[gmx-users] protonated histidine with Martini
Dear gromacs users, I want to use Martini force field for my simulation. The simulation is supposed to be performed at acidic environment (pH2.6). In this environment His is protonated. I want to add protonate Hisidine in itp file. Where exactly should I put the charge on S2c or on S3c? Maybe I should put 0.5 on each CG bead? Thank you in advance. Regina This message was sent using IMP, the Internet Messaging Program. -- 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] minimization problem (Martini simulation)
Thank you very much. It worked. Regina Quoting "Justin A. Lemkul" : pol...@fh.huji.ac.il wrote: Dear Justin, Thank you very much for your answer. Can you please explain me what do you mean by saying "EM wasn't sufficient". What information do you need in order be able to help? I run EM with emtol=60 and I got the following energies: Steepest Descents converged to Fmax < 60 in 2256 steps Potential Energy = -1.2244622e+07 Maximum force = 4.7755444e+01 on atom 1659 Norm of force = 6.3245118e-01 This was the information I wanted to see. Without it, no one had any idea if your EM converged reasonably. Everything seems ok. Indeed it does. After that I run MD using mdp file attached and I got the following error: Started mdrun on node 0 Tue Jun 28 00:10:12 2011 Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) Bond G96Angle Improper Dih. LJ (SR) Coulomb (SR) 6.39093e+03 9.79589e+03 3.77765e+02 -1.22386e+07 -1.82773e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -1.22239e+07 1.25745e+00 -1.22239e+07 2.55766e-04 -1.14611e+03 Here's your problem. The initial temperature is ridiculously small, indicating something has gone wrong. Cons. rmsd () 4.25390e-06 DD step 9 load imb.: force 3.0% --- Program mdrun_mpi, VERSION 4.0.3 Any reason you're using a really old version of Gromacs? Here's your problem. The combination of: tcoupl = Berendsen and gen_vel = no is generally not stable. You should set "gen_vel = yes" to start a reasonable equilibration period. -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 This message was sent using IMP, the Internet Messaging Program. -- 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] minimization problem (Martini simulation)
Dear Justin, Thank you very much for your answer. Can you please explain me what do you mean by saying "EM wasn't sufficient". What information do you need in order be able to help? I run EM with emtol=60 and I got the following energies: Steepest Descents converged to Fmax < 60 in 2256 steps Potential Energy = -1.2244622e+07 Maximum force = 4.7755444e+01 on atom 1659 Norm of force = 6.3245118e-01 Everything seems ok. After that I run MD using mdp file attached and I got the following error: Started mdrun on node 0 Tue Jun 28 00:10:12 2011 Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) Bond G96Angle Improper Dih. LJ (SR) Coulomb (SR) 6.39093e+03 9.79589e+03 3.77765e+02 -1.22386e+07 -1.82773e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -1.22239e+07 1.25745e+00 -1.22239e+07 2.55766e-04 -1.14611e+03 Cons. rmsd () 4.25390e-06 DD step 9 load imb.: force 3.0% --- Program mdrun_mpi, VERSION 4.0.3 Source code file: nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. --- "Step Aside, Butch" (Pulp Fiction) I found that this error is connected to problems with minimization but unfortunately I don't know how to fix it. I will appreciate very much any help. Thank you. Regina mdp file used: ; VARIOUS PREPROCESSING OPTIONS = title= Martini cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 0.0 dt = 0.030 nsteps = 4000 ; number of steps for center of mass motion removal = nstcomm = 1 ; Groups for center of mass motion removal comm-grps= System ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 0 xtc_precision= 100 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = Protein_PSE W_ION ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r= 15 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths= rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = Berendsen ; Groups to couple separately = tc-grps = Protein_PSE W_ION ; Time constant (ps) and reference temperature (K) = tau_t= 1.0 1.0 ref_t= 300 300 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 5.0 5.0 compressibility = 3e-4 3e-4 ref_p= 1.0 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 300 gen_seed = 473529 ; OPTIONS FOR BONDS = constraints = none ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 30 Quoting "Justin A. Lemkul" : pol...@fh.huji.ac.il wrote: Dear Gromacs users and developers, I forgot to note that I'm talking about a Martini simulation. I'm trying to set up simulation. I have a big simulation of something like half million CG atoms. The problem is that I have a minimization problem. I'm getting the following error: Converged to machine precision, but not to the requested precision Fmax < 10 This is not really an error: http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_
[gmx-users] minimization problem
