[gmx-users] coupling to center of mass

How to apply temp coupling only to the center-of-mass motion of water molecules in mdp file. -- Sree lakshmi ramesh Ph.D student Center for Computational Natural Sciences and Bioinformatics International Institute of Information Technology, Hyderabad Gachibowli, Hyderabad 500032 ph: +91 40 665319

Re: [gmx-users] understanding the output of REMD

trjcat -f *.trr -demux replica_index.xvg -o final.trr now how to produce temp evolution over time with these concatenated trajectories thanks in advance, sree. On Thu, Jul 28, 2011 at 6:53 AM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> after having enoug

Re: [gmx-users] understanding the output of REMD

please. Regards, sree. On Wed, Jul 27, 2011 at 4:58 PM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> dear all , >> I am new to ReMD simulations.And i done a trial run of 100 ps for 7 >> replicas . if i view the log file for output i get something like th

[gmx-users] understanding the output of REMD

dear all , I am new to ReMD simulations.And i done a trial run of 100 ps for 7 replicas . if i view the log file for output i get something like this for every replica for one of the replica the log file looks like this Replica exchange at step 1000 time 2 Repl 0 <-> 1 dE = 6.793e+02 dpV = 0.0

[gmx-users] monte carlo simulation in gromacs

Dear all, I wanted to do perform a Monte carlo simulation of RNA using coarse grained force filedn in gromacs.when i do pdb2gmx i dont get option for Coarse grained ff.is mC integrator availble in gromacs? thanks in advance, sree. -- gmx-users mailing listgmx-users@gromacs.or

[gmx-users] umbrella sampling pull_group0 adn pull_group1

Dear all, i wanted to do umbrella sampling on petide which is completely folded.now in mdp file there is a option pull_group0 and pull_group1 i just know the ref group and the one to which pulling force has to be applied in pdb file their atom numbers are 201 adn 61 .how should i ment

[gmx-users] missing topology file adn creating a new one

Dear all, i am doing a sampling method and in a stage of completion But unfortunatelymy topol.top file is missing and am really helpless .i cant continue the simulation.i have the tpr file adn pdb file at last step.i tried to create the top file from *g_x2top -f beta_md17.tpr -o topo

[gmx-users] need tip3p.gro for charmm force field

Dear all, am trying to do a simulation with charmm forcefield adn tip3p water model when i use gen box command adn mention tip3p gromacs gives a error that the tip3p file is not found.any help please regrds, sree -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailm

Re: [gmx-users] Re: error during equilibriation

wrote: > > > sreelakshmi ramesh wrote: > >> >> >> -- Forwarded message ------ >> From: *sreelakshmi ramesh* > sree.laks...@research.iiit.ac.in>> >> Date: Sat, Jun 11, 2011 at 4:37 PM >> Subject: Re: error during equilibria

[gmx-users] Re: error during equilibriation

-- Forwarded message -- From: sreelakshmi ramesh Date: Sat, Jun 11, 2011 at 4:37 PM Subject: Re: error during equilibriation To: Discussion list for GROMACS users here goes my mdp file.The when i attach the top file by mail is getting bounced back.Thanks in adcvance title

[gmx-users] error during equilibriation

Dear all, am trying to simulate a cnt double walled in tip 4p water .had no problem till minimization but during equilibri i got the following errorany suggestions please. *A list of missing interactions: Angle of 2097 missing 14 Ryckaert-Bell. of 1286 missing

[gmx-users] Atoms in the .top are not numbered consecutively from 1

Dear all, when i run energy minimization i get the following error. the topology file was created from the starting pdb file using g_x2top *grompp -f em.mdp -c out.gro -p carbon.top -o o.tpr -maxwarn 3* Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = 348,

[gmx-users] Invalid angle type 0 error during minimization.

