Re: [gmx-users] temperature problem
Hi everyone I want to ask a question ... Like If I have Metal parameters i.e non-bonded parameters ...and I want to define its interactions with others for example a water molecule .having O and H non-bonded parameters ... Can I define their interaction by following combination rules for particular force field ...Or Some thing more than that needed to be done to define their interaction in non-bonded file !!! Thanks and Regards Lovika On Mon, Jun 22, 2015 at 6:16 PM, Lovika Moudgil lovikamoud...@gmail.com wrote: Thanks Justin Regrads Lovika On Mon, Jun 22, 2015 at 6:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/22/15 7:55 AM, Lovika Moudgil wrote: Hi everyone Can anybody tell from where I will get this tip3p.gro file ...I have tip4p.gro and tip5p.gro ...but not tip3p.gro Error is :: *Library file tip3p.gro not found in current dir nor in default directories.(You can set the directories to search with the GMXLIB path variable)* I am not being able to find this gro file . Use spc216.gro. Both are 3-point water models; there's no reason for redundancy. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] temperature problem
Hi everyone Can anybody tell from where I will get this tip3p.gro file ...I have tip4p.gro and tip5p.gro ...but not tip3p.gro Error is :: *Library file tip3p.gro not found in current dir nor in default directories.(You can set the directories to search with the GMXLIB path variable)* I am not being able to find this gro file . Thanks and Regards Lovika On Fri, Jun 19, 2015 at 7:45 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/19/15 10:13 AM, Lovika Moudgil wrote: Hi .. Can anybody tell me about *nrdf* (*radial distribution functions*) value that is in log file . How it effect our system !! Any link that I can follow to understand its role more clearly !!! nrdf in this context is the number of degrees of freedom, nothing to do with radial distribution functions. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] temperature problem
Hi .. Can anybody tell me about *nrdf* (*radial distribution functions*) value that is in log file . How it effect our system !! Any link that I can follow to understand its role more clearly !!! Thanks and Regards Lovika On Wed, Jun 17, 2015 at 10:54 AM, Lovika Moudgil lovikamoud...@gmail.com wrote: Thanks Justin . Your suggestions helped me a lot I got it . Regards Lovika On Sun, Jun 7, 2015 at 7:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/6/15 2:03 AM, Lovika Moudgil wrote: Hi Justin ... Thanks for being so supportive . I tried things as you said and figured out that my slab is having problem with water . I have one more question ... As I am working with golp ff parameters .. and it's parameters are fine for water . Like if I put one water molecule on my slab ..and run my system ...Its doing well ...but if I do same things with box full of water ... its not working !!! Is this possible?? Could it be because of parameters compatibility Or could be because of my slab Could be either. Maybe the definition of the water-slab parameters is wrong, such that one water only infrequently interacts and the crash is rare, whereas with a full box, the bad interaction comes up frequently. But at least it sounds like you've identified the problem. Now the issue is how to properly implement the GOLP parameters; if you did this yourself, check your work carefully. If you got the parameters from somewhere else, ask the person who created the files. -Justin Thanks and Regards Lovika On Fri, Jun 5, 2015 at 10:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/5/15 8:09 AM, Lovika Moudgil wrote: Hi Justin... Yes I agree my system is behaving absurdly . But I am wondering why !!I have done minimization without any error ..here is the result ... Steepest Descents converged to Fmax 1000 in 1004 steps Potential Energy = -9.6667906e+05 Maximum force = 9.7920349e+02 on atom 796 Norm of force = 1.7943926e+01 ... I have One gold slab ...with golp parameters ..and amino acid on it ...in box with water and Na , Cl ions Freezing is for gold only So simplify the system - remove the gold layer and see if the remainder works, do a system of water + gold, etc. Your system is more complex than you're likely giving it credit for. Break it down - be scientific! System is not that big . And thing is temperature remain at the value (that is 300K) for few time after some time it start behaving weird . If system is wrong why its working even for one step ?? Probably because the starting configuration is fine, but the trajectory evolves in such a way that it produces unreasonable physics. Freezing is a pretty severe perturbation. Investigate the validity of the force field. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] temperature problem
Thanks Justin . Your suggestions helped me a lot I got it . Regards Lovika On Sun, Jun 7, 2015 at 7:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/6/15 2:03 AM, Lovika Moudgil wrote: Hi Justin ... Thanks for being so supportive . I tried things as you said and figured out that my slab is having problem with water . I have one more question ... As I am working with golp ff parameters .. and it's parameters are fine for water . Like if I put one water molecule on my slab ..and run my system ...Its doing well ...but if I do same things with box full of water ... its not working !!! Is this possible?? Could it be because of parameters compatibility Or could be because of my slab Could be either. Maybe the definition of the water-slab parameters is wrong, such that one water only infrequently interacts and the crash is rare, whereas with a full box, the bad interaction comes up frequently. But at least it sounds like you've identified the problem. Now the issue is how to properly implement the GOLP parameters; if you did this yourself, check your work carefully. If you got the parameters from somewhere else, ask the person who created the files. -Justin Thanks and Regards Lovika On Fri, Jun 5, 2015 at 10:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/5/15 8:09 AM, Lovika Moudgil wrote: Hi Justin... Yes I agree my system is behaving absurdly . But I am wondering why !!I have done minimization without any error ..here is the result ... Steepest Descents converged to Fmax 1000 in 1004 steps Potential Energy = -9.6667906e+05 Maximum force = 9.7920349e+02 on atom 796 Norm of force = 1.7943926e+01 ... I have One gold slab ...with golp parameters ..and amino acid on it ...in box with water and Na , Cl ions Freezing is for gold only So simplify the system - remove the gold layer and see if the remainder works, do a system of water + gold, etc. Your system is more complex than you're likely giving it credit for. Break it down - be scientific! System is not that big . And thing is temperature remain at the value (that is 300K) for few time after some time it start behaving weird . If system is wrong why its working even for one step ?? Probably because the starting configuration is fine, but the trajectory evolves in such a way that it produces unreasonable physics. Freezing is a pretty severe perturbation. Investigate the validity of the force field. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] temperature problem
Hi Justin ... Thanks for being so supportive . I tried things as you said and figured out that my slab is having problem with water . I have one more question ... As I am working with golp ff parameters .. and it's parameters are fine for water . Like if I put one water molecule on my slab ..and run my system ...Its doing well ...but if I do same things with box full of water ... its not working !!! Is this possible?? Could it be because of parameters compatibility Or could be because of my slab Thanks and Regards Lovika On Fri, Jun 5, 2015 at 10:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/5/15 8:09 AM, Lovika Moudgil wrote: Hi Justin... Yes I agree my system is behaving absurdly . But I am wondering why !!I have done minimization without any error ..here is the result ... Steepest Descents converged to Fmax 1000 in 1004 steps Potential Energy = -9.6667906e+05 Maximum force = 9.7920349e+02 on atom 796 Norm of force = 1.7943926e+01 ... I have One gold slab ...with golp parameters ..and amino acid on it ...in box with water and Na , Cl ions Freezing is for gold only So simplify the system - remove the gold layer and see if the remainder works, do a system of water + gold, etc. Your system is more complex than you're likely giving it credit for. Break it down - be scientific! System is not that big . And thing is temperature remain at the value (that is 300K) for few time after some time it start behaving weird . If system is wrong why its working even for one step ?? Probably because the starting configuration is fine, but the trajectory evolves in such a way that it produces unreasonable physics. Freezing is a pretty severe perturbation. Investigate the validity of the force field. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] temperature problem
Hi Justin... Yes I agree my system is behaving absurdly . But I am
wondering why !!I have done minimization without any error ..here is the
result ...
