[gmx-users] gmx gangle in the development version of gromacs

Hello gromacs users, I want to analyze a liquid interface by producing a series of histograms that profile different slices of my simulation along the cartesian z axis. In each histogram, I want to bin the angles between the z-axis and the normal vector defined by a plane of three atoms in a flat

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 119, Issue 23

-OJQxxZRa5QXmn4QSq0VKc3sg3LQe= hqi8...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hello, On Wed, Mar 5, 2014 at 1:30 AM, Eric Smoll ericsm...@gmail.com wrote: Assuming I define a given slice to be between 0 and 1 on the z axis, I believe the command that will produce what I want is: gmx

[gmx-users] compile single src file

Hello, I have a working gromacs install (in /home/gromacs/4.5.3) but I am interested in editing the source and want to start by toying with individual c files in src/mdlib. I added a main function to qm_orca.c and tried to compile as follows: gcc qm_orca.c -o qm_orca -lm

[gmx-users] Question about atom field in .top / .itp file vs ffnonbonded.itp

Hello Gromacs Users, Can the atom field (e.g., H) of a .top / .itp file differ from the atom field of the .gro file and, for instance, the ffnonbonded.itp file? What are the restrictions here? My guess is that the .top /.itp will reference with the ffnonbonded.itp with the type field only

[gmx-users] g_sas

Hello, I am interested in using g_sas in gromacs 4.6.5. I have a few questions: 1.) Is it advisable to use this tool to compute the vacuum accessible surface area for a liquid? 2.) I ran a test using .gro / .trr / .tpr output from a production run in my workflow as shown follows: { g_sas -f

Re: [gmx-users] g_sas

Regards, On Sat, Aug 16, 2014 at 9:01 PM, Eric Smoll ericsm...@gmail.com wrote: Hello, I am interested in using g_sas in gromacs 4.6.5. I have a few questions: 1.) Is it advisable to use this tool to compute the vacuum accessible surface area for a liquid? 2.) I ran a test using

Re: [gmx-users] g_sas

made of? I am not sure what you mean when you say trajectory like information. g_sas prints out information for every time step. Regards, On Saturday, August 16, 2014, Justin Lemkul jalem...@vt.edu wrote: On 8/16/14, 1:40 PM, Eric Smoll wrote: Rajat, Thank you for the rapid

Re: [gmx-users] g_sas area

Hello Yao, Running g_sas -h will print out some helpful information. It reads: The calculation group should always consists of all the non-solvent atoms in the system. The output group can be the whole or part of the calculation group. Best, Eric On Mon, Aug 18, 2014 at 10:00 AM, xy21hb

[gmx-users] centering with trjconv

Hello GROMACS users, I have created an infinite liquid film system by building a slab of molecules in a 3D periodic unit cell where two dimensions of the film (x and y) extend out to the edge of the unit cell and one (z) does not. I found the slab drifts along the z-dimension during MD and I am

Re: [gmx-users] centering with trjconv

. Best, Eric On Tue, Aug 26, 2014 at 1:49 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey :) What about -pbc nojump -center ? Cheers, Tsjerk On Tue, Aug 26, 2014 at 8:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/26/14, 12:30 PM, Eric Smoll wrote: Hello GROMACS users

[gmx-users] Monitor distance between atoms

Hello Gromacs Users, Is there a way to output the distance between and atom X and all atoms within distance R of atom X along a trajectory? I am paging through the manual but I can't seem to find anything like this. I would settle for the coordinates of all atoms within a distance R of atom X

[gmx-users] MD exit condition

Hello Gromacs users, I am using Gromacs 4.6.5 Is there a way to set an exit condition during a simulation? I am interested in terminating dynamics when two groups are separated by a certain distance. If it is not possible to set an exit condition, I suspect I can post process the trajectory

[gmx-users] QM / MM assistance

Hello Gromacs users, As far as I understand, the most up-to-date reference for compiling gromacs for QM/MM calculations is shown here: http://wwwuser.gwdg.de/~ggroenh/qmmm.html I am trying to follow the MOPAC instructions with Gromacs 4.6.7. When I try to use the provided precompiled library,