Dear all, i am trying to simulate a double walled cnt in tip4p water using oplsaa force field. first i used *g_x2top -f carbon.pdb -o carbon.top* ( successfully created the topology) * editconf -f carbon.pdb -o carbon_newbox.gro -c -box 3.41840 3.44350 5.5965 genbox

[gmx-users] creating topology using g_x2top

Dear all , I want to simulate a double walled nano tube in spc water i had made the pdb file now if i use g_x2top for creating the topology file it gives me the following error . Now if i run * g_x2top -f out.pdb -o out.top -ff oplsaa* it gives the following error *Can not find forcef

[gmx-users] carbon nano tubes pdb file

Dear all, I need to create a starting pdb file for doble walled Carbon nano tube of desired radius with two graphene sheets.I already have one but when i use pdb2gmx gromacs The pdb file looks something like this.. RYST10.0000.0000.000 90.00 90.00 90.00 P 1

Re: [gmx-users] regarding table for water water interactions

25, 2011 at 3:21 PM, Mark Abraham wrote: > On 25/05/11, *sreelakshmi ramesh * > wrote: > > Hai all, > My system is just a water Spc model. > I am trying to create a table.xvg which would deal with nonbonded > intearction for water-water for say SPC mod

[gmx-users] regarding table for water water interactions

Hai all, My system is just a water Spc model. I am trying to create a table.xvg which would deal with nonbonded intearction for water-water for say SPC model. If i have to calculate the potential i have to consider the interaction between 1.O of water1--O of water 2(LJ+COLOUMB

Re: [gmx-users] Water molecule starting at atom X can not be settled.

ya sorry i actually meant to say that the starting pdb file had just NA and Cl.I then solvated it with tip4p water.Anad then try to minimize it. On Sun, May 22, 2011 at 11:59 AM, Mark Abraham wrote: > On 22/05/2011 3:35 PM, sreelakshmi ramesh wrote: > > my starting structure has just

Re: [gmx-users] Water molecule starting at atom X can not be settled.

my starting structure has just two atoms one Na and one Cl and they are seperated by a distance of 3 angstroms.Its not a huge system. On Sun, May 22, 2011 at 10:30 AM, Mark Abraham wrote: > On 22/05/2011 2:43 PM, sreelakshmi ramesh wrote: > > Dear gmx-users, >

[gmx-users] Water molecule starting at atom X can not be settled.

Dear gmx-users, I have a problem during minimization and shows a error that water molecules starting at atom X cannot be settled i had attached the output of mdrun below. I read the earlier post for same problem faced by other gmx users.tried to reduce the timestep stil

[gmx-users] energy minimization error

Dear all, I am using tabulated potential do simulate nacl in water .when i was doing my energy minimization it gives me the following error.Any help please.. WARNING: For the 1498 non-zero entries for table 2 in table_NA_CL.xvg the forces deviate on average 39% from minus the numeri

[gmx-users] segmentation fault.

dear gmx-users, During equilibriation i get the following error.Any suggestions please. *grompp* WARNING 1 [file npt.mdp]: The sum of the two largest charge group radii (2.369582) is larger than rlist (1.00) This run will generate roughly 73 Mb of data There wa

Re: [gmx-users] problem during energy minimization

, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> Dear Gmx users, >> I am trying to do minimization of my system .i >> have no problem wehen i grompp it but when i do the mdrun its giving me some >> segmentation error.I h

[gmx-users] problem during energy minimization

Dear Gmx users, I am trying to do minimization of my system .i have no problem wehen i grompp it but when i do the mdrun its giving me some segmentation error.I had attached the output of grompp and mdrun below.Any suggestions please.Thanks in advance *OUTPUT OF GROMPP*

Re: [gmx-users] regarding nacl simulation in water using tabulated potentials

ond params WARNING 3 [file tol.top, line 15]: Too few parameters on line (source file toppush.c, line 315) On Tue, May 10, 2011 at 4:25 AM, Mark Abraham wrote: > On 10/05/2011 2:20 AM, sreelakshmi ramesh wrote: > > i had three tables one for solvent na and solvent cl ions (obeyi

Re: [gmx-users] regarding nacl simulation in water using tabulated potentials

: > On 9/05/2011 4:01 PM, sreelakshmi ramesh wrote: > > i had followed the instructions in themnaual for ninbonded interactions adn > had created two tables one for nacl adn other table for water ion > interations... > > > That's not "I really don't have any id