Steepest Descents converged to Fmax 1000 in 1004 steps
Potential Energy = -9.6667906e+05
Maximum force = 9.7920349e+02 on atom 796
Norm of force = 1.7943926e+01
... I have One gold slab ...with golp parameters ..and amino acid on it
...in box with water and Na , Cl ions Freezing is for gold only
System is not that big . And thing is temperature remain at the value (that
is 300K) for few time after some time it start behaving weird . If system
is wrong why its working even for one step ??
Thanks and Regards
Lovika
On Thu, Jun 4, 2015 at 6:27 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/4/15 8:52 AM, Lovika Moudgil wrote:
HiiiHere is my .mdp file below ...
title= OPLS Lysozyme NVT equilibration
define= -DPOSRES; position restrain the protein
; Run parameters
integrator= md; leap-frog integrator
nsteps= 200; 2 * 5 = 100 ps
dt= 0.001; 2 fs
; Output control
nstxout= 500; save coordinates every 1.0 ps
nstvout= 500; save velocities every 1.0 ps
nstenergy= 500; save energies every 1.0 ps
nstlog= 500; update log file every 1.0 ps
nstxtcout = 500 ; [steps] freq to write
coordinates
to xtc trajectory
xtc_precision = 1000 ; [real] precision to write xtc
trajectory
comm_mode= Linear
comm_grps = Protein Non-Protein ; group(s) for center of
mass motion removal
; Bond parameters
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
; 7.3.9 Neighbor Searching
cutoff-scheme = Verlet
nstlist = 10 ; [steps] freq to update neighbor
list
ns_type = grid ; method of updating neighbor list
pbc = xyz ; periodic boundary conditions in
all directions
rlist = 1.0 ; [nm] cut-off distance for the
short-range neighbor list
; 7.3.10 Electrostatics
coulombtype = PME ; Particle-Mesh Ewald
electrostatics
rcoulomb= 1.0 ; [nm] distance for Coulomb
cut-off
; 7.3.11 VdW
rvdw= 1.0 ; [nm] distance for LJ cut-off
DispCorr= Ener ; apply long range dispersion
corrections
; 7.3.13 Ewald
fourierspacing = 0.12 ; [nm] grid spacing for FFT grid
when using PME
pme_order = 4 ; interpolation order for PME, 4 =
cubic
ewald_rtol = 1e-5 ; relative strength of
Ewald-shifted potential at rcoulomb
; Temperature coupling is on
tcoupl= nose-hoover; modified Berendsen thermostat
tc-grps= Protein Non-Protein
tau_t= 0.1 0.1 ; time constant, in ps
ref_t= 300 300 ; reference temperature, one for each
group, in K
; Pressure coupling is off
pcoupl= no ; no pressure coupling in NVT
; Velocity generation
gen_vel= yes; assign velocities from Maxwell distribution
gen_temp= 300; temperature for Maxwell distribution
gen_seed= -1; generate a random seed
; To keep au surface in place, freeze Au atoms.
; The AU group has been defined via make_ndx
; to contains all the AU atoms ('a AU').
freezegrps = AUS AUB AUI
freezedim= Y Y Y Y Y Y Y Y Y
And in one part of log file temperature is getting high..without
error
and it keeps on increasing ...
Energies (kJ/mol)
AngleProper Dih. Ryckaert-Bell. LJ-14
Coulomb-14
2.91339e+013.23884e-018.52437e+001.65299e+01
2.68992e+02
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
Potential
5.70551e+05 -6.29186e+03 -8.96225e+054.42542e+03
-3.27216e+05
Kinetic En. Total Energy Conserved En.*Temperature* Pres. DC
(bar)
9.71936e+099.71903e+092.71970e+19 * 2.35145e+07*
0.0e+00
Ask yourself whether or not this is even reasonable. A temperature of
10^7? That's 4000x hotter than the surface of the sun. There's no way
that's real. Your system is physically nonsensical. You'll have to
describe in complete detail what it is you're trying to do, but the
combination of multiple comm-grps, freezing (which is a pretty massive
perturbation in and of itself), restraints, etc. is quite complex and any
number of things could be causing a problem. It could be something as
simple as insufficient minimization
Re: [gmx-users] temperature problem
HiiiHere is my .mdp file below ...
