[gmx-users] Re: gmx-users Digest, Vol 114, Issue 75
> > "Not working" is too vague a symptom for anyone to guess what the problem > > is, sorry. > > > > Mark > > On Oct 24, 2013 9:39 AM, "Santu Biswas" > wrote: > > > > > dear users, > > > > > > I am performing 500ps mdrun in vacuum for > > polypeptide(formed > > > by 10-residues leucine) using gromacs_4.5.5(double- precision) using > > > opls-aa/L force field.Input file for 500ps mdrun is given below > > > > > > > > > title= peptide in vaccum > > > cpp= /lib/cpp > > > > > > ; RUN CONTROL > > > integrator = md > > > comm_mode= ANGULAR > > > nsteps = 50 > > > dt= 0.001 > > > ; NEIGHBOR SEARCHING > > > nstlist = 0 > > > ns_type = simple > > > pbc = no > > > rlist = 0 > > > ; OUTPUT CONTROL > > > nstxout = 1000 > > > nstvout = 1000 > > > nstxtcout = 0 > > > nstlog= 1000 > > > constraints = none > > > nstenergy = 1000 > > > ; OPTION FOR ELECTROSTATIC AND VDW > > > rcoulomb = 0 > > > ; Method for doing Van der Waals > > > rvdw= 0 > > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > > > tcoupl = V-rescale > > > tc_grps= Protein > > > tau_t= 0.1 > > > ref_t = 300 > > > gen_vel= yes > > > gen_temp = 300 > > > > > > Using the 500ps trajectory if i run g_hbond_d for calculating the > number > > of > > > hydrogen bonds as a function of time using index file(where atom O and > > atom > > > N H is used) it is not working. > > > Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is > also > > > not working. > > > I do not know why this is happening. > > > > > > -- > > > santu > > > -- > > Thanks Mark for your reply. > > > >Using the 500ps trajectory i want to calculate the number of hydrogen > bonds as a function of time in vacuum .For this calculation i > > > have uesd > > g_hbond_d -f traj_0-500ps.trr -s 500ps.tpr -n index.ndx -num > > hbond-num.xvg -dist dist.xvg -ang angle.xvg > > With what groups? Can there be any hydrogen bonds between those groups? Is there a bug fixed in a version of g_hbond that isn't 2 years old? Did a shorter trajectory work because it took less time? Does doing only one of three analyses help things to work? You'd be much closer to a solution if you'd tried some simplifications and done some detective work already ;-) > > Programm was running .After 1 hour it was still running but there was no > > output. > > > > If I calculate the number of hydrogen bonds as a function of time in > water (no vacuum) using the same command line then there was no problem. > >Same problem when I used g_rdf in vacuum.The commad line I have used >g_rdf_4.5.5 -f traj.trr -s 500ps.tpr -n index.ndx -o rdf.xvg and also > checked with -nopbc with the same command line. > RDF of what, in vacuum? What groups did you use? >The programm is running but in the output file nothing is written. >If I used g_rdf in water using the same command line there was no > problem. > OK - but does your analysis make sense in vacuum? Mark Thanks Mark for your reply In the index file I mentioned C=O oxygen atom and N-H hydrogen atom. Now I want to calculate the distance between O atom and N-H hydrogen atom using g_rdf in vacuum. Similarly using the same index file I want to calculate the number of hydrogen bonds as a function of time in vacuum using g_hbond. Yes there is a H bond between C=O oxygen atom of i-th residue and N-H hydrogen of i+4-th residue. I also checked with shorter trajectory there is also same problem . Please let me know If there are any mistakes. - santu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 114, Issue 64
> > > > "Not working" is too vague a symptom for anyone to guess what the problem > is, sorry. > > Mark > On Oct 24, 2013 9:39 AM, "Santu Biswas" wrote: > > > dear users, > > > > I am performing 500ps mdrun in vacuum for > polypeptide(formed > > by 10-residues leucine) using gromacs_4.5.5(double-precision) using > > opls-aa/L force field.Input file for 500ps mdrun is given below > > > > > > title= peptide in vaccum > > cpp= /lib/cpp > > > > ; RUN CONTROL > > integrator = md > > comm_mode= ANGULAR > > nsteps = 50 > > dt= 0.001 > > ; NEIGHBOR SEARCHING > > nstlist = 0 > > ns_type = simple > > pbc = no > > rlist = 0 > > ; OUTPUT CONTROL > > nstxout = 1000 > > nstvout = 1000 > > nstxtcout = 0 > > nstlog= 1000 > > constraints = none > > nstenergy = 1000 > > ; OPTION FOR ELECTROSTATIC AND VDW > > rcoulomb = 0 > > ; Method for doing Van der Waals > > rvdw= 0 > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > > tcoupl = V-rescale > > tc_grps= Protein > > tau_t= 0.1 > > ref_t = 300 > > gen_vel= yes > > gen_temp = 300 > > > > Using the 500ps trajectory if i run g_hbond_d for calculating the number > of > > hydrogen bonds as a function of time using index file(where atom O and > atom > > N H is used) it is not working. > > Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is also > > not working. > > I do not know why this is happening. > > > > -- > > santu > > -- > Thanks Mark for your reply. > Using the 500ps trajectory i want to calculate the number of hydrogen bonds as a function of time in vacuum .For this calculation i > have uesd > g_hbond_d -f traj_0-500ps.trr -s 500ps.tpr -n index.ndx -num > hbond-num.xvg -dist dist.xvg -ang angle.xvg > > Programm was running .After 1 hour it was still running but there was no > output. > If I calculate the number of hydrogen bonds as a function of time in water (no vacuum) using the same command line then there was no problem. Same problem when I used g_rdf in vacuum.The commad line I have used g_rdf_4.5.5 -f traj.trr -s 500ps.tpr -n index.ndx -o rdf.xvg and also checked with -nopbc with the same command line. The programm is running but in the output file nothing is written. If I used g_rdf in water using the same command line there was no problem. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_hbond and g_rdf in vacuum
dear users, I am performing 500ps mdrun in vacuum for polypeptide(formed by 10-residues leucine) using gromacs_4.5.5(double-precision) using opls-aa/L force field.Input file for 500ps mdrun is given below title= peptide in vaccum cpp= /lib/cpp ; RUN CONTROL integrator = md comm_mode= ANGULAR nsteps = 50 dt= 0.001 ; NEIGHBOR SEARCHING nstlist = 0 ns_type = simple pbc = no rlist = 0 ; OUTPUT CONTROL nstxout = 1000 nstvout = 1000 nstxtcout = 0 nstlog= 1000 constraints = none nstenergy = 1000 ; OPTION FOR ELECTROSTATIC AND VDW rcoulomb = 0 ; Method for doing Van der Waals rvdw= 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS tcoupl = V-rescale tc_grps= Protein tau_t= 0.1 ref_t = 300 gen_vel= yes gen_temp = 300 Using the 500ps trajectory if i run g_hbond_d for calculating the number of hydrogen bonds as a function of time using index file(where atom O and atom N H is used) it is not working. Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is also not working. I do not know why this is happening. -- santu -- 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] SR-coulomb energy
Dear users,
I have performed an simulation of polypeptide(5-residues of
alanine) in vacuum using gmx_4.5.5 (Double Precision). For this, I am using
all cutoff=0 with no pbc. The input mdp file for the simulation is given
below
title= peptide in vaccum
cpp = /lib/cpp
define = -DFLEXIBLE
; RUN CONTROL
integrator = md
comm_mode = ANGULAR
nsteps = 100
dt = 0.0005
; NEIGHBOR SEARCHING
nstlist = 0
ns_type = simple
pbc = no
rlist = 0
; OUTPUT CONTROL
nstxout = 1000
nstvout = 1000
nstxtcout= 0
nstlog = 1000
constraints = none
nstenergy= 1000
; OPTION FOR ELECTROSTATIC AND VDW
rcoulomb = 0
; Method for doing Van der Waals
rvdw = 0
; OPTIONS FOR WEAK COUPLING ALGORITHMS
tcoupl = V-rescale
tc_grps = Protein
tau_t= 0.1
ref_t= 300
The output (.log) file is
Step Time Lambda
00.00.0
Group rest with mass 4.28491e+02, Ekrot 6.48028e+00 Det(I) = 4.27209e+03
COM: 1.82773 1.85017 1.82461
P:0.0 -0.0 0.0
V:0.0 -0.0 0.0
J: -0.82095 -13.54870 -19.02024
w:0.02012 -0.41432 -0.38715
Inertia tensor (3x3):
Inertia tensor[0]={ 1.34454e+01, -6.11374e+00, 2.21534e+00}
Inertia tensor[1]={-6.11374e+00, 2.88115e+01, -6.31417e+00}
Inertia tensor[2]={ 2.21534e+00, -6.31417e+00, 1.36527e+01}
Energies (kJ/mol)
Bond AngleProper Dih. Ryckaert-Bell. LJ-14
4.93368e+001.49038e+011.00713e+003.83183e+017.57789e+01
Coulomb-14LJ (SR) Coulomb (SR) PotentialKinetic En.
7.82758e+02 -6.47030e+01 -1.48187e+03 -6.28870e+022.30892e+02
Total Energy Conserved En.Temperature Pressure (bar)
-3.97978e+02 -3.97978e+023.08553e+020.0e+00
gen_vel = yes
gen_temp = 300
Now the problem is with Coulomb (SR) value.To check this value, I have
calculated coulomb interactions beyond 1-4 interaction by the following
equation
energ=(f*q1*q2)/r ; where f=138.935485
but the value which I obtain for step 0 is -170.10733 and this not the same
as the log file. I do not know how Gromacs calculate coulomb (SR) value.
Please suggest if I am missing something.
