[gmx-users] OPLS forcefield for Alkane and ethers?

Hi, I was wondering whether OPLS supports force-field for alkane chain or ethers . One of the molecule I am looking forward to using is ethylene glycol ( CH2-O-CH2-O-CH2 ). But, I was wondering whether it is available in OPLS forcefield . Any help will be appreciated . Sanku -- gmx-

[gmx-users] dipole moment of a charged peptide

Hi, I have a long-chain peptide which has a net charge of +5 . I was wondering whether the g_dipole will give any reasonable dipole moment for a molecule with a net charge. Is there any suggestion I should follow regarding calculation of dipole-moment of a charged molecule . I found that in

[gmx-users] integral equation theory in gromacs?

Hi, I was wondering whether there is any way in gromacs so that one can perform integral equation theory or RISM theory of a system . Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

[gmx-users] g_dipoles and index file

Hi, I was trying to calculate the dipole moment of part of my peptide. In other words, if I have a 10-residue peptide, I was interested in calculating the dipole-moment contribution of the backbone. So, I made an index file which have a group containing backbone atoms. But, if I try to use g_d

[gmx-users] problem with g_dipoles and index file

Hi, I was trying to calculate the dipole moment of part of my peptide. In other words, if I have a 10-residue peptide, I was interested in calculating the dipole-moment contribution of the backbone. So, I made an index file which have a group containing backbone atoms. But, if I try to use g_d

[gmx-users] how to define charge group?

Hi, I am trying to write a topology in gromacs format for a recently developed molecule in OPLS format. From the parameterization-paper, I know the partial charges on each of the atom in that molecule from the corresponding paper . But, I am not sure how to split the molecule topology into se

[gmx-users] rigid tetrahedral molecule

Hi, I am interested in simulating a anionic molecule BF4(-) ( Boron tetrafluoride). In the paper which developed the parameters for this molecule, it is mentioned that it has been used as 'rigid' molecule i.e the molecule only has non-bonding interaction but there was no intramolecular motion

Re: [gmx-users] rigid tetrahedral molecule

25:05 PM Subject: Re: [gmx-users] rigid tetrahedral molecule Sanku M wrote: > Hi, > I am interested in simulating a anionic molecule BF4(-) ( Boron >tetrafluoride). In the paper which developed the parameters for this >molecule, >it is mentioned that it has been used as '

Re: [gmx-users] rigid tetrahedral molecule

23 5 5 1 23 4 From: Mark Abraham To: Discussion list for GROMACS users Sent: Wed, April 27, 2011 8:39:23 PM Subject: Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 11:25 AM, Justin A. Lemkul wrote: > > > Sanku M wro

Re: [gmx-users] rigid tetrahedral molecule

GROMACS users Sent: Wed, April 27, 2011 11:14:34 PM Subject: Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 1:54 PM, Sanku M wrote: Hi, > I tried to keep the geometry of the BF4 fixed by using constraints >using lincs. But , unfortunately, my simulation is cr

Re: [gmx-users] rigid tetrahedral molecule

: Mark Abraham To: Discussion list for GROMACS users Sent: Thu, April 28, 2011 1:00:42 AM Subject: Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 3:49 PM, Sanku M wrote: I went through the LINCS manual . But, I am still struggling with coming up with the idea of putting correct

[gmx-users] vdw cutoff options for opls forcefield

Hi, I was wondering whether someone can comment on what vdw-cutoff scheme will be suitable when using a molecule under OPLS/AA force field . Also, providing some details about what cut-off value one should use will be really helpful. Thanks Sanku-- gmx-users mailing listgmx-users@gromacs

Re: [gmx-users] rigid tetrahedral molecule

ill be incorrect! You can achieve a solution with the right number of d.o.f. by using vsites as well. How to do this is left as an exercise for the reader. > I hope this helps. > > best, > Gyorgy > > > Citando Sanku M : > >> Thanks. The molecule was developed as a p

[gmx-users] trjconv problem

Hi, I am having a problem with trjconv to get a single snap-shot from a trajectory file. I am using gromacs 4.0.7 . If I try to get a snapshot corresponding to 14 ps, I was trying to use "-b 14 -e 14 " command as follows. But, If I issue this command as shown below trjconv --f traj.xtc -o c