title= OPLS Lysozyme NVT equilibration
define= -DPOSRES; position restrain the protein
; Run parameters
integrator= md; leap-frog integrator
nsteps= 200; 2 * 5 = 100 ps
dt= 0.001; 2 fs
; Output control
nstxout= 500; save coordinates every 1.0 ps
nstvout= 500; save velocities every 1.0 ps
nstenergy= 500; save energies every 1.0 ps
nstlog= 500; update log file every 1.0 ps
nstxtcout = 500 ; [steps] freq to write coordinates
to xtc trajectory
xtc_precision = 1000 ; [real] precision to write xtc
trajectory
comm_mode= Linear
comm_grps = Protein Non-Protein ; group(s) for center of
mass motion removal
; Bond parameters
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
; 7.3.9 Neighbor Searching
cutoff-scheme = Verlet
nstlist = 10 ; [steps] freq to update neighbor
list
ns_type = grid ; method of updating neighbor list
pbc = xyz ; periodic boundary conditions in
all directions
rlist = 1.0 ; [nm] cut-off distance for the
short-range neighbor list
; 7.3.10 Electrostatics
coulombtype = PME ; Particle-Mesh Ewald electrostatics
rcoulomb= 1.0 ; [nm] distance for Coulomb cut-off
; 7.3.11 VdW
rvdw= 1.0 ; [nm] distance for LJ cut-off
DispCorr= Ener ; apply long range dispersion
corrections
; 7.3.13 Ewald
fourierspacing = 0.12 ; [nm] grid spacing for FFT grid
when using PME
pme_order = 4 ; interpolation order for PME, 4 =
cubic
ewald_rtol = 1e-5 ; relative strength of
Ewald-shifted potential at rcoulomb
; Temperature coupling is on
tcoupl= nose-hoover; modified Berendsen thermostat
tc-grps= Protein Non-Protein
tau_t= 0.1 0.1 ; time constant, in ps
ref_t= 300 300 ; reference temperature, one for each
group, in K
; Pressure coupling is off
pcoupl= no ; no pressure coupling in NVT
; Velocity generation
gen_vel= yes; assign velocities from Maxwell distribution
gen_temp= 300; temperature for Maxwell distribution
gen_seed= -1; generate a random seed
; To keep au surface in place, freeze Au atoms.
; The AU group has been defined via make_ndx
; to contains all the AU atoms ('a AU').
freezegrps = AUS AUB AUI
freezedim= Y Y Y Y Y Y Y Y Y
And in one part of log file temperature is getting high..without error
and it keeps on increasing ...
Energies (kJ/mol)
AngleProper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
2.91339e+013.23884e-018.52437e+001.65299e+012.68992e+02
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
5.70551e+05 -6.29186e+03 -8.96225e+054.42542e+03 -3.27216e+05
Kinetic En. Total Energy Conserved En.*Temperature* Pres. DC
(bar)
9.71936e+099.71903e+092.71970e+19 * 2.35145e+07*
0.0e+00
Pressure (bar) Constr. rmsd
Thanks and Regards
Lovika
On Thu, Jun 4, 2015 at 5:09 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/4/15 12:39 AM, Lovika Moudgil wrote:
Hi...Justin Thanks for explaining .. I just want to ask could
there be any other reasons too?? ...Because I have tried it with PME
too...and still I am not getting desired temperature
You'll have to provide a full .mdp file and quantitative evidence of what
you're seeing. There are plenty of things that could be going on, but I'm
not going just blindly guess.
-Justin
Thanks and Regards
Lovika
On Wed, Jun 3, 2015 at 5:29 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/3/15 3:46 AM, Lovika Moudgil wrote:
Hi...thanks for reply Peter and Mark I tried with temperature
coupling
. But things are still same ...
Hi ... Mark would you like to explain this factor to me ??
Using a plain cutoff in the condensed phase is outdated methodology
that
is very inaccurate. Cutoff artifacts lead to accumulation of heat in the
system. Use something sensible like PME.
-Justin
Thanks and Regards
Lovika
On Tue, Jun 2, 2015 at 2:23 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
Runaway heating is the only useful feature of cutoff electrostatics.
Use
an
actual model physics.
Mark
On Tue, Jun 2, 2015 at 10:19 AM Peter Kroon p.c.kr...@rug.nl wrote:
On 02/06/15 09:43
Re: [gmx-users] temperature problem
Hi...thanks for reply Peter and Mark I tried with temperature coupling
. But things are still same ...
Hi ... Mark would you like to explain this factor to me ??
Thanks and Regards
Lovika
On Tue, Jun 2, 2015 at 2:23 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
Runaway heating is the only useful feature of cutoff electrostatics. Use an
actual model physics.
Mark
On Tue, Jun 2, 2015 at 10:19 AM Peter Kroon p.c.kr...@rug.nl wrote:
On 02/06/15 09:43, Lovika Moudgil wrote:
Hi everyone
I am having some problem in my md run .In my system temperature of
system
is abruptly increasing .I have done nvt for 50 picoseconds ..nd then
using
it for further md simulation .I am not getting any error for this
temperature increase .But when I plot temperature graph ,
temperature
is not same as nvt and is very high in md .I am having gold slab and
amino
acid in my system . Mdp file for md run is below Is their any error
in
my mdp file ???what could be the reason for this ???Please suggest
; Run parameters
integrator= md; leap-frog integrator
nsteps= 3000; 2 * 5 = 100 ps
dt= 0.001; 2 fs
; Output control
; Output control
nstxout= 500; save coordinates every 1.0 ps
nstvout= 500; save velocities every 1.0 ps
nstenergy= 500; save energies every 1.0 ps
nstlog= 500; update log file every 1.0 ps
nstxtcout = 500 ; [steps] freq to write
coordinates
to xtc trajectory
xtc_precision = 1000 ; [real] precision to write xtc
trajectory
xtc_grps= System; group(s) to write to xtc
trajectory
energygrps = System; group(s) to write to energy
file
; Bond parameters
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
cutoff-scheme = Verlet
ns_type= grid; search neighboring grid cells
nstlist= 10; 20 fs, largely irrelevant with Verlet
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = cut-off
pme_order= 4; cubic interpolation
fourierspacing= 0.12; grid spacing for FFT
; Temperature coupling is on
tcoupl= nose-hoover; modified Berendsen
thermostat
tc-grps= Protein AUS AUB AUI SOL NA CL; two coupling
groups -
more accurate
tau_t= 0.1 0.1 0.1 0.1 0.1 0.1 0.1 ; time constant,
in ps
ref_t= 300 300 300 300 300 300 300; reference
temperature, one for each group, in K
You have too many temperature coupling groups. (What Not To Do on
http://www.gromacs.org/Documentation/Terminology/Thermostats)
I'd stick to one for proteins, and one for the rest.