Re: [gmx-users] QM / MM assistance

, Eric Smoll ericsm...@gmail.com wrote: Hello Gromacs users, As far as I understand, the most up-to-date reference for compiling gromacs for QM/MM calculations is shown here: http://wwwuser.gwdg.de/~ggroenh/qmmm.html I am trying to follow the MOPAC instructions with Gromacs 4.6.7

Re: [gmx-users] QM / MM assistance

/mkl/include This compiles nicely with no errors on the machine I am using. Thank you for the guidance. Best, Eric On Sun, Sep 14, 2014 at 11:14 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/14/14 12:59 PM, Eric Smoll wrote: Hello Johnny, Thanks for the suggestion. I dumped the contents

Re: [gmx-users] .gro file units

Hello Nilesh, The coordinates and the box vectors are specified in nanometers. The various elements of the .gro file format are specified here: http://manual.gromacs.org/current/online/gro.html. Best, Eric On Thu, Oct 16, 2014 at 1:43 PM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Hello,

[gmx-users] OPLSAA

Hello Gromacs users, Here is a quote from a JPCB paper with over 500 citations: In fact, in the specification of the OPLS-AA force field, sites within the same molecule separated by *more than* three bonds interact by Lennard-Jones and electrostatic potentials scaled by a factor of 0.5 Am I

[gmx-users] Parameter dump

Hello Gromacs users, Is there an easy, readable way to dump all parameters loaded by gromacs when a topology files is read in? Will -debug do this? Best, Eric -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] Question

Hello Gromacs users, If I have all the files that were used to generate a trajectory file, what is the proper procedure to update the atomnames in the trajectory. My best guess is below. Is this problematic? # remove first frame of trajectory cat EOF tmp.ndx [ FIRSTFRAME ] 1 EOF trjconv -fr

Re: [gmx-users] Question

Thanks for the guidance, Justin. -Eric On Thu, Oct 23, 2014 at 2:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/23/14 4:29 PM, Eric Smoll wrote: Hello Gromacs users, If I have all the files that were used to generate a trajectory file, what is the proper procedure to update

[gmx-users] trjconv gets stuck on frame

Hello Gromacs users, I have a trajectory file script18_o.trr that I am trying to process. Using gmxcheck, this file appears to be complete. When I execute the command below trjconv -f ../script18/script18_o.trr -s ../script17/script17_o.tpr -o tmp1.trr -pbc whole EOF 0 EOF the code moves

Re: [gmx-users] trjconv gets stuck on frame

problem area. Mark On Oct 26, 2014 6:59 PM, Eric Smoll ericsm...@gmail.com wrote: Hello Gromacs users, I have a trajectory file script18_o.trr that I am trying to process. Using gmxcheck, this file appears to be complete. When I execute the command below trjconv -f ../script18

Re: [gmx-users] trjconv gets stuck on frame

speed. Best, Eric On Mon, Oct 27, 2014 at 5:33 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Sun, Oct 26, 2014 at 11:44 PM, Eric Smoll ericsm...@gmail.com wrote: Hi Mark, Thank you for responding so rapidly. I should note that identical processing (I use a script

[gmx-users] pdb2gmx

Hello Gromacs users, I would like to add a molecule as a residue in the aminoacids.rtp file and I have a few questions. As far as I understand, a residue in a gro file can multiple atoms with the same atom name. What links every atom in this residue to parameters in the top [ atoms ] directive

Re: [gmx-users] How to implement LJ 6-12 function form?