Re: [gmx-users] trjconv problem

utput, trajectory ended at 14' Any help will be appreciated. Sanku From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Thu, May 5, 2011 10:22:38 AM Subject: Re: [gmx-users] trjconv problem Sanku M wrote: > Hi, > I am having a problem wit

Re: [gmx-users] trjconv problem

I found it will work if I use -b 13.9 -e 14.1 From: Sanku M To: jalem...@vt.edu; Discussion list for GROMACS users Sent: Thu, May 5, 2011 10:33:19 AM Subject: Re: [gmx-users] trjconv problem Hi Justin, In many of the frames, if I use -b and -e to be same

[gmx-users] query regarding replica exchange

Hi, I am planning to run replica exchange simulation using gromacs 4.0.7 . I have read the manual about REMD. Only thing I wanted to know is that how I can specify the name of host-machines where I am planning to run the simulations. I have 10 different quad-core computers each intra-connect

Re: [gmx-users] query regarding replica exchange

to be on the same machine. The above approach will generally achieve that. Mark > -- Josh > > On Wed, 2011-05-25 at 11:50 -0700, Sanku M wrote: >> Hi, >> >> >>I am planning to run replica exchange simulation using gromacs >> 4.0.7 . I have read the manual a

[gmx-users] Restarting replica exchange simulation

Hi, I was running a replica exchange simulation in a PBS queue which was killed as my simulation crossed the maximum time limit. I was planning to restart the simulation. I am using gromacs 4.0.7 I was wondering what should be the command line arguement for the multiple .cpt file for resta

[gmx-users] Dreiding force field in Gromacs ?

Hi, I was wondering whether Gromacs can be used to perform simulation using Dreiding force field developed by Goddard and co-workers ( J.Phys.Chem. ,94,8897,1990). If someone can share some experience in porting this force field in gromacs, that will be very helpful. Sanku-- gmx-users mail

[gmx-users] g_rdf: how to change grid spacing for structure factor

Hi, I am using gromacs_4.0.7 to calculate the Scattering Intensity as a function of scattering vectors(q) using g_rdf -sq command . But, I found that there is no way that one can increase/decrease the grid spacing for structure factor calculation. I tried using -bin option , but that does not

[gmx-users] g_rdf problem

Hi, I am using gromacs_4.0.7 to calculate the Scattering Intensity as a function of scattering vectors(q) using g_rdf -sq command . But, I found that there is no way that one can increase/decrease the grid spacing for structure factor calculation. I tried using -bin option , but that does not

[gmx-users] Transition path sampling

Hi , I was wondering whether current GROMACS versions can perform transition path sampling to study rare events ? Sanku -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Li

[gmx-users] helix dihedral constraint

Hi, I wanted to run an atomistic simulation where I would like to constrain helicity of a helical peptide( i.e the initial configuration is an ideal helix) . I was wondering whether there is a way to constrain the helix dihedral angles in Gromacs. Also, if there is any other option to keep the

[gmx-users] dipole-dipole interaction energy

Hi, I am trying to calculate the dipole-dipole interaction energy of two charged molecules. But, I was looking for a method/formula to do that. I have the .xtc file from which I can calculate the dipole moment of each of the molecule using g_dipole . But, then how will I calculate the dipole-d

[gmx-users] trjorder and index

Hi, I am trying to use trjorder command to generate a sorted trajectory where all the water molecules are certain distance away. I can use the trjorder command to generate the sorted trajectory where all waters are sorted based on distance but I am looking for method for creating a index fil

[gmx-users] query on 1-4 interaction

Hi,    I have a question regarding how the 1-4 interaction works in GROMACS4.5.4 with charmm force field and its relation with number of exclusions ( nrexcl)  If we choose charmm forcefield ( or opls forcefield) in pdb2gmx, it writes down the topology file topol.top    with nrexcl 3 . If I try t

[gmx-users] average force on solute

Hi,   I am simulating a peptide in a box of water in gromacs 4.5.4 . From the trajectory, I want to compute the time-averaged force acting on the peptide.  I found g_traj tool can provide information on force upon supplying the traj.trr file  and g_traj help menu also suggests that using -af opti