; 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
; Velocity generation
gen_vel= yes; assign velocities from Maxwell
distribution
gen_temp= 300; temperature for Maxwell distribution
gen_seed= -1; generate a random seed
; To keep au surface in place, freeze Au atoms.
; The AU group has been defined via make_ndx
; to contains all the AU atoms ('a AU').
freezegrps = AUS AUB AUI
freezedim= Y Y Y Y Y Y Y Y Y
comm_mode= None
Thanks and Reagrds
Lovika
Peter
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Re: [gmx-users] temperature problem
Hi...Justin Thanks for explaining .. I just want to ask could
there be any other reasons too?? ...Because I have tried it with PME
too...and still I am not getting desired temperature
Thanks and Regards
Lovika
On Wed, Jun 3, 2015 at 5:29 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/3/15 3:46 AM, Lovika Moudgil wrote:
Hi...thanks for reply Peter and Mark I tried with temperature coupling
. But things are still same ...
Hi ... Mark would you like to explain this factor to me ??
Using a plain cutoff in the condensed phase is outdated methodology that
is very inaccurate. Cutoff artifacts lead to accumulation of heat in the
system. Use something sensible like PME.
-Justin
Thanks and Regards
Lovika
On Tue, Jun 2, 2015 at 2:23 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
Runaway heating is the only useful feature of cutoff electrostatics. Use
an
actual model physics.
Mark
On Tue, Jun 2, 2015 at 10:19 AM Peter Kroon p.c.kr...@rug.nl wrote:
On 02/06/15 09:43, Lovika Moudgil wrote:
Hi everyone
I am having some problem in my md run .In my system temperature of
system
is abruptly increasing .I have done nvt for 50 picoseconds ..nd then
using
it for further md simulation .I am not getting any error for this
temperature increase .But when I plot temperature graph ,
temperature
is not same as nvt and is very high in md .I am having gold slab and
amino
acid in my system . Mdp file for md run is below Is their any error
in
my mdp file ???what could be the reason for this ???Please suggest
; Run parameters
integrator= md; leap-frog integrator
nsteps= 3000; 2 * 5 = 100 ps
dt= 0.001; 2 fs
; Output control
; Output control
nstxout= 500; save coordinates every 1.0 ps
nstvout= 500; save velocities every 1.0 ps
nstenergy= 500; save energies every 1.0 ps
nstlog= 500; update log file every 1.0 ps
nstxtcout = 500 ; [steps] freq to write
coordinates
to xtc trajectory
xtc_precision = 1000 ; [real] precision to write xtc
trajectory
xtc_grps= System; group(s) to write to xtc
trajectory
energygrps = System; group(s) to write to energy
file
; Bond parameters
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
cutoff-scheme = Verlet
ns_type= grid; search neighboring grid cells
nstlist= 10; 20 fs, largely irrelevant with Verlet
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = cut-off
pme_order= 4; cubic interpolation
fourierspacing= 0.12; grid spacing for FFT
; Temperature coupling is on
tcoupl= nose-hoover; modified Berendsen
thermostat
tc-grps= Protein AUS AUB AUI SOL NA CL; two coupling
groups -
more accurate
tau_t= 0.1 0.1 0.1 0.1 0.1 0.1 0.1 ; time constant,
in ps
ref_t= 300 300 300 300 300 300 300; reference
temperature, one for each group, in K
You have too many temperature coupling groups. (What Not To Do on
http://www.gromacs.org/Documentation/Terminology/Thermostats)
I'd stick to one for proteins, and one for the rest.
; 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
; Velocity generation
gen_vel= yes; assign velocities from Maxwell
distribution
gen_temp= 300; temperature for Maxwell distribution
gen_seed= -1; generate a random seed
; To keep au surface in place, freeze Au atoms.
; The AU group has been defined via make_ndx
; to contains all the AU atoms ('a AU').
freezegrps = AUS AUB AUI
freezedim= Y Y Y Y Y Y Y Y Y
comm_mode= None
Thanks and Reagrds
Lovika
Peter
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[gmx-users] temperature problem
Hi everyone
I am having some problem in my md run .In my system temperature of system
is abruptly increasing .I have done nvt for 50 picoseconds ..nd then using
it for further md simulation .I am not getting any error for this
temperature increase .But when I plot temperature graph , temperature
is not same as nvt and is very high in md .I am having gold slab and amino
acid in my system . Mdp file for md run is below Is their any error in
my mdp file ???what could be the reason for this ???Please suggest
; Run parameters
integrator= md; leap-frog integrator
nsteps= 3000; 2 * 5 = 100 ps
dt= 0.001; 2 fs
; Output control
; Output control
nstxout= 500; save coordinates every 1.0 ps
nstvout= 500; save velocities every 1.0 ps
nstenergy= 500; save energies every 1.0 ps
nstlog= 500; update log file every 1.0 ps
nstxtcout = 500 ; [steps] freq to write coordinates
to xtc trajectory
xtc_precision = 1000 ; [real] precision to write xtc
trajectory
xtc_grps= System; group(s) to write to xtc
trajectory
energygrps = System; group(s) to write to energy file
; Bond parameters
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
cutoff-scheme = Verlet
ns_type= grid; search neighboring grid cells
nstlist= 10; 20 fs, largely irrelevant with Verlet
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = cut-off
pme_order= 4; cubic interpolation
fourierspacing= 0.12; grid spacing for FFT
; Temperature coupling is on
tcoupl= nose-hoover; modified Berendsen thermostat
tc-grps= Protein AUS AUB AUI SOL NA CL; two coupling groups -
more accurate
tau_t= 0.1 0.1 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps
ref_t= 300 300 300 300 300 300 300; 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
; Velocity generation
gen_vel= yes; assign velocities from Maxwell distribution
gen_temp= 300; temperature for Maxwell distribution
gen_seed= -1; generate a random seed
; To keep au surface in place, freeze Au atoms.
