mdrun It looks fine, but I still cannot use multi flag, and it is still the same error. I don't know what the problem is and what I should do next. Thank you for help! With that program suffix, you need to use mdrun_mpiq Mark -- Message: 2 Date: Thu, 1 Mar 2012 20:42:06 -0500 From: Juliette N. joojoojo...@gmail.com Subject: Re: [gmx-users] dihedral distributions To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: cagdqh4os1kuuogwlncznyxrf9sra_+a8s0eku2bum6cojvz...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Skipped content of type multipart/alternative-- next part -- A non-text attachment was scrubbed... Name: RB1.88.PNG Type: image/png Size: 9359 bytes Desc: not available Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20120301/e812dbaf/RB1.88.png -- next part -- A non-text attachment was scrubbed... Name: RB1.46.PNG Type: image/png Size: 9580 bytes Desc: not available Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20120301/e812dbaf/RB1.46.png -- -- 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! End of gmx-users Digest, Vol 95, Issue 10 * -- 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: Re: Re: Re: mdrun -multi flag (Mark Abraham) (Justin A. Lemkul)
Thank you for help! Is that possible to run REMD on a PC with only one processor? Bo bo.shuang wrote: Hi, Mark, Thank you for help. It works. But now I have new fatal error: Fatal error: The number of nodes (1) is not a multiple of the number of simulations (2) MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. What does it mean about nodes? Thank you! Running multiple simulations requires multiple processors. For 2 simulations, you need at least 2 processors (one for each simulation). More can be used, but it must be a multiple of the number of simulations, as the error message indicates. -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] mdrun -multi flag
Hello, all, I am trying to do REMD simulation. So I used command: mdrun -s t2T.tpr -multi 2 -replex 1000 And gromacs gives error report: Fatal error: mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Then I tried re-install mdrun: ./configure --enable-mpi --program-suffix=_mpiq make mdrun make install-mdrun It looks fine, but I still cannot use multi flag, and it is still the same error. I don't know what the problem is and what I should do next. Thank you for help! Bo -- 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] change simulation temperature
Hi, all, I have a question about change the temperature in simulation. When I change the ref_t and gen_temp only, (from 300 to 400) I cannot see any difference. I am thinking if I need to change tau_t also, since diffusivity constant is also related to temperature. Am I right? Here is my mdp file: title= OPLS Lysozyme NVT equilibration ;define= -DPOSRES; position restrain the protein ; Run parameters integrator= bd; leap-frog integrator nsteps= 50; 2 * 50 = 1000 ps dt= 0.002; 2 fs ; Output control nstxout= 100; save coordinates every 0.2 ps nstvout= 100; save velocities every 0.2 ps nstenergy= 100; save energies every 0.2 ps nstlog= 100; update log file every 0.2 ps ; Bond parameters continuation= yes; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= system; two coupling groups - more accurate tau_t= 0.01; time constant, in ps ref_t= 400 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl= no ; no pressure coupling in NVT ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distributionchanged gen_temp= 400; temperature for Maxwell distribution gen_seed= 100; generate a random seed ld_seed=-1 Thank you! Bo -- 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: gmx-users Digest, Vol 94, Issue 185
When I use explicit solvent, and set tau_t=2, it looks OK. The ions move
faster when I increase the temperature. But when I use implicit solvent, it
seems not change at all. Also, I am using sd instead of bd. I forgot to
change it back. And in my understanding, the diffusive constant of Brown
motion should be linear dependent on temperature, as shown below. Thank you!
[image: \frac{\overline{x^2}}{2t}=D=\mu k_BT=\frac{\mu
RT}{N}=\frac{RT}{6\pi\eta rN}.]
Bo
On Tue, Feb 28, 2012 at 8:36 PM, gmx-users-requ...@gromacs.org wrote:
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than Re: Contents of gmx-users digest...
Today's Topics:
1. Re: change simulation temperature (Justin A. Lemkul)
2. Re: change simulation temperature (Mark Abraham)
3. NaN error using mdrun-gpu (Adam Jion)
4. NaN error for mdrun-gpu (Adam Jion)
--
Message: 1
Date: Tue, 28 Feb 2012 20:47:22 -0500
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] change simulation temperature
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4f4d83aa.3010...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
bo.shuang wrote:
Hi, all,
I have a question about change the temperature in simulation. When I
change the ref_t and gen_temp only, (from 300 to 400) I cannot see any
difference. I am thinking if I need to change tau_t also, since
diffusivity constant is also related to temperature. Am I right?
You're using a bd integrator, so the relationships here are not as
straightforward as with md or sd integrators. I'm not experienced enough
to
comment on the implications of various settings for bd, but I would refer
you to
the manual, where the relationships are described (and how some of the .mdp
keywords are used in special ways).
Generally speaking, if you want to conduct a simulation at a different
temperature, changing gen_temp and ref_t are indeed all that are required.
The
value of tau_t controls how tight the coupling is, nothing more.
-Justin
Here is my mdp file:
title= OPLS Lysozyme NVT equilibration
;define= -DPOSRES; position restrain the protein
; Run parameters
integrator= bd; leap-frog integrator
nsteps= 50; 2 * 50 = 1000 ps
dt= 0.002; 2 fs
; Output control
nstxout= 100; save coordinates every 0.2 ps
nstvout= 100; save velocities every 0.2 ps
nstenergy= 100; save energies every 0.2 ps
nstlog= 100; update log file every 0.2 ps
; Bond parameters
continuation= yes; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy atom-H bonds)
constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 10 fs
rlist= 1.0; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= PME; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT
; Temperature coupling is on
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= system; two coupling groups - more accurate
tau_t= 0.01; time constant, in ps
ref_t= 400 ; reference temperature, one for each group,
in K
; Pressure coupling is off
pcoupl= no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc= xyz; 3-D PBC
; Dispersion correction
DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
gen_vel= yes; assign velocities from Maxwell
distributionchanged
gen_temp= 400; temperature for Maxwell distribution
gen_seed= 100; generate a random seed
ld_seed=-1
Thank you!
Bo
--
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