Thanks
Santu
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 105, Issue 43
thank you Justin.Now it is fine. > -- > > Message: 1 > Date: Wed, 9 Jan 2013 22:50:13 +0530 > From: SANTU BISWAS > Subject: [gmx-users] energy-mimisation-problem > To: gmx-users@gromacs.org > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > dear users, > > I am performing an energy minimization of > apolypeptide(formed by alanine-10-residues) in vacuum box by using > Steepest Descent(initially) and then Conjugate Gradient methods in > gromacs_4.5.5_doubleprecision.The chain length of > alanine-10-mer is around 1.5 nm.Here i want to see only the sort-range > interactions.so i use cutoff 2.0 nm .But in the > output (.log )file there is a contribution of energy for long-range > interactions(in both energy minimisation methods). > I do not understand why this is happening. > > the input file for energy minimisation is, > > ;title= > cpp = /lib/cpp > ;include =-I../top/ > define = -DFLEXIBLE > ; Input file > integrator = steep/cg > nsteps = 1 > nstlist = 1 > rlist = 1.0 > rcoulomb= 2.0 > rvdw= 2.0 > ; Energy minimizing stuff > emtol = 0.001 > emstep = 0.1 > nstcgsteep = 10 > > > the output(.log )file is, > > Energies (kJ/mol) >Bond AngleProper Dih. > Ryckaert-Bell. LJ-14 > 8.48244e+002.10205e+012.39409e+00 9.86941e+01 > 1.47894e+02 > Coulomb-14LJ (SR)LJ (LR) Coulomb (SR) > Coulomb (LR) > 1.63221e+03 -1.64038e+02 -4.97232e-01 -3.00455e+03 -1.00138e+01 > Potential Pressure (bar) >-1.26841e+030.0e+00 > > > santu > > > -- > > Message: 2 > Date: Wed, 09 Jan 2013 12:30:06 -0500 > From: Justin Lemkul > Subject: Re: [gmx-users] energy-mimisation-problem > To: Discussion list for GROMACS users > Message-ID: <50eda91e.2070...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 1/9/13 12:20 PM, SANTU BISWAS wrote: >> dear users, >> >>I am performing an energy minimization of >> apolypeptide(formed by alanine-10-residues) in vacuum box by using >> Steepest Descent(initially) and then Conjugate Gradient methods in >> gromacs_4.5.5_doubleprecision.The chain length of >> alanine-10-mer is around 1.5 nm.Here i want to see only the sort-range >> interactions.so i use cutoff 2.0 nm .But in the >> output (.log )file there is a contribution of energy for long-range >> interactions(in both energy minimisation methods). >> I do not understand why this is happening. >> >> the input file for energy minimisation is, >> >> ;title= >> cpp = /lib/cpp >> ;include =-I../top/ >> define = -DFLEXIBLE >> ; Input file >> integrator = steep/cg >> nsteps = 1 >> nstlist = 1 >> rlist = 1.0 >> rcoulomb= 2.0 >> rvdw= 2.0 >> ; Energy minimizing stuff >> emtol = 0.001 >> emstep = 0.1 >> nstcgsteep = 10 >> >> > > You haven't set a value for the pbc keyword, so it takes the default value > (xyz). The result is that you're not really minimizing in vacuo, but rather > in > some sort of pseudo-crystal state that probably has lots of periodicity > artifacts. That's probably the source of the energy terms - your peptide > interacting with itself. > > -Justin > >> the output(.log )file is, >> >> Energies (kJ/mol) >> Bond AngleProper Dih. >> Ryckaert-Bell. LJ-14 >> 8.48244e+002.10205e+012.39409e+00 9.86941e+01 >> 1.47894e+02 >> Coulomb-14LJ (SR)LJ (LR) Coulomb (SR) >> Coulomb (LR) >> 1.63221e+03 -1.64038e+02 -4.97232e-01 -3.00455e+03 -1.00138e+01 >>Potential Pressure (bar) >> -1.26841e+030.0e+00 >> >> >> santu >> > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department
[gmx-users] Re: energy-mimisation-problem
On Sun, Nov 25, 2012 at 9:08 PM, SANTU BISWAS wrote: > dear users, > >When performing a energy minimization of a > polypeptide(formed by lysine-5-residues) in vacuum box by using > Steepest Descent and also Conjugate Gradient methods in gromacs double > precision,i noted that GROMACS never converges to emtol values under > about 0.1 kj/mol/nm.I have used the .mdp file which is given below > > > > title= > cpp = /lib/cpp > ;include =-I../top/ > define = -DFLEXIBLE > > ; RUN CONTROL PARAMETERS = > integrator = steep > ; start time and timestep in ps = > tinit= 0 > dt = 0.001 > nsteps = 1000 > rlist= 0.9 > rcoulomb = 0.9 > ; Method for doing Van der Waals > vdw-type = Cut-off > ; cut-off lengths > rvdw_switch = 0 > rvdw = 0.9 > ; Neighbour searching > nstlist = 1 > ; ENERGY MINIMIZATION OPTIONS = > emtol= 0.1 > emstep = 0.1 > nstcgsteep = 1000 > > > > > santu -- 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