; The AU group has been defined via make_ndx
; to contains all the AU atoms ('a AU').
freezegrps = AUS AUB AUI
freezedim= Y Y Y Y Y Y Y Y Y
comm_mode= None
Thanks and Reagrds
Lovika
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[gmx-users] nvt problem
Hi Everyone ,
I am having a problem in NVT of system . In my system I have Gold and
aminoacid . For Gold I am using GolP forcefield and for aminoacid using
OPLSAA forcefield . I have done energy minimization of my system but when I
am doing NVT I am getting error of water is not getting settled . I am
confused How it got minimize if water is not settled in system .I have
tried changing parameters of NVT.mdp file but noting worked . Can any body
help me what can be the root cause for this . I will be thankful for
guidance .
My NVT.mdp
; 7.3.2 Preprocessing
define = -DPOSRES ; defines to pass to the
preprocessor
; 7.3.3 Run Control
integrator = md; md integrator
tinit = 0 ; [ps] starting time for run
dt = 0.001 ; [ps] time step for
integration
nsteps = 25000 ; maximum number of steps
to integrate, 0.001 * 25,000 = 25 ps
nstcomm = 1 ; [steps] frequency of mass
motion removal
comm_grps = Protein Non-Protein ; group(s) for center of
mass motion removal
; 7.3.8 Output Control
nstxout = 25000 ; [steps] freq to write coordinates
to trajectory
nstvout = 25000 ; [steps] freq to write velocities
to trajectory
nstfout = 25000 ; [steps] freq to write forces to
trajectory
nstlog = 50 ; [steps] freq to write energies to
log file
nstenergy = 100 ; [steps] freq to write energies to
energy file
nstxtcout = 100 ; [steps] freq to write coordinates
to xtc trajectory
xtc_precision = 1000 ; [real] precision to write xtc
trajectory
xtc_grps= System; group(s) to write to xtc
trajectory
energygrps = System; group(s) to write to energy file
; 7.3.9 Neighbor Searching
nstlist = 1 ; [steps] freq to update neighbor
list
ns_type = grid ; method of updating neighbor list
pbc = xyz ; periodic boundary conditions in
all directions
rlist = 1.4 ; [nm] cut-off distance for the
short-range neighbor list
; 7.3.10 Electrostatics
coulombtype = PME ; Particle-Mesh Ewald electrostatics
rcoulomb= 1.4 ; [nm] distance for Coulomb cut-off
; 7.3.11 VdW
vdwtype = cut-off ; twin-range cut-off with rlist
where rvdw = rlist
rvdw= 1.4 ; [nm] distance for LJ cut-off
DispCorr= EnerPres ; apply long range dispersion
corrections
; 7.3.13 Ewald
fourierspacing = 0.10 ; [nm] grid spacing for FFT grid
when using PME
pme_order = 4 ; interpolation order for PME, 4 =
cubic
ewald_rtol = 1e-5 ; relative strength of
Ewald-shifted potential at rcoulomb
; 7.3.14 Temperature Coupling
tcoupl = nose-hoover ; temperature
coupling with Berendsen-thermostat
tc_grps = ProteinNon-Protein; groups to couple
seperately to temperature bath
tau_t = 0.10.1; [ps] time
constant for coupling
ref_t = 310310; [K] reference
temperature for coupling
; 7.3.17 Velocity Generation
gen_vel = no ; generate velocities according to
Maxwell distribution of temperature
gen_temp= 310 ; [K] temperature for Maxwell
distribution
gen_seed= -1; [integer] used to initialize
random generator for random velocities
; 7.3.18 Bonds
constraints = all-bonds ; convert all bonds to constraints
constraint_algorithm= LINCS ; LINear Constraint Solver
lincs_order = 4 ; highest order in the expansion of
the contraint coupling matrix
lincs_iter = 1 ; number of iterations to correct
for rotational lengthening
lincs_warnangle = 80; [degrees] maximum angle that a
bond can rotate before LINCS will complain
; To keep au surface in place, freeze Au atoms.
; The AU group has been defined via make_ndx
; to contains all the AU atoms ('a AU').
freezegrps = AU AUI
freezedim= Y Y Y Y Y Y
comm_mode = none
Regards
Lovika
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Re: [gmx-users] itp file
Thanks for reply Lalit , Actually my system have citrate anion and I want .itp for citrate and further I will use OPLA/SS force field!! It can't be generated be pdb2gmx!! Regards Lovika On Thu, Sep 11, 2014 at 3:35 PM, Lalita Shaki lalitash...@gmail.com wrote: Hi Lovika, You can't use the .itp file from GROMOS for other forcefield. Which kind of molecule are you studying? For generating the .itp file is usually use the pdb2gmx tool. Regards Lalita Message: 1 Date: Thu, 11 Sep 2014 10:22:39 +0530 From: Lovika Moudgil lovikamoud...@gmail.com To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: [gmx-users] itp file Message-ID: CANz=wd= ccwj65te2vc5ezf_3k_nos0yfxrkusx+bf1wzkgr...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi everyone , Need some help . I am using OPLS/AA force field . I am generating .itp file from external tool , But these tools are using GROMOS force fields . Is it fine to use these .itp files with OPLS/AA force field ?? Or if its not fine to use these file with different force field than how can I generate .itp files for OPLS/AA ? Thanks and Regards Lovika -- Lalita S. Uribe. European Master in Theoretical Chemistry and Computational Modeling. PhD student. Johannes Gutenberg-Universität Mainz -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] itp file
Thanks Justin ... I will try as you said!! Regards Lovika On Thu, Sep 11, 2014 at 6:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/14 6:09 AM, Lovika Moudgil wrote: Thanks for reply Lalit , Actually my system have citrate anion and I want .itp for citrate and further I will use OPLA/SS force field!! It can't be generated be pdb2gmx!! The OPLS-AA strategy is generally similar to GROMOS - you can piece the molecule together from existing functional groups. Since the force field already covers everything you need for citrate, assigning charges and atomtypes is straightforward. You can create an .rtp entry for it and have pdb2gmx do all the work of assigning the bonded interactions (you need to specify the [bonds], pdb2gmx does the rest). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Integrator problem
Hi everyoneI want to ask one question...In my .mdp file if I use md intergrator for energy minimisation .then system is fine...but if I use steep integrator...my system got error of more force on one atomI not clear why this is happeingcan any body guide me please.. Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Status of MD simulation
Hi...I think the best way is to check log file If I m wrong please do correct me!! Regards Lovika On 8 Sep 2014 19:21, ankit agrawal aka...@gmail.com wrote: hi I am running a 5ns simulation using mdrun command. So this will take a day to complete. So I want to know that how to check the status of simulation in between the run whether it is going in right direction or not? thanks regards ankit -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Integrator problem
Oo.thanks for guiding Mark !!! Regards Lovika On 8 Sep 2014 19:45, Mark Abraham mark.j.abra...@gmail.com wrote: The md integrator does MD, not EM... Mark On Sep 8, 2014 4:11 PM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi everyoneI want to ask one question...In my .mdp file if I use md intergrator for energy minimisation .then system is fine...but if I use steep integrator...my system got error of more force on one atomI not clear why this is happeingcan any body guide me please.. Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] non-zero charge