Dear Gromacs users and developers, I'm trying to set up simulation. I have a big simulation of something like half million atoms. The problem is that I have a minimization problem. I'm getting the following error: Converged to machine precision, but not to the requested precision Fmax < 10 I tried to use a bigger emtol(emtol=20) and it still didn't converge.However I still run the MD with dt = 0.03 and nstxout = 1. after something like 100 steps the system blow up. I will appreciate any help with this issue. Many thanks in advance. P.S May it help if I minimize a smaller system and replicate it after that. How exactly can I do replication? This message was sent using IMP, the Internet Messaging Program. -- 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] minimization problem (Martini simulation)
Dear Gromacs users and developers, I forgot to note that I'm talking about a Martini simulation. I'm trying to set up simulation. I have a big simulation of something like half million CG atoms. The problem is that I have a minimization problem. I'm getting the following error: Converged to machine precision, but not to the requested precision Fmax < 10 I tried to use a bigger emtol(emtol=20) and it still didn't converge.However I still run the MD with dt = 0.03 and nstxout = 1. after something like 100 steps the system blow up. I will appreciate any help with this issue. Many thanks in advance. P.S May it help if I minimize a smaller system and replicate it after that. How exactly can I do replication? This message was sent using IMP, the Internet Messaging Program. -- 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] minimization and simulation problems
Quoting pol...@fh.huji.ac.il:
Dear gromacs users,
my box dimensions are 368A and when I run the simulation with
nsteps=1 it works fine. The mdp files used for minimization and
post-em simulation are attached.
Thanks again for your help.
Regina
Quoting chris.ne...@utoronto.ca:
What are your initial box dimensions prior to em? Also, please copy
and paste your .mdp options. Also, what happens when you run the
same post-em simulation with nsteps=1 ?
-- original message --
Dear all,
I'm trying to run simulation of 30 proteins in water using the Martini
force field. I used water.gro file in order to solvate the proteins.
For minimization I used the em.mdp file published at Martini site
(http://md.chem.rug.nl/cgmartini/index.php/home). When I set the emtol
parameter to 10 the system can't converge. So I used emtol 100 and
then the system converged. I use it as an input for the simulation.
The file can't be attached as it is too big nut I can send it if needed.
However, the sumulation crushes when I'm trying to run MD using md.mdp
also from the Martini site. I'm getting the following warnings and
errors:
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
---
"It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 8
gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0[cli_0]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
---
Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 1 out of 8
gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3[cli_3]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5[cli_5]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5
gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4[cli_4]:
aborting job:
applicati
Re: [gmx-users] minimization and simulation problems
my box dimensions are 368A
Quoting chris.ne...@utoronto.ca:
What are your initial box dimensions prior to em? Also, please copy
and paste your .mdp options. Also, what happens when you run the
same post-em simulation with nsteps=1 ?
-- original message --
Dear all,
I'm trying to run simulation of 30 proteins in water using the Martini
force field. I used water.gro file in order to solvate the proteins.
For minimization I used the em.mdp file published at Martini site
(http://md.chem.rug.nl/cgmartini/index.php/home). When I set the emtol
parameter to 10 the system can't converge. So I used emtol 100 and
then the system converged. I use it as an input for the simulation.
The file can't be attached as it is too big nut I can send it if needed.
However, the sumulation crushes when I'm trying to run MD using md.mdp
also from the Martini site. I'm getting the following warnings and
errors:
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
---
"It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 8
gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0[cli_0]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
---
Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 1 out of 8
gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3[cli_3]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5[cli_5]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5
gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4[cli_4]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4
gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6[cli_6]
[gmx-users] minimization and simulation problems
Dear all,
I'm trying to run simulation of 30 proteins in water using the Martini
force field. I used water.gro file in order to solvate the proteins.
For minimization I used the em.mdp file published at Martini site
(http://md.chem.rug.nl/cgmartini/index.php/home). When I set the emtol
parameter to 10 the system can't converge. So I used emtol 100 and
then the system converged. I use it as an input for the simulation.
The file can't be attached as it is too big nut I can send it if needed.