Hello Kester, Setting the first value in the defaults directive to 1 indicates that you want to use the 6-12 LJ potential. As far as I understand, setting N is only necessary if you want the repulsive LJ term to be something other than 12. I don't think you need to do anything else. The first

Re: [gmx-users] pdb2gmx

and examples in Chapter 5 of the manual. Mark On Wed, Oct 29, 2014 at 1:11 AM, Eric Smoll ericsm...@gmail.com wrote: Hello Gromacs users, I would like to add a molecule as a residue in the aminoacids.rtp file and I have a few questions. As far as I understand, a residue in a gro file can

Re: [gmx-users] pdb2gmx

input methods are making use of the same parameters and that these parameters are correct. If you are aware of any sanity checks the user can preform, that would be most useful. Best, Eric On Wed, Oct 29, 2014 at 10:55 AM, Eric Smoll ericsm...@gmail.com wrote: Hi Mark, Thanks for your help. I am

[gmx-users] trjcat

Hello Gromacs users, I ran a 2 ns simulation (using A.mdp and A.top) and obtained the files A.trr, and A.cpt, and A.gro. I would like to continue the simulation over an identical interval with identical settings. I executed the following commands: grompp -f A.mdp -c A.gro

Re: [gmx-users] trjcat

Rajesh On Fri, Oct 31, 2014 at 3:18 PM, Eric Smoll ericsm...@gmail.com wrote: Hello Gromacs users, I ran a 2 ns simulation (using A.mdp and A.top) and obtained the files A.trr, and A.cpt, and A.gro. I would like to continue the simulation over an identical interval with identical

Re: [gmx-users] Making index file

Hello, Can you index your residues so that each residue gets a unique number. pdb2gmx has an option -renum that will do this for you. Best, Eric On Tue, Nov 4, 2014 at 10:33 PM, bharat gupta bharat.85.m...@gmail.com wrote: Thank you for your response. But in the gro file there are no names

Re: [gmx-users] Axis

Hello Lloyd, Try the editconf -rotate flag: editconf -f in.gro -o out.gro -rotate 0 90 0 Run editconf -h for more information. Best, Eric On Tue, Nov 4, 2014 at 11:55 PM, lloyd riggs lloyd.ri...@gmx.ch wrote: Dear Gromacs users, Is there a way to change the x y z axis as read by the

[gmx-users] ffout

Hello Gromacs users, What is the purpose of the ffout flag for mdrun version 4.6.5? It does not produce output, it appears to have has no impact on my simulations, and it is not documented in the manual. Best, Eric -- Gromacs Users mailing list * Please search the archive at

[gmx-users] content of trr / xtc files + -b/-e flag question + tpr question

Hello Gromacs users. I have a few questions. I ran two small trajectories: trajectory 1: dt = 0.0008 nsteps=10 nstxout=2 nstxtcout=3 trajectory 2: dt = 0.0008 nsteps=10 nstxout=3 nstxtcout=2 We can examine the content of each trajectory using trajconv -sep -nzeros 1. The initial frame is

Re: [gmx-users] trjconv during transfer of .trr

Hello Johnny, Try gmxcheck -f file.trr - Eric On Sun, Dec 14, 2014 at 3:58 PM, Johnny Lu johnny.lu...@gmail.com wrote: seems to be fine for slurm resource manager... so far. On Sun, Dec 14, 2014 at 5:50 PM, Johnny Lu johnny.lu...@gmail.com wrote: Alternatively, is there a way to

Re: [gmx-users] Reg: topology and parameter files for dichlormethane

Hello Akshay, Perhaps try http://virtualchemistry.org/molecules/75-09-2/index.php Best, Eric On Fri, Jan 2, 2015 at 10:24 PM, Akshay Bhatnagar akshaybhatnagar2...@gmail.com wrote: Hello I want to simulate an amino acid in dichloromethane as solvent. can anyone provide me with the topology

[gmx-users] g_sas question

Hello, I am using the Gromacs 4.6.5 g_sas tool with custom radii for each atom as specified with a local vdwradii.dat file. Are the surface areas reported in -or atomarea.xvg on a sphere defined by R_VDW or at R_VDW + R_probe? Similarly, is the -minarea # flag a threshold value that applies to

[gmx-users] Gromacs precision and the precision of values set in the mdp file

Hello Gromacs users, What is the precision limit for values entered in an mdp file for a single precision gromacs simulation? Does this increase when using gromacs is compiled in double precision? Best, Eric -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Constraints and Energy Minimization