Thanks everyone for help Regards Lovika On Fri, Sep 5, 2014 at 3:34 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/5/14, 3:27 AM, Indu Kumari wrote: Good afternoon, No, if your system is showing some charge then it gives a note not an error. So the reason is something else, check your .mdp file. In this case, a fractional net charge of this magnitude indicates a serious topology error. It is a note rather than a warning because of floating-point math, which can lead to very small, meaningless fractional charges (on the order of 0.0001 or so, usually), so we cannot with certainty always say that a fractional charge is wrong (and hence an error). -Justin With regards, Indu On Fri, Sep 5, 2014 at 11:14 AM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi Everyone , I want to ask one question , that my system have non-zero total charge and its not an integer too . System has non-zero total charge: -0.255000 Is this one of the reason that my system is blowing up . Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] water not getting settle
Hi everyone , I am getting an error about water i.e step 168: Water molecule starting at atom 5226 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. I have already tried reducing timestep ..but it didn't worked . If I freeze water things work fine . But what if I do not want to freeze it !! What is the other way to get it settled ? Thanks and Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] coordinates don't match
Thanks Lalita and Rinu for reply ...I got the point!!! Regards lovika On Wed, Aug 27, 2014 at 3:51 PM, RINU KHATTRI nickname.mi...@gmail.com wrote: firstly check your topology file i think you forgot to add either ligand or any molecule which is present in your pdb . in maximum steps of gromacs you have to update your topology file otherwise in maximum steps you will get error coordinates does not match On Wed, Aug 27, 2014 at 3:43 PM, Lalita Shaki lalitash...@gmail.com wrote: Hi Lovika, If the coordinates do not match it usually means you have more molecules in your pdb file than in the top. It will be easier to know which is the problem if you tell us which is the system and how the top file look like. Regards, lalita Hi everyone , I have a question , If coordinates of my .pdb file and .top file are not matching than what is the right way to correct it ! Like if I have one coordinate more in .pdb than in .top and I delete one from .pdb ...and it get fine !!! Will it be a problem in future or its fine to do this ?? Is there any other way to correct it ...without deleting !! Thanks and Regards Lovika -- Lalita S. Uribe. European Master in Theoretical Chemistry and Computational Modeling. PhD student. Johannes Gutenberg-Universität Mainz -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] coordinates don't match
Hi everyone , I have a question , If coordinates of my .pdb file and .top file are not matching than what is the right way to correct it ! Like if I have one coordinate more in .pdb than in .top and I delete one from .pdb ...and it get fine !!! Will it be a problem in future or its fine to do this ?? Is there any other way to correct it ...without deleting !! Thanks and Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun error
I am trying to have a system of GNPs with aminoacid and stabilizer i.e Sodium Citrate ...and this hydrogen is of Sodium Citrate . moving molecule is not working for me!!! Regards Lovika On Mon, Aug 25, 2014 at 10:52 AM, Kester Wong kester2...@ibs.re.kr wrote: If the H-atom is constituent of a molecule (e.g. H2O), then you could also try moving the molecule coordinates and see how it goes. I had a similar issue, but moving the molecule by an angstrom worked in my case. Good luck! Regards, Kester - 원본 메일 - *보낸사람* : Lovika Moudgil lovikamoud...@gmail.com *받는사람* : gmx-us...@gromacs.org *받은날짜* : 2014년 8월 25일(월) 13:52:49 *제목* : Re: [gmx-users] mdrun error Thanks for reply Justin and Kester...Ya my geometry is getting distorted and I tried to change the coordinates of atom 19 i.e Hydrogen ...but the error is same Regards Lovika On Mon, Aug 25, 2014 at 7:09 AM, Kester Wong wrote: Dear Lovika, Have you looked into atom 19 specifically? Perhaps, changing the coordinate of atom 19 manually, and let it do another minimisation run would solve the issue? Regards, Kester - 원본 메일 - *보낸사람* : Lovika Moudgil *받는사람* : *받은날짜* : 2014년 8월 24일(일) 18:28:06 *제목* : [gmx-users] mdrun error Hi everyone , Need some help .I have got an error in my mdrun . Upto grompp every thing was fine but when I give command for mdrun ,It stops with this ... Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=1 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.08534e+18 Fmax= inf, atom= 19 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.0853354e+18 Maximum force =inf on atom 19 Norm of force = 1.7429674e+18 constraints are all ready none ...Please help me what should I do to solve this . Thanks and Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] mdrun error
Hi everyone , Need some help .I have got an error in my mdrun . Upto grompp every thing was fine but when I give command for mdrun ,It stops with this ... Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=1 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.08534e+18 Fmax= inf, atom= 19 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.0853354e+18 Maximum force =inf on atom 19 Norm of force = 1.7429674e+18 constraints are all ready none ...Please help me what should I do to solve this . Thanks and Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun error
Thanks for reply Justin and Kester...Ya my geometry is getting distorted and I tried to change the coordinates of atom 19 i.e Hydrogen ...but the error is same Regards Lovika On Mon, Aug 25, 2014 at 7:09 AM, Kester Wong kester2...@ibs.re.kr wrote: Dear Lovika, Have you looked into atom 19 specifically? Perhaps, changing the coordinate of atom 19 manually, and let it do another minimisation run would solve the issue? Regards, Kester - 원본 메일 - *보낸사람* : Lovika Moudgil lovikamoud...@gmail.com *받는사람* : gmx-us...@gromacs.org *받은날짜* : 2014년 8월 24일(일) 18:28:06 *제목* : [gmx-users] mdrun error Hi everyone , Need some help .I have got an error in my mdrun . Upto grompp every thing was fine but when I give command for mdrun ,It stops with this ... Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=1 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.08534e+18 Fmax= inf, atom= 19 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.0853354e+18 Maximum force =inf on atom 19 Norm of force = 1.7429674e+18 constraints are all ready none ...Please help me what should I do to solve this . Thanks and Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pH simulation
Hi everyone... I want to do pH simulation in gromacs . I didn't found any specific link that I can follow for calculation regarding pH . Can you please guide me ..Any link that can help me... Thanks in advance Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] merge two .top file
