[gmx-users] detailed energies per interaction
Hi, How can I get detailed energies per interaction (that is bonding and non-bonding terms for each pair/threesome/foursome of atoms) in Gromacs? 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
Re: [gmx-users] detailed energies per interaction
On 18/11/2010 6:32 PM, Efrat Noy wrote: Hi, How can I get detailed energies per interaction (that is bonding and non-bonding terms for each pair/threesome/foursome of atoms) in Gromacs? Thanks, Efrat Please search the archives before posting. There have been several threads on this in the last fortnight. Basically, you can't get the bonded terms easily. 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] Reg: Unit Of Surface Tension
All output is in gromacs units, so it is bar*nm 1 bar*nm = 0.1 mN/m = 0.1 dyn/cm That is exactly what the two posts are explaining. Sven vinothkumar mohanakrishnan schrieb: Hi all What is the unit of Surface tension that one obtains from Gromacs using the g_energy command?. I searched the mailing list and i found two posts but the answers seems to be contradictory. Because in one post it was said that mN/m and in the other bar nm. below are the link of the two post. any help is highly appreciated. http://oldwww.gromacs.org/pipermail/gmx-users/2006-September/024028.html http://www.mail-archive.com/gmx-users@gromacs.org/msg09748.html Regards Vinoth -- 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] DNA didnot wrap around CNT
Siamkhanthang Neihsial wrote: Hi friends, I have a DNA sequence (5'-GAG TCT GTG GAG GAG GTA GTC-3') and a CNT(6,5) of 90 Angstroms in length. I kept the DNA CNT at a distance of 1 angstrom. Solvents molecules(water) inside CNT are removed at a radius of CNT at 4.2 . Equilibration at 1000 steps, results in diminished quality of CNT (like bonds between carbons are no more visible!), i repeat equilibration with larger steps( 5000), the same Bonds cannot break or form in molecular mechanics. Whatever you're seeing is a visualization artifact. problem result. Also,the DNA is suppose to wraped around the CNT, but it didnot seems to happen. I am using GROMACS. Any help will be highly appreciated. If your model is not reproducing the correct behavior, then there's probably something wrong with the model. My equil.mdp file is What you've got here is an energy minimization, not equilibration, input file. No large-scale changes are going to happen during EM. I would suggest you go through some tutorial material to understand a proper Gromacs workflow in order to run actual MD. -Justin ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization of - ; Title of run ; The following lines tell the program the standard locations where to find certain files Define=-Dflexible cpp = cpp; Preprocessor ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0; Stop minimization when the maximum force 1.0 kJ/mol nsteps= 1000; Maximum number of (minimization) steps to perform nstenergy = 5; Write energies to disk every nstenergy steps nstxtcout= 10; Write coordinates to disk every nstxtcout steps xtc_grps = Protein SOL ; Which coordinate group(s) to write to disk energygrps = Protein SOL ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 5; Frequency to update the neighbor list and long range forces ns_type = simple; Method to determine neighbor list (simple, grid) coulombtype= PME-switch ; Treatment of long range electrostatic interactions rcoulomb = 0.9; long range electrostatic cut-off rlist = 1.0; Cut-off for making neighbor list (short range forces) vdwtype = Shift rvdw= 0.9; long range Van der Waals cut-off constraints = all-bonds; Bond types to replace by constraints pbc = xyz; Periodic Boundary Conditions (yes/no) constraint_algorithm=LINCS lincs_order =4 lincs_iter=2 periodic_molecules = yes nstcomm = 1 comm_mode = Linear comm_grps= Protein SOL -- Best Regards, Siam Theoretical Sciences Unit, JNCASR, (Lab) +91-080-2208-2581, (M) +91-8971001405 e-mail: skt...@gmail.com mailto:skt...@gmail.com, s...@jncasr.ac.in mailto:s...@jncasr.ac.in -- 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] Parameterization
You could use GLYCAM which is in AMBER so the parameters are already there in the correct format (but not in the AMBER ported to GROMACS) and convert that to GROMACS topology. It'll save you some time :) I had problems converting the improper dihedral that holds the NAc group planar using amb2gmx.pl so keep an eye on it. Good Luck, Oliver On 15 November 2010 22:15, Anthony Cruz Balberdi anthony.cr...@upr.eduwrote: Dear Yuvraj: There is a protocol to find the charges and force field parameters for new molecules for the AMBER force field. The best way is to try to find the parameters from a publication. If you dont find anything then use RED to find the charges (http://q4md-forcefieldtools.org/RED/). Then use ambertools to find the necessary force field parameters and generate an AMBER topology. After that use acpype to transform the amber topology to a GROMACS topology. From the GROMACS topology the create an itp file to use in your GROMACS TOPOLOGY. To better understand what I said please read the reference for the force field, the GROMACS manual and the RED tutorial. Best Regards, Anthony On Mon, Nov 15, 2010 at 5:13 PM, YUVRAJ UBOVEJA yuvrajthe...@gmail.com wrote: How to parametrize N-acetyl Glucosamine present in my PDB file with AMBER force field to use in GROMACS. Please suggest some solutions. Thanks -- Yuvraj -- 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 -- 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] cutoff values for amber ff