[gmx-users] How to find Hbonding partner

Hi,    I am wondering whether there is any way in GROMACS that one can find which groups are the main Hbonding partners in a trajectory. For example, if I simulate a peptide in water, I want to know during the simulation, which particular atoms in the peptides are making most of the Hbonds with

[gmx-users] query on g_sorient

Hi,   I am trying to understand what are the angles g_sorient plans to compute.  The manual says that the theta1 is "the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3" .  But, I wonder what is the reference position of this angle  ? In ot

[gmx-users] FEP for ligand mutation

Hi,   Is it possible in GROMACS4.5 to perform computation of relative binding free energy of a ligand to a protein due to mutation in the ligand ( or due tio mutation in the protein)?  I have done the computation of solvation free energy of a solute in a solvent using FEP but looking for some su

Re: [gmx-users] isodensity surface

You can load your gromacs trajectory file in  VMD 1.9 and then use Volume-map tool in the "analysis" section  to calculate the isodensity surface. The GUI of the Volume-map tool is pretty user-friendly. From: Nidhi Katyal To: gmx-users@gromacs.org Sent: Satur

[gmx-users] gromacs installation with mpi

Hi,  I am using a cluster where user/local/bin has some old mpi executable. But, I have installed openmpi-1.3 in my own home directory so that I can use that for installing gromacs4.5.4 parallel version. I have also updated the path with the openmpi bin directory and library directory in the bas

[gmx-users] cutting a cylinder from simulation box

Hi,   I have run a simulation of a fixed object in water using gromacs. Now, I want to analyze only water molecules which are present within a cylinder of certain radius (smaller than simulation box dimension in XY plane). I wonder whether gromacs has any particular tool which can identify the p

[gmx-users] Umbrella sampling along Radius of gyration

Hi,   Is there any way in gromacs to use radius of gyration of a polymer as reaction coordinate for umbrella sampling ? Thanks Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/M

[gmx-users] Charmm27.ff with FEP

Hi,  Is there any known issue/problem in running FEP calculations with charm27.ff in gromacs4.5.4 ? I tried running an FEP calculation using charmm27.ff by interpolating A state and B state but it gives error that dihedral terms with multiple values can not be interpolated..One need to write all

[gmx-users] any method to determine gaussian curvature of phase

Hi,   I wanted to numerically determine the gaussian curvature of a phase obtained by self-assembly of surfactants. I was wondering whether any one can suggest any tool or any program which can create a 3D grid and then calculate the gaussian curvature on points on the 3D grid . Thanks Sanku-

[gmx-users] Number of native contacts rho

Hi,   Is there any tool in gromacs that can compute the fraction of native contacts  "rho" ( i,e  the typical parameter that quantifies how close the folding protein is to the native ) ? Thanks Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

[gmx-users] problem with plumed version of gromacs in replica exchange

Dear Users ,   I am trying to use PLUMED with gromacs4.5.4 to perform umbrella sampling simulation using replica exchange as implemented within gromacs. I am using radius of gyration as the collective variable along which umbrella sampling is being performed. However, I find that whenever I try

[gmx-users] simulating protein in gas-phase

Dear Gromacs users,   I am trying to perform a MD simulation in gromacs 4.5.4 using a protein and ligand in gas phase. I have previously run the simulation in water without any problem. Now, I want to compare the result to see the effect of solvent. But for running the same simulation after stri

[gmx-users] mdp option for implicit solvent simulation

Hi,   I am trying to do implicit solvent simulation for a protein in gas-phase. I have a few questions : 1) should I use sd integrator? 2) should I also use no periodic condition considering continuum dielectric ? 3) in the JCTC 2010 paper by Lindahl and co-worker, it is mentioned that no cutof

Re: [gmx-users] mdp option for implicit solvent simulation

Hi Erik,   That statement was a typo. The simulation will be done in implicit solvent ( not in gas phase). Sanku From: Erik Marklund To: Sanku M ; Discussion list for GROMACS users Sent: Friday, January 11, 2013 5:04 AM Subject: Re: [gmx-users] mdp option