Hi everyone Can anybody tell me that how can I merge two different .top (topology) files Thanks and Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] merge two .top file
Thanks Justin:) On Tue, May 27, 2014 at 5:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/27/14, 7:39 AM, Lovika Moudgil wrote: Hi everyone Can anybody tell me that how can I merge two different .top (topology) files A .top file is a system topology, so it's hard to merge them. What you can do is compile the necessary components by making them into .itp files (i.e. removing system-level directives) and using the #include mechanism to put everything together, along with a unified [molecules] directive. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] constraint error
Hi everyone... Can any body help me ...As i have an .itp file in which I have defined constraint and then I am defining this .itp file in my .top fileAnd with grompp command I got this error . I think I have defined constraints on right place. Than why this error ??Where I need to move constraints ??Please help me to understand this ... Fatal error: [ file gold_bulk.itp, line 16 ]: Atom index (2) in constraints out of bounds (1-1). This probably means that you have inserted topology section constraints in a part belonging to a different molecule than you intended to. In that case move the constraints section to the right molecule. Thanks and Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] constraint error
Thanks for reply Justin . Yes ...I get your point . Regards Lovika On Sat, May 24, 2014 at 4:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/24/14, 4:46 AM, Lovika Moudgil wrote: Hi everyone... Can any body help me ...As i have an .itp file in which I have defined constraint and then I am defining this .itp file in my .top fileAnd with grompp command I got this error . I think I have defined constraints on right place. Than why this error ??Where I need to move constraints ??Please help me to understand this ... Fatal error: [ file gold_bulk.itp, line 16 ]: Atom index (2) in constraints out of bounds (1-1). This probably means that you have inserted topology section constraints in a part belonging to a different molecule than you intended to. In that case move the constraints section to the right molecule. It seems that you have only 1 atom defined in the [moleculetype], but then you are defining a constraint involving atom 2, which does not exist. The error is similar to a common mistake involving positions restraints: http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_ restraints_out_of_bounds If you need more specific advice, please provide us with the content of the problematic topology. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to generate .top file
Hi everyone.. I have a .pdb file with protein and gold slab .Problem is I can generate .top file for my protein with pdb2gmx but I want my slab in the same system .I can generate .gro file for both but what about .top file . Can any body help me with this issue .Thanks in advance. Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to generate .top file
Thanks for reply Abhijit... .I will definitely try this . Hey Tsjerk ... Is it possible , if I define all this in a different .itp and than define that .itp file in .top file ? On Fri, May 23, 2014 at 3:45 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lovika, IIRC your gold is frozen, right? So you have a moleculetype definition for one gold atom (atomtype, mass, charge). You can just put it in the .top file after the #includes of the force field, like #include forcefield.itp #include protein.itp [ moleculetype ] AU 1 [ atoms ] 1 AU 1 UA UA 1 0196.96655 [ system ] Protein with gold [ molecules ] ... Hmm, I wonder, should one account for the gravitational effects of gold. Pretty heavy stuff :p Cheers, Tsjerk On Fri, May 23, 2014 at 11:39 AM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi everyone.. I have a .pdb file with protein and gold slab .Problem is I can generate .top file for my protein with pdb2gmx but I want my slab in the same system .I can generate .gro file for both but what about .top file . Can any body help me with this issue .Thanks in advance. Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to generate .top file
Thanks Tsjerk [?] Regards Lovika On Fri, May 23, 2014 at 4:17 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lovika, Yes, you can #include gold.itp or something along those lines. Cheers, Tsjerk On Fri, May 23, 2014 at 12:44 PM, Lovika Moudgil lovikamoud...@gmail.com wrote: Thanks for reply Abhijit... .I will definitely try this . Hey Tsjerk ... Is it possible , if I define all this in a different .itp and than define that .itp file in .top file ? On Fri, May 23, 2014 at 3:45 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lovika, IIRC your gold is frozen, right? So you have a moleculetype definition for one gold atom (atomtype, mass, charge). You can just put it in the .top file after the #includes of the force field, like #include forcefield.itp #include protein.itp [ moleculetype ] AU 1 [ atoms ] 1 AU 1 UA UA 1 0196.96655 [ system ] Protein with gold [ molecules ] ... Hmm, I wonder, should one account for the gravitational effects of gold. Pretty heavy stuff :p Cheers, Tsjerk On Fri, May 23, 2014 at 11:39 AM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi everyone.. I have a .pdb file with protein and gold slab .Problem is I can generate .top file for my protein with pdb2gmx but I want my slab in the same system .I can generate .gro file for both but what about .top file . Can any body help me with this issue .Thanks in advance. Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun error
Thanks for help Justin. Regards Lovika On Tue, May 20, 2014 at 2:49 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/19/14, 11:24 AM, Lovika Moudgil wrote: Hiii Everyone I need some helpAs in my grompp command I am getting warning about charge group and rlist Can any body help me to understand this ... Warning is WARNING 2 [file gro.mdp]: The sum of the two largest charge group radii (5.930022) is larger than rlist (1.80) and my .mdp file is Something is inconsistent; your error message says rlist is 1.8, but your .mdp says it is 1.0. Regardless, either you have some very nasty charge groups (way too large) or you simply have groups broken across PBC, which is not actually a problem. Recent versions of grompp are smart enough to deal with PBC, so this would only show up with an old version of Gromacs. http://www.gromacs.org/Documentation/Errors#The_sum_ of_the_two_largest_charge_group_radii_(X)_is_larger_ than.c2.a0rlist_-_rvdw.2frcoulomb -Justin ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/roe include = ; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 0 ; For exact run continuation or redoing part of a run init_step= 0 ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 ; number of steps for center of mass motion removal nstcomm = 10 ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 10 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 100 nstvout = 100 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 100 nstcalcenergy= -1 nstenergy= 100 ; Output frequency and precision for .xtc file nstxtcout= 0 xtc-precision= 1000 ; 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 = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns-type = Grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1 ; long-range cut-off for switched potentials rlistlong= -1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb = 1 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = No ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 1 ; Dielectric coefficient