However, the sumulation crushes when I'm trying to run MD using md.mdp
also from the Martini site. I'm getting the following warnings and
errors:
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
---
"It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 8
gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0[cli_0]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
---
Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 1 out of 8
gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3[cli_3]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5[cli_5]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5
gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4[cli_4]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4
gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6[cli_6]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6
gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2[cli_2]:
aborting job:
applicati
[gmx-users] Simulation using Martini force field
regarding "parameterization of phosphorylated serine " I checked the Martini papers and I couldn't find how it is done. Can somebody please instruct me. In addition in JCTC paper from 2008 I saw that they simulated pentapeptides without imposing secondary structure. How can I do it? The problem is that there is no good tutorial how to use Martini (something general). If I still want to use Martini without imposing secondary structure how should I do it? What tutorial is better to use the one for lipids or the one for proteins in water. I think I should explain what exactly I want to do. I want to simulate casein protein that is natively unstructured. The only thing that is known about this protein that it creates micelles. I just want to see if it possible to create micelles with Martini and I'm trying to understand what is the better way to run Martini taking into consideration the limitations of the force field and my system. As I'm not an expert in Gromacs neither in Martini force field I will appreciate very much any help for setting this simulation. Thank you very much in advance. Regina n Feb 14, 2011, at 11:43 PM, pol...@fh.huji.ac.il wrote: Thank you very much for you reply. Can you please explain me why do i need secondary structure file at all and why "secondary structure is pre-defined and thus static throughout a simulation"? I didn't see that something like this defined for lipids. Have look at the Martini paper for protein (JCTC-2009) you might find some stuff quite instructive in there :)) FYI lipids do not have secondary structure or something that would succgest they could have different interacting behavior in function of their conformation. How do I use do_dssp to build the needed file? I saw that I need a topology file in rder to use do_dssp. Where can I find this topology file? I hope this is ok that I'm asking so many questions. Thank you very much for your help. No problem it just shows how it was a good idea to make a tutorial :)) have look there cgmartini.nl Regina Quoting "XAvier Periole" : Dear Regina, You have two problems: 1- the parameterization of phosphorylated serine should be done following the same philosophy of Martini. Check the Martini papers to see how this is done. In short partitioning is of primary importance. 2- you want to simulate unfolded protein ... indeed there is evidently no persistent structure in such system and therefore the choice for secondary structure would be coil in the Martini force field. However the definition of "coil" for Martini has not been parameterize to reproduce anything even close to what an unfolded protein, assuming that we know what it looks like :)) The Martini "coil" is simply something flexible. I am afraid Martini is just not ready for simulating unfolded proteins. Any outcome of a simulation would have to be interpreted with CARE! XAvier. On Feb 14, 2011, at 2:09 PM, pol...@fh.huji.ac.il wrote: Dear Gromacs users and developers, I'm interested to run simulation of natively unstructured protein (casein), that can self assembly and create micelles, using Martini force field. The initial structure of the monomer was created and minimized using Sybyl. This protein includes also 4 phosporylated serines. I'm trying to understand how should I set my system. I started from the tutorial (http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-water) but I found that have no idea how to create a phosphorylated serine inCG structure (I have it in my initial pdb). In addition, I found that I need a secondary structure of the protein and I don't have something like this. Moreover, this protein doesn't have one. I will appreciated very much if somebody can help me and guide me a little. Thank you very much in advance. Regina This message was sent using IMP, the Internet Messaging Program. -- 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 thewww 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users P
Re: [gmx-users] Simulation using Martini force field
Thank you very much for you reply. Can you please explain me why do i need secondary structure file at all and why "secondary structure is pre-defined and thus static throughout a simulation"? I didn't see that something like this defined for lipids. How do I use do_dssp to build the needed file? I saw that I need a topology file in rder to use do_dssp. Where can I find this topology file? I hope this is ok that I'm asking so many questions. Thank you very much for your help. Regina Quoting "XAvier Periole" : Dear Regina, You have two problems: 1- the parameterization of phosphorylated serine should be done following the same philosophy of Martini. Check the Martini papers to see how this is done. In short partitioning is of primary importance. 