[gmx-users] Removing external bias apart from umbrella potential

Hi, I am recently trying to perform an umbrella sampling simulation along a particular reaction coordinate on a system where I have also put position restraint on certain atoms of the system... So, for each umbrella sampling window, I have an extra potential on certain atoms ( due to the positi

[gmx-users] PMF and jacobian correction

Dear Gromacs user,   I was having a question on when need to use jacobian coorection of -2KTln(r) ( gromacs manual chapter 6) term when calculating PMF. I understand for a 3-dimensional radial coordinate like distance between two groups, this term need to taken care of. But, if the PMF is comput

[gmx-users] query on replica exchange

Hi,   I am wondering if there is a way I can use twice more number of replica than the number of CPU is available so that each replica will run at 50 % CPU usage..For example if I have 48 replica and have 24 CPUs, is it a possibility to perform Replica exchange in gromacs ? I was using gromacs4.

[gmx-users] query on table potential

Hi,   I am trying to use a table potential implementing Weeks-Chandler-Anderson (WCA) interaction between a solute and all atoms of a solvent like TIP3P water ( with nonzero interaction in the Hydrogen atoms) . But, I am having a trouble in specifying energy groups required for table potential. 

[gmx-users] problem with pull code

Hi all,   I am trying to do an umbrella sampling of a fairly extended state of the protein along end-to-end distance of it. I am using a rectangular box ( elongated along x ) of dimension 20 nm X 8nm X 8 nm. I am doing the simulation in NVT ensemble. gromacs 4.5.4 is being used. But, even after

[gmx-users] Using umbrella sampling at constant force

Hi,   I am trying to compute free energy of a polymer in presence of a constant force. If I understand correctly, I need to use two pull-option here in gromacs: one for performing umbrella sampling and other for applying  constant force. But, as far as I know I can not specify two pull option in

[gmx-users] carbohydrate forcefield in gromacs

Hi,   Is carbohydrate forcefield in Charmm or Amber included in gromacs4.5.5 topology folders ?  Sanku -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before p

Re: [gmx-users] fraction of native contacts calculation

Bipin,   There might be a workaround. You might want to check out Plumed plugin in latest versions of VMD for calculating fractions of native contact. You can load the gromacs trajectory along with the native .gro file in VMD and use Plumed plugin inbuilt in VMD . You need to install plumed most

[gmx-users] g_bar and second law violations

Hi,   I am trying to compute the free energy change using g_bar: I am using two-stage decoupling process as in Justin Lemkul's tutorial. But , I get following warning in all cases regarding violation of second law of thermodynamics. Can someone explain what is this error about and which lambda I

[gmx-users] Replica exchange and wham

Hi, Occasionally I hear that one need to use WHAM( weighed histogram analysis) method in collaboration with Temperature-Replica exchange simulation. But, I was not understanding why one need to use WHAM with temperature-remd simulation. Can someone explain me ? Does one need to use any sor

[gmx-users] residence time calculation

Hi , I am planning to calculate the residence time of a counter-ion near the charged head group of surfactant. I was wondering whether some one can suggest how one can calculate residence time in gromacs? Thanks Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

Re: [gmx-users] residence time calculation

residence time. Is it ? Sanku From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Tue, July 12, 2011 9:13:20 PM Subject: Re: [gmx-users] residence time calculation Sanku M wrote: > Hi , > I am planning to calculate the residence time of a c

[gmx-users] XTC I/O error in replica exchange

Hi, I am running a replica exchange simulation using 64 replicas ( using gromacs4.0.7) in a super computer using 2 nodes ( each having 32 processors). But, what happens is that after running for a day or so, the simulation crashes with error like 'XTC error, may be you are out of quota'. But,

[gmx-users] g_dist with multiple chains of molecules

Hi, I am running a simulation where I have 100 chains of molecule in a box . I am trying to calculate the distance between two particular atoms ( present in each molecule) averaged over all the chains of molecule. i.e If I have atom C1 and C2 in each of the molecule-chain, I want to calculate

[gmx-users] Poisson-Boltzmann free energy in gromacs?