[gmx-users] Need guidance
Hi Everyone, Need guidance and help. As I am doing md simulation for Lysozyme in presence of gold i.e Au(111) with force field oplsaa and Golp parameters . What I am doing is first generating .top file for protein with oplsaa force field and then using Golp gold .itp and .gro file parameters adding them to protein generated .top file. The .itp files for gold , I am adding are of surface ,bulk ,virtual . Coordinates that I am using are all taken from Golp force field .gro file . Mdp file that I am using is also from Golp in which Au and AUI Group is freezed. Changes that I am making are in .top file generated by pdb2gmx and adding gold coordinates to the protein.pdb file .But my system is giving error in grompp The sum of the two largest charge group radii is larger than rlist or DD cell error .. Please guide me where I am wrong ..Is there any thing serious that I am missing in my system . Please guide... Thanks and Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun error
= 0 userint3 = 0 userint4 = 0 userreal1= 0 userreal2= 0 userreal3= 0 userreal4= 0 Please guide me .. Regards and Thanks Lovika On Sun, May 18, 2014 at 9:54 AM, Lovika Moudgil lovikamoud...@gmail.comwrote: Mark thanks for your reply and support . [?] Regards Lovika On Sat, May 17, 2014 at 5:23 PM, Mark Abraham mark.j.abra...@gmail.comwrote: No, the .mdp file mostly describes your model physics (but there are some implementation details that affect parallelization in there). Your GROMACS CMake configuration, mdrun command line and the attributes of your hardware are the biggest factors that determine how mdrun will try to parallelise. There's a lot of diagnostic reporting in the log file, but you are initially looking for the number of cells in the domain decomposition (DD). And you need to know how big your simulation system is. For example, a 900-molecule water system won't parallelise over a whole 32-core compute server with a domain per core. Background info here http://www.gromacs.org/Documentation/Acceleration_and_parallelization Mark On Sat, May 17, 2014 at 9:02 AM, Lovika Moudgil lovikamoud...@gmail.com wrote: Thanks for quick reply Mark...what information you are asking for?Should I search for this my .mdp file?? Thanks Lovika On Sat, May 17, 2014 at 11:35 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Your simulation seems too small to parallelize in the way you/mdrun tried. But we need more information to be sure. Mark On May 17, 2014 7:33 AM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi Everyone I need some help. With my mdrun command I am getting this following error . Program mdrun, VERSION 4.6.5 Source code file: /home/itlab/Documents/gromacs/gromacs-4.6.5/src/mdlib/domdec_con.c, line: 722 Fatal error: DD cell 0 0 1 could only obtain 1 of the 2 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Please help me to understand this error.What this error is all about ? Where should I search to resolve this error ? Thanks Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun error
Thanks for quick reply Mark...what information you are asking for?Should I search for this my .mdp file?? Thanks Lovika On Sat, May 17, 2014 at 11:35 AM, Mark Abraham mark.j.abra...@gmail.comwrote: Your simulation seems too small to parallelize in the way you/mdrun tried. But we need more information to be sure. Mark On May 17, 2014 7:33 AM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi Everyone I need some help. With my mdrun command I am getting this following error . Program mdrun, VERSION 4.6.5 Source code file: /home/itlab/Documents/gromacs/gromacs-4.6.5/src/mdlib/domdec_con.c, line: 722 Fatal error: DD cell 0 0 1 could only obtain 1 of the 2 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Please help me to understand this error.What this error is all about ? Where should I search to resolve this error ? Thanks Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun error
Mark thanks for your reply and support . [?] Regards Lovika On Sat, May 17, 2014 at 5:23 PM, Mark Abraham mark.j.abra...@gmail.comwrote: No, the .mdp file mostly describes your model physics (but there are some implementation details that affect parallelization in there). Your GROMACS CMake configuration, mdrun command line and the attributes of your hardware are the biggest factors that determine how mdrun will try to parallelise. There's a lot of diagnostic reporting in the log file, but you are initially looking for the number of cells in the domain decomposition (DD). And you need to know how big your simulation system is. For example, a 900-molecule water system won't parallelise over a whole 32-core compute server with a domain per core. Background info here http://www.gromacs.org/Documentation/Acceleration_and_parallelization Mark On Sat, May 17, 2014 at 9:02 AM, Lovika Moudgil lovikamoud...@gmail.com wrote: Thanks for quick reply Mark...what information you are asking for?Should I search for this my .mdp file?? Thanks Lovika On Sat, May 17, 2014 at 11:35 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Your simulation seems too small to parallelize in the way you/mdrun tried. But we need more information to be sure. Mark On May 17, 2014 7:33 AM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi Everyone I need some help. With my mdrun command I am getting this following error . Program mdrun, VERSION 4.6.5 Source code file: /home/itlab/Documents/gromacs/gromacs-4.6.5/src/mdlib/domdec_con.c, line: 722 Fatal error: DD cell 0 0 1 could only obtain 1 of the 2 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Please help me to understand this error.What this error is all about ? Where should I search to resolve this error ? Thanks Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] mdrun error
Hi Everyone I need some help. With my mdrun command I am getting this following error . Program mdrun, VERSION 4.6.5 Source code file: /home/itlab/Documents/gromacs/gromacs-4.6.5/src/mdlib/domdec_con.c, line: 722 Fatal error: DD cell 0 0 1 could only obtain 1 of the 2 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Please help me to understand this error.What this error is all about ? Where should I search to resolve this error ? Thanks Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] need guidance
Hi Everyone , I need some help . gromacs software is new for me . I want to know how can I run my protein in presence of gold atoms . What force field should be there that is compatible with gold atoms and what changes i need to do .Is there any link that I can follow ? Please guide me . Thanks in advance. Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