Dear all, I am setting-up a simulation of a protein-DNA complex using amber force field. In the manual (v4.5.3) I have found the recommended cutoff distances for electrostatics - coulombtype using PME (rcoulomb=rlist=rvdw = 0.9nm) with Gromos ff. However, I am aware the cutoff values are specific for different forcefield and also the simulated system. Since I am using the amber ff with Gromacs, I wanted to ensure I set-up the correct cutoffs to prevent any potential artifacts, so I have searched the manual, gmx-users old posts (gromacs wiki links do not work any more) and papers, and I found all sorts of distances for the non-bonded interactions tratment with PME (ranging from 1.0 to 1.4 nm). With respect to the amber ff, I found a value of 0.8nm cutoff for the PME in the Amber manual. Could you please advise me on what would be the reasonable cutoff values to choose for the protein-DNA system, with the use of Gromacs 4.5.3 and amber ff? All your comments will be greatly appreciated. Thank you Jarmila Jarmila Husby, PhD Candidate CRUK PPI Drug Discovery/ BMSG Group Department of Pharm Biol Chemistry The School of Pharmacy, University of London email: jarmila.hu...@live.pharmacy.ac.uk tel: (44) 0207 753 5996 -- 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] cutoff values for amber ff
Jarmila Husby wrote: Dear all, I am setting-up a simulation of a protein-DNA complex using amber force field. In the manual (v4.5.3) I have found the recommended cutoff distances for electrostatics - coulombtype using PME (rcoulomb=rlist=rvdw = 0.9nm) with Gromos ff. However, I am aware the cutoff values are specific for different forcefield and also the simulated system. Since I am using the amber ff with Gromacs, I wanted to ensure I set-up the correct cutoffs to prevent any potential artifacts, so I have searched the manual, gmx-users old posts (gromacs wiki links do not work any more) and papers, and I found all sorts of distances for the non-bonded interactions tratment with PME (ranging from 1.0 to 1.4 nm). With respect to the amber ff, I found a value of 0.8nm cutoff for the PME in the Amber manual. Could you please advise me on what would be the reasonable cutoff values to choose for the protein-DNA system, with the use of Gromacs 4.5.3 and amber ff? All your comments will be greatly appreciated. You haven't searched in the most important location yet - the primary literature for your chosen force field (and there are subtle differences among the different Amber force fields). It is generally recommended to follow the protocols used to derive the force field, in the absence of any subsequent modifications that demonstrate better results. -Justin Thank you Jarmila Jarmila Husby, PhD Candidate CRUK PPI Drug Discovery/ BMSG Group Department of Pharm Biol Chemistry The School of Pharmacy, University of London email: jarmila.hu...@live.pharmacy.ac.uk tel: (44) 0207 753 5996 -- 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] Gromacs Quotes
Hi I am wondering where can I find the file containing all the Gromacs Quotes , which are printed at the end of program run? thanks sikandar -- 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] Gromacs Quotes
On 2010-11-18 20.48, Sikandar Mashayak wrote: Hi I am wondering where can I find the file containing all the Gromacs Quotes , which are printed at the end of program run? thanks sikandar share/gromacs/top/gurgle.dat -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] genion writes a log file?
Hi,
When using versions 4.5.2 and 4.5.3, I have noticed that genion now outputs a
file called genion.log (or genion_node0.log with 4.5.2) that appears to
contain the header information normally found in an md.log file produced by
mdrun (see below). Is this normal? There really isn't any use to this file,
from what I can tell, so I suspect it shouldn't be written, but I can't find the
relevant code change that would have caused it.
-Justin
genion.log:
===
Log file opened on Thu Nov 18 15:12:15 2010
Host: justin-lemkuls-macbook.local pid: 19469 nodeid: 0 nnodes: 1
The Gromacs distribution was built Thu Nov 18 15:00:26 EST 2010 by
jus...@justin-lemkuls-macbook.local (Darwin 9.8.0 i386)
Input Parameters:
integrator = steep
nsteps = 5
init_step= 0
ns_type = Grid
nstlist = 1
ndelta = 2
nstcomm = 10
comm_mode= Linear
nstlog = 100
nstxout = 100
nstvout = 100
nstfout = 0
nstcalcenergy= -1
nstenergy= 100
nstxtcout= 0
init_t = 0
delta_t = 0.001
xtcprec = 1000
nkx = 50
nky = 54
nkz = 48
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 = No
nsttcouple = -1
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
rlistlong= 1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
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 = No
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 = 0
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 = 1000
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
[gmx-users] Using Charmm FF with implicit solvent on gromacs
Dear all, I would like to know if anyone has experience on running simulations using the Charmm FF and implicit solvent model on gromacs. I have found that gromacs has three implementations for GB models - Still - Hawkins-Cramer-Truhlar (HCT) - Onufriev-Bashford-Case (OBC) The charmm FF has been extensively tested with the GBSW* implementation (in Charmm program) for which the backbone phi/psi cross-term (CMAP) and the atomic input radii were specifically optimized (Chan, Im and Brooks, JACS, 2006). Is there a way to perform the same calculation on gromacs? * W. Im, M.S. Lee, and C.L. Brooks III Generalized Born Model with a Simple Smoothing Function. J. Comput. Chem. 24:1691-1702 (2003). -- 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] Cumulative coordination number?
Dear all, I am trying to calculate the cumulative coordination number of solvents around my solute as a function of distance but the result obtained seem not reasonable. I used the following command. g_rdf -f DD.xtc -s DD.gro -n DD.ndx -cn -b 18000 -e 2-o CNDD.xvg My solvent molecule is heptane and want to see how many heptane molecule are there in the first shell (from RDF). Can anybody shed a light on this. Is this method work for a molecule or only valid for a single atom type in the molecule. what method is the correct for calculating the solvent molecules around my solute. Thank you Rob -- 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] Area per lipid calculation
Dear gromacs users, I have a protein embedded in a lipid bilayer. After sufficient equilibration of the system ( i.e. size of box X and Box Y became quite constant), I would now like to assess the area per lipid of my system. However, (I think) I could not simply do this ( average size of box X * average size of box Y/ number of lipids per monolayer) because there is a protein in the middle of the bilayer. Ideally I would first like to calculate the area occupied by the protein then take the difference between the two as my answer. I notice this is how the inflategro script calculates the estimated area per lipid during the shrinking process. I have had a search through the mailing list to look for an answer but to no avail. It seems I might need a script to perform that? Thank you for your help. HW This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK Malaysia legislation. -- 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] 4-site rigid body model
Hi, I have a molecule consisting of 4 sites which have fixed relative positions interacting only through LJ and coulomb interaction. I was wondering how can I do MD simulation in GROMACS keeping the geometry unchanged . Is just putting constraints along all the possible distances and using LINCS good enough for maintaining the geometry ? Or , Does one need to also make sure the angles are also unchanged but I am not sure how to do that ? I was wondering what will be an optimum ways of dealing with such a 4-site system. I guess, Settle can not be used for such a 4-site system. Thanks Sanku -- 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] Area per lipid calculation
NG HUI WEN wrote: Dear gromacs users, I have a protein embedded in a lipid bilayer. After sufficient equilibration of the system ( i.e. size of box X and Box Y became quite constant), I would now like to assess the area per lipid of my system. However, (I think) I could not simply do this ( average size of box X * average size of box Y/ number of lipids per monolayer) because there is a protein in the middle of the bilayer. Ideally I would first like to calculate the area occupied by the protein then take the difference between the two as my answer. I notice this is how the inflategro script calculates the estimated area per lipid during the shrinking process. I have had a search through the mailing list to look for an answer but to no avail. It seems I might need a script to perform that? Shameless self-promotion: http://www.bevanlab.biochem.vt.edu/GridMAT-MD/ -Justin Thank you for your help. HW This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK Malaysia legislation. -- 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] 4-site rigid body model
Sanku M wrote: Hi, I have a molecule consisting of 4 sites which have fixed relative positions interacting only through LJ and coulomb interaction. I was wondering how can I do MD simulation in GROMACS keeping the geometry unchanged . Is just putting constraints along all the possible distances and using LINCS good enough for maintaining the geometry ? Or I suspect it is, and I would imagine it would be easy enough to determine that with a short test. , Does one need to also make sure the angles are also unchanged but I am not sure how to do that ? I was wondering what will be an optimum ways You can also set constraints = all-angles in the .mdp file. of dealing with such a 4-site system. I guess, Settle can not be used for such a 4-site system. Nope, SETTLE shouldn't be relevant here. -Justin Thanks Sanku -- 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] Using Charmm FF with implicit solvent on gromacs
On 19/11/2010 8:49 AM, César Ávila wrote: Dear all, I would like to know if anyone has experience on running simulations using the Charmm FF and implicit solvent model on gromacs. I have found that gromacs has three implementations for GB models * Still * Hawkins-Cramer-Truhlar (HCT) * Onufriev-Bashford-Case (OBC) The charmm FF has been extensively tested with the GBSW* implementation (in Charmm program) for which the backbone phi/psi cross-term (CMAP) and the atomic input radii were specifically optimized (Chan, Im and Brooks, JACS, 2006). Is there a way to perform the same calculation on gromacs? * W. Im, M.S. Lee, and C.L. Brooks III Generalized Born Model with a Simple Smoothing Function. J. Comput. Chem. 24:1691-1702 (2003). There's http://dx.doi.org/10.1021/ct900549r from the people who implemented CHARMM+implicit solvation in GROMACS 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