Hi, I was wondering whether, in gromacs, there is any way of calculating the electrostatic free energy using poisson Boltzmann equation. Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs

Re: [gmx-users] Poisson-Boltzmann free energy in gromacs?

-Boltzmann free energy in gromacs? Sanku M wrote: > Hi, > I was wondering whether, in gromacs, there is any way of calculating the >electrostatic free energy using poisson Boltzmann equation. > There is no mention of such a feature in the manual, so I would suspect the answer is

[gmx-users] How to read XTC file in fortran code

Hi, I was planning to do some analysis by reading in a XTC file using Fortran code . I was wondering what is the best possible option I can have . Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.

[gmx-users] query on Free energy perturbation

Hi, I was planning to use Thermodynamic integration to calculate solvation free energy of a molecule in a solvent. I was following Justin Lemkul's online tutorial. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html . I found that a) a sd int

[gmx-users] umbrella sampling using replica exchange

Hi, I was wondering whether in gromacs 4, one can use replica exchange simulation in combination with umbrella sampling. Thanks Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support

[gmx-users] Problem with temperature and stochastic dynamics in FEP

Hi, I am trying to calculate the solvation free energy using thermodynamic integration(TI) method . I am using gromacs 4.0.7 . But, I am having a problem in getting accurate average temperature . The following is what I did: I found that when doing TI, grompp recommends using 'sd' ( stochast

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

ust 2, 2011 8:08:20 PM Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP Sanku M wrote: > Hi, > I am trying to calculate the solvation free energy using thermodynamic >integration(TI) method . I am using gromacs 4.0.7 . But, I am having a problem >in

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

___ From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Tue, August 2, 2011 8:26:16 PM Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP Justin A. Lemkul wrote: > > > Sanku M wrote: >> Hi Justin, >> I first performed t

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Tue, August 2, 2011 8:40:21 PM Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP Sanku M wrote: > Hi Justin, > So, do you suggest that after minimization, I should generate the velocity >

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

and stochastic dynamics in FEP Sanku M wrote: > OKK, But, before, I have tried using md as integrator where I start the > initial >velocity as 280K ( which makes sense as the minimized configuration is >essentially at low temperature) and have used Nose-hoover at 300K and I

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

as time-step. From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Tue, August 2, 2011 10:16:17 PM Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP Sanku M wrote: > Hi Justin, >I did calculate the a

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

nku From: Mark Abraham To: Discussion list for GROMACS users Sent: Tue, August 2, 2011 11:46:21 PM Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP On 3/08/2011 2:23 PM, Sanku M wrote: > >Finally, I achieved the desired 300K

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

Sent: Wed, August 3, 2011 11:00:30 AM Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP On 4/08/2011 1:51 AM, Sanku M wrote: Hi Mark and Justin, > I did investigate on the rvdw=rlist issue. But, I found even if I >make rvdw < rlist and still keep t

[gmx-users] possible bug in structure factor calculation in g_rdf?

Hi,    I was using gromacs 4.0.7 to calculate the scattering intensity of polymer solvated in a solvent. But, I found a discrepancy in the normalization of the calculation when considering only a subset   of  the entire system ( e.g . only solute from the entire solution) : This is what I found:

[gmx-users] Hamiltonian replica exchange ?

Hi,    I was wondering whether hamiltonian replica exchange simulation has been implemented in latest version of  gromacs . Or, is there any other way of performing the hamiltonian replica exchange using some variants of lambda-dynamics ? Sanku-- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Hamiltonian replica exchange?

Hi,    I was wondering whether hamiltonian replica exchange simulation has been implemented in latest version of  gromacs . Or, is there any other way of performing the hamiltonian replica exchange using some variants of lambda-dynamics ? Sanku-- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Force field for thiocyanate ions

Hi,   Does anyone know about availability of MM pair-wise additive forcefield for thiocyanate anion ( SCN- ) , either in CHARMM or OPLS format ? Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gro

[gmx-users] problem with g_density -center

Hi,   I am trying to calculate the density profile of  head group of bilayer normal to z direction using gromacs 4.0.7. I was trying to center the density profile about dx/2.dy/2,0 . But, I am finding problem with using center option. I find using -center option does not shift the bilayer to 0.