2- you want to simulate unfolded protein ... indeed there is evidently no persistent structure in such system and therefore the choice for secondary structure would be coil in the Martini force field. However the definition of "coil" for Martini has not been parameterize to reproduce anything even close to what an unfolded protein, assuming that we know what it looks like :)) The Martini "coil" is simply something flexible. I am afraid Martini is just not ready for simulating unfolded proteins. Any outcome of a simulation would have to be interpreted with CARE! XAvier. On Feb 14, 2011, at 2:09 PM, pol...@fh.huji.ac.il wrote: Dear Gromacs users and developers, I'm interested to run simulation of natively unstructured protein (casein), that can self assembly and create micelles, using Martini force field. The initial structure of the monomer was created and minimized using Sybyl. This protein includes also 4 phosporylated serines. I'm trying to understand how should I set my system. I started from the tutorial (http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-water) but I found that have no idea how to create a phosphorylated serine inCG structure (I have it in my initial pdb). In addition, I found that I need a secondary structure of the protein and I don't have something like this. Moreover, this protein doesn't have one. I will appreciated very much if somebody can help me and guide me a little. Thank you very much in advance. Regina This message was sent using IMP, the Internet Messaging Program. -- 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 thewww 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists This message was sent using IMP, the Internet Messaging Program. -- 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] Simulation using Martini force field
Dear Gromacs users and developers, I'm interested to run simulation of natively unstructured protein (casein), that can self assembly and create micelles, using Martini force field. The initial structure of the monomer was created and minimized using Sybyl. This protein includes also 4 phosporylated serines. I'm trying to understand how should I set my system. I started from the tutorial (http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-water) but I found that have no idea how to create a phosphorylated serine inCG structure (I have it in my initial pdb). In addition, I found that I need a secondary structure of the protein and I don't have something like this. Moreover, this protein doesn't have one. I will appreciated very much if somebody can help me and guide me a little. Thank you very much in advance. Regina This message was sent using IMP, the Internet Messaging Program. -- 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_rdf
Dear gromacs users, I want to calculate radial distribution function around my protein. I want to get g_rdf for water molecules (OW) around my protein and g_rdf for COM of some solutes around my protein. The numbers should be averaged over all the frames. I tried to look at the mailing list but there is some error and as a result I can't open it. Can someone help me with it and give me the command I should use. Regina This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] center peptide in simulation box
Dear Gromacs users and developers, I'm trying to visualize .trr from md simulation using VMD. I see that starting from some point (probable as a result of a peptide drift ) my peptide splits and it seems like one part appears at one side of the box and the other on the opposite side. Both parts are connected with a very long bond. I want to center the peptide in the box and of course I want all the molecules to be wrapped accordingly. I checked the mailing list and I found that I can use trjconv (trjconv -f *.xtc -s *.tpr -o center.xtc -center -pbc nojump). I tried to use this command with .trr (trjconv -f *.trr -o center.trr -center -pbc) as a result the peptide is still not centered and all the water molecules diffuse out of my rectangular box. Am I doing something wrong? I'm trying to center the molecule not only for visualization but also because I want to analyze the simulation using VMD and scripts I made for analysis of NAMD simulations (I worked with NAMD for a long time and I need to work with gromacs because of SPCE water). Is it possible to perform analysis with VMD (I need commands like measure distance, measure angle, cut molecules at some radius from predefined residue and pbcwrap around some molecule or peptide)? Regina This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] simulation settings
Dear Gromacs users and developers, I want to perform simulation of peptide dissolved in water using NPT. For constant temperature I use Berendsen temperature coupling. Do I have to define tc-grps for 2 groups (protein and solvent) or I may use tc-grps =System. What is the difference? The person who introduced gromacs to me uses tc-grps = Protein Sol_Ions but he is not sure why it should be in this way if at all Can you, please elucidate this issue to me. Thank you a lot. Regina This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] MD simulation with glycerol
Dear Gromacs users, I'm completely new in Gromacs. I would like to perform a simulation of a peptide in water (SPCE) in glycerol presence using OPLS-AA. I want to know where can I find the parameter and topology file in order to create a solvation box that includes glycerol. Should I construct glycerol from some building blocks? If yes what files do I need to update? A similar message was posted once on the Gromacs mailing list but there was no answer on how to do it. I found a paper "OPLS all atom force field for carbohydrates" and a couple of papers that cite this paper so maybe the parameters from this paper are already implemented to Gromacs. In addition, I used NAMD to perform this simulation so I have a pdb file that contains my peptide dissolved in water box (TIP3P) with glycerol molecules presented as well. Can I use this file in some way to generate files for simulation in Gromacs. If yes, what should I change and how should I proceed in order to perform the simulation? I'm using Gromacs VERSION 4.0.3. Thank you a lot for your help Regina This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