Re: [gmx-users] regarding nacl simulation in water using tabulated potentials

On 9/05/2011 3:46 PM, sreelakshmi ramesh wrote: > >> dear gmx users, >>i have to simulate nacl in water...the system is >> acubic box with just one na adn one cl ion in tip3p water.i wanted to use a >> buckingham potential for na adn cl interacti

[gmx-users] regarding nacl simulation in water using tabulated potentials

dear gmx users, i have to simulate nacl in water...the system is acubic box with just one na adn one cl ion in tip3p water.i wanted to use a buckingham potential for na adn cl interaction and lennard jones for water -ion intercation.i really dont have any idea on how to do

[gmx-users] regarding creating tabulated potentials

dear gmx users, -- 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 s

Re: [gmx-users] The sum of the O-H distancesof the backbone hydrogen bonds ROH

Thanks a lot for your reply.. On Mon, Jan 3, 2011 at 6:07 PM, Mark Abraham wrote: > On 2/01/2011 2:18 PM, sreelakshmi ramesh wrote: > >> Dear all, >> I have a protein in water and i have simulated it for few >> nanoseconds and i now i wanted to monitor

[gmx-users] distance between two atoms of diff protein residue

hai all, can anyone help me out on how to find distance using g_dist between two atoms in two diff residues . -- 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_List

[gmx-users] The sum of the O-H distancesof the backbone hydrogen bonds ROH

Dear all, I have a protein in water and i have simulated it for few nanoseconds and i now i wanted to monitor the The sum of the O-H distances (in Å) of the backbone hydrogen bonds ROH:i dono how to extract the value from the trajectory file.Any siuggestion please.Thanks in advance r

[gmx-users] average pressure too high

Dear users, I did nvt equil and after that npt equilbriation and i am using parinello rahman as the barostat but the prob is even after 200 ps of equil the avg pressure is 1.5 bar .can anybody hepl me out with the issue.Any suggestions please. sree. -- gmx-users mailing listg

[gmx-users] velocity rescaling

what is velocity rescaling and how to use it in nve simulations. thanks in advance. -- 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

[gmx-users] simulation at constant temprature

Dear Gmx users, I wanted to do a simulation with NVE ensemble but i want the temprature to be always around 300k but in my simulation the temp is 380k.I am usng leap frog as integrator .can anyone help me out with this.how to do the velocity rescaling regards, sree. --

[gmx-users] nve simulation

Dear Gmx users, I wanted to do a simulation with NVE ensemble but i want the temprature to be always around 300k but in my simulation the temp is 380k.can anyone help me out with this. regards, sree. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

Re: [gmx-users] buckingham potentials

A under c12 and how should i declare B. thanks sree. On Wed, Dec 22, 2010 at 10:04 AM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> Dear justin, >> >> I have no clues about rewriting a force field so i >> think i can t pro

Re: [gmx-users] buckingham potentials

Dear justin, I have no clues about rewriting a force field so i think i can t proceed with this anymore. thanks a lot for your patient reply. sree. On Wed, Dec 22, 2010 at 9:32 AM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > &g

Re: [gmx-users] buckingham potentials

Do u mean to say that all the force fields available in gromacs are default to be used only for LJ potential. On Wed, Dec 22, 2010 at 9:32 AM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> Dear justin, >> I am sorry the file is ff

Re: [gmx-users] buckingham potentials

Dear justin, I am sorry the file is ffG43a1nb.itp.It was a typing mistake. On Wed, Dec 22, 2010 at 9:26 AM, Justin A. Lemkul wrote: > > > Justin A. Lemkul wrote: > >> >> >> sreelakshmi ramesh wrote: >> >>> I am using gromos force fi

Re: [gmx-users] buckingham potentials

e 144]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) any help appreciated. On Wed, Dec 22, 2010 at 8:40 AM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> >> so if i set vdwtype =cut off and specify 2 in default section (2 is for >&

Re: [gmx-users] buckingham potentials

so if i set vdwtype =cut off and specify 2 in default section (2 is for buck and 1 for LJ ) of topology file will gromacs makes suer that i want the calculation with bucking ham potential. On Wed, Dec 22, 2010 at 8:32 AM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >

Re: [gmx-users] buckingham potentials

tions please. sree. On Tue, Dec 21, 2010 at 6:02 PM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> can anyone tell me how to alter the parameter B OF buckingham potential. >> >> > Manual, chapter 5, especially table 5.4, which specifically lists all

[gmx-users] buckingham potentials

can anyone tell me how to alter the parameter B OF buckingham potential. regards, sree -- 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 do

[gmx-users] reagrding huggins meyer potential

Dear all, I wanted to simulate Nacl in water using huggins meyer potential as vdw type.since gromacs has just LJ OR BJ potential i wanted to know if somebody had done it with huggins meyer potential.I read the manual and since i am not good in c or fortran i dono how to create a user

Re: [gmx-users] reagarding polarisable force field in gromacs

, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> Dear justin , >> I read the manual and i didnt get it thats why i sought >> the help of people here.i want to know how to use those polarisable force >> field. >> >> > T

Re: [gmx-users] reagarding polarisable force field in gromacs

Dear justin , I read the manual and i didnt get it thats why i sought the help of people here.i want to know how to use those polarisable force field. On Mon, Dec 20, 2010 at 9:15 AM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> Dear all,

[gmx-users] reagarding polarisable force field in gromacs

Dear all, can anyone tell me if there are polarisable force field available in gromacs.I need to use dang chang force field which is polarisable force field for my work.I have used classical force fields before can anyone help me out regaring this. thanks in advance , shree -- gmx-u

Re: [gmx-users] changing the velocity in trajectory file

dear all, can anybody tell me what happens to the velocity of intial config when i use the stochastic integrator like bd or sd. reagrds, sree. On Tue, Nov 30, 2010 at 11:11 AM, Lutz Maibaum wrote: > On Nov 29, 2010, at 8:52 PM, sreelakshmi ramesh wrote: > > Lutz ya you

Re: [gmx-users] changing the velocity in trajectory file

Lutz ya you are true but as you said how can i change the velocity for a config every move as in TPS?since i have not done tps i have no idea abt this. sree On Tue, Nov 30, 2010 at 9:15 AM, Lutz Maibaum wrote: > On Nov 29, 2010, at 5:58 PM, sreelakshmi ramesh wrote: > > Basically i

Re: [gmx-users] changing the velocity in trajectory file

so everytime when the same trajectory file is read is it possible to randomize the velocity by a small amount so that i may end up with different trajectory? sree. On Tue, Nov 30, 2010 at 7:28 AM, sreelakshmi ramesh < sree.laks...@research.iiit.ac.in> wrote: > Basically i have bee

Re: [gmx-users] changing the velocity in trajectory file

On 30/11/2010 2:16 AM, sreelakshmi ramesh wrote: > > so can anybody tell me how to hack the trr file so that i can change the > velocity parameter in it > > > You've expressed no reason to need to do that rather than generate > independent random sets of velocities. If you'

Re: [gmx-users] changing the velocity in trajectory file

so can anybody tell me how to hack the trr file so that i can change the velocity parameter in it On Mon, Nov 29, 2010 at 8:40 PM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> so if i use gen_vel = yes ad seed -1 i get diff traj.But what would happen >>

Re: [gmx-users] changing the velocity in trajectory file

so if i use gen_vel = yes ad seed -1 i get diff traj.But what would happen if read the postion and velocity from traj file(input file) On Mon, Nov 29, 2010 at 8:08 PM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> i am reading the velocities from trajectory f

Re: [gmx-users] changing the velocity in trajectory file

o generate the velocity? > > > On 11/29/2010 02:55 PM, sreelakshmi ramesh wrote: > > Dear all, > > could anybody help me out with the following issue. I have > a > > trajectory file.i have to used that file at a particular frame as the > > input to c

[gmx-users] changing the velocity in trajectory file

Dear all, could anybody help me out with the following issue. I have a trajectory file.i have to used that file at a particular frame as the input to continue the simulation and i need to use that file for 20 independent simulations.since the starting file for the 20 simulations are

[gmx-users] regrding sampling in transtion path sampling

Dear sir, i have been doing something like transition path sampling.i have the order parameter and i have to monitor the distance between the ions how do i monitor the distace between the ions during the course of simulation.should i include the order parameters in the mdp file. --