[gmx-users] BD with Hydrodynamic interactions?

Hi,   I was wondering whether BD simulation integrator in Gromacs also have option of including hydrodynamic interactions. Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Maili

Re: [gmx-users] BD with Hydrodynamic interactions?

simulation. From: Sanku M To: Dommert Florian Sent: Monday, September 26, 2011 6:07 AM Subject: Re: [gmx-users] BD with Hydrodynamic interactions? I did not mean lattice boltzmann by BD.  By BD I meant Brownian Dynamics. In general, for accuracy in dynamics, one uses

[gmx-users] query on OPLS-2005

Hi,   I wanted to check what is actually OPLS-2005 forcefield that is recently being referred often for md simulation. However, I also see that whenever, OPLS-2005 is being referred, it cites a 2001 paper by Jorgensen on OPLS forcefield. So, what is actually OPLS-2005? So, I wonder what version

[gmx-users] How to convert a gromacs trajectory to Desmond trajectory format

Hi,     I was looking for some way out for converting the trajectory-files back and forth between two softwares between gromacs and Desmond.  More specifically, if I run a simulation for a particular system using gromacs 4.5.4 , how can I convert it into Desmond trajectory file format ? Sanku--

Re: [gmx-users] How to convert a gromacs trajectory to Desmond trajectory format

gromacs trajectory to Desmond trajectory format On 28/10/2011 9:46 AM, Sanku M wrote: Hi, >    I was looking for some way out for converting the trajectory-files back >and forth between two softwares between gromacs and Desmond.  >More specifically, if I run a simulation for a particul

[gmx-users] problem with compiling fftw

Hi,   When trying to compile fftw3.3.3 in our cluster I got following error. Apparently, it try to guess the build-type by trying to create a directory in scratch. I am not sure why it will try to create a directory there and then it fails. I was wondering whether there is any way-out to avoid t

Re: [gmx-users] query on OPLS-2005

Hi Cara,    Thanks for a  very clarifying email. It helps a lot. Sanku From: Cara Kreck To: gmx-users@gromacs.org Sent: Friday, October 28, 2011 3:50 AM Subject: RE: [gmx-users] query on OPLS-2005 Hi Sanku According to the Schrodinger Knowledge Base, this

[gmx-users] pdb2gmx problem with ACE N-cap

Hi,   I have a protein pdb file with ACE as N-cap and I am trying to use pdb2gmx ( within gromacs 4.5.4 ) to generate a topology file using opls/AA . the ACE is present in opls aminoacids.rtp files. But, on issuing the pdb2gmx command, I get following error message: Program pdb2gmx_44, VERSION

[gmx-users] problem with Threading during run

Hi,  I just compiled gromacs 4.5.4 in a cluster. But, I find that if I try to make use of threading introduced in gromacs 4.5.x series, it does not work.   After issuing command like mdrun -v -s , I expected that for my 8-core processor which is not running any other jobs, the threading will show

[gmx-users] Jarzinsky's inequality from SMD simulation

Hi,   I have done some steered MD simulation and I want to construct the potential of mean force from these pull-profile using Jarzinsky's inequality. I wanted to see whether, in updated version of gromacs, there is any implementation of   extracting PMF from SMD simulations.  If not, can anyone

Re: [gmx-users] Jarzinsky's inequality from SMD simulation

F from sMD simulations using the weighted histogram analysis method (WHAM) in gromacs- Justin Lemkul's tutorial does a nice job of explaining it: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html - Laura On 10/31/2011 11:05 AM, Sanku M wrote: Hi, >

[gmx-users] Steered MD in reverse direction?