On Sat, Apr 25, 2015 at 8:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/25/15 10:25 PM, Eric Smoll wrote: Hello Gromacs Users, I am studying a forcefield where certain bond force constants were not specified because the associated bond lengths were constrained. What do I need to do

[gmx-users] Constraints and Energy Minimization

Hello Gromacs Users, I am studying a forcefield where certain bond force constants were not specified because the associated bond lengths were constrained. What do I need to do to run a simulation that is consistent with the way this forcefield was designed? Will LINCS constraints satisfy this

[gmx-users] Molecule specific explosion

Hello Gromacs Users, I have constructed a multi-component solution and, during energy minimization, one molecule type is radically deforming under ~ 0.2 ps. All molecules of this type explode simultaneously. Looking over the topology, all the atoms in this molecules appear to have correct

Re: [gmx-users] Constraints and Energy Minimization

, I have an equilibrium distance but I do not have a force-constant. Is it irrelevant what value I choose for the force constant if I apply constraints to that bond? Best, Eric On Sat, Apr 25, 2015 at 9:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/25/15 11:01 PM, Eric Smoll wrote: Hello

Re: [gmx-users] Molecule specific explosion

On Sun, Apr 26, 2015 at 2:08 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Look at the whole molecule topology. Don't ignore any warnings. Mark On 26/04/2015 9:38 am, Eric Smoll ericsm...@gmail.com wrote: Hello Gromacs Users, I have constructed a multi-component solution

Re: [gmx-users] which file to use to analyze trajectory using code

Hello Sahithya, Here is one solution: http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library Best, Eric On Mon, Jun 8, 2015 at 9:56 PM, Sahithya S Iyer sah2...@gmail.com wrote: Dear users, If one wanted to analyze the trajectory obtained on production run for a property of the

Re: [gmx-users] Molecule specific explosion

at http://www.gromacs.org/Documentation/Terminology/Blowing_Up Mark On Tue, Apr 28, 2015 at 8:09 AM, Eric Smoll ericsm...@gmail.com wrote: Hi Mark, Thanks for the reply. In my previous message, one molecular component of my liquid solution greatly-deforms (explodes) on energy

Re: [gmx-users] Question

, On Wed, Aug 12, 2015 at 9:47 PM Eric Smoll ericsm...@gmail.com wrote: Hello gromacs users, I am running a set of MD simulations where we are only interested in logging the coordinates and kinetic energy of a specific group in the system. I want to write the coordinates and energy

Re: [gmx-users] simulations of ice beginning to spin

Hello Nathan, Did you set comm-mode and nstcomm http://manual.gromacs.org/online/mdp_opt.html#run in your mdp file? Best, Eric On Thu, Aug 20, 2015 at 3:37 PM, Nathan K Houtz nho...@purdue.edu wrote: Hello, I'm sorry to submit a query twice, but I have not received a reply since last week.

[gmx-users] a few detailed questions about the topology file format

Hello Gromacs users, As far as I understand, values listed in the top file override any information pulled from share/gromacs/top. However, ff an atom type (e.g., opls_100) serves as a references to information contained in the share/gromacs/top directory, is it necessary to include a value for

[gmx-users] Question about redundancy in forcefield files and dihedral parameterization

Hello GROMACS users, In the *types directives, what impact does redundancy have? Does a later specification override an earlier specification? For a concrete example, consider a bondtypes entry: [ bondtypes ] A B 1 1.0 2.0 A B 1 1.0 3.0 Which specification will be used? What impact does

[gmx-users] Question about forcefield files

Hello GROMACS users, In the OPLS atomtypes.atp file, is it problematic to define atom type names (e.g., opls_XXX) with nonconsecutive integers? For example, opls_1000 ... opls_1100 ... opls_1050 ... Best, Eric -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Add new integrator

Hello GROMACS users, I am interested in adding a fifth/sixth order predictor/corrector integrator to GROMACS. Is this possible? If so, any guidance on which files need to be updated is much appreciated. Best, Eric -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Gromacs 4