Hi,   I am performing steered Molecular dynamics simulation to pull a molecule out of a complex. I am using gromacs 4.5.4 to perform the constant rate pulling..I have done the steered MD simulation in a particular direction i.e hav pulled the molecule out of complex. But, to check the convergenc

Re: [gmx-users] Steered MD in reverse direction?

from pullf.xvg will provide the work . Or, will it be force ( obtained from pullf.xvg) multiplied by pulling rate multiplied by time ? From: Justin A. Lemkul To: Sanku M ; Discussion list for GROMACS users Sent: Thursday, November 3, 2011 9:27 PM Subject: Re

Re: [gmx-users] Steered MD in reverse direction?

from pullf.xvg will provide the work . Or, will it be force ( obtained from pullf.xvg) multiplied by pulling rate multiplied by time ? From: Justin A. Lemkul To: Sanku M ; Discussion list for GROMACS users Sent: Thursday, November 3, 2011 9:27 PM Subject: Re

[gmx-users] How to calculate work

Hi, I am performing steered MD simulation using gromacs.  I was wondering how one can get the time profile of the irreversible work from the gromacs pull-code out put . From constant pulling-rate SMD, we get time profile of force pullf.xvg and pullx.xvg. I wonder does multiplying the the value f

Re: [gmx-users] Gromacs error message

Did you create/have any .mdp file called 'minim.mdp' . The grompp is looking for the run parameter file and not finding it as you may not have created one. From: Salvatore Guccione To: gmx-users@gromacs.org Sent: Saturday, November 5, 2011 2:33 PM Subject: [gmx

[gmx-users] g_wham and entropic subtraction

Hi,   I just wanted to check whether g_wham ( in gromacs4.5.4) already subtract the entropic contribution ( -2KTlog(r) term ) term when unbiasing the histogram obtained from umbrella sampling using distance in 3D as a reaction coordinate. Thanks Sanku-- gmx-users mailing listgmx-users@gromac

[gmx-users] Query on restraining center of mass of a protein

Hi,   I have a system containing water and a large protein. In the simulation, I do not want the protein center of mass to drift away. I was wondering what will be the reasonable method in gromacs to fix the position of the center of mass of the protein in its original position . I was thinking

[gmx-users] query on partial charge entry in topology

Hi,   I find that in the ffnonbonded.itp under OPLS forcefield ( inside opls.ff directory), for each particle-type, there is a partial charge assigned to it. However, again in the .rtp file, for each residue, under each charge group, each of the atom is assigned  another partial charge assigned

[gmx-users] density of confined water

Hi,   I would like to know if there is a way in gromacs to calculate the time-averaged density of solvent which is confined between two objects , say, two plates or another example will be water confined between ligand and binding-pocket. I was thinking about two ways for going about this but in

[gmx-users] output logfile

Hi,  It might be a very minor issue but I find in versions of gromacs 4.5.4, the output log file ( in verbose mode) writes the progress of the simulation in a single line ( unlike in previous gromacs 4.0.7 version) where it used to write the progress in a new lines. As a result, in gromacs4.5.4,

Re: [gmx-users] output logfile

Hi,   This has been compiled and installed in same machine which runs Linux. It never happens in any other version lower than gromacs4.5. Sanku From: "Broadbent, Richard" To: Sanku M ; Discussion list for GROMACS users Sent: Saturday, December 3,

[gmx-users] good reference for PCA in gromacs

Hi,   I am wondering whether someone can suggest a reference paper based on which all gromacs principal component analysis (PCA) analysis ( i.e g_covar and g_anaeig tools) tools are based . Or, any other review articles on  PCA analysis  is based will also be useful. Thanks Sanku-- gmx-users ma

[gmx-users] umbrella sampling with replica exchange

Hi,   I have a technical question regarding feasibility of  combining replica exchange with umbrella sampling or any other pulling simulations in gromacs. Since the umbrella sampling or any other pulling simulations are non-equilibrium simulation due to presence of external bias, I wonder whether

[gmx-users] combining umbrella sampling with replica exchange

Hi,   I sent this email few weeks back and thought sending it again in case someone can give some opinion. I have a technical question regarding feasibility of  combining replica exchange with umbrella sampling or any other pulling simulations in gromacs. Since the umbrella sampling or any other

[gmx-users] maining helix conformation

Hi,   I have a pair of polypeptides which are generated as ideal helix. I want to carry out their assembly/dis-assembly simulation by maintaining the helicity of them. I wonder which of the methods for retaining helicity is better : 1. use a harmonic restraints using [bonds] directive using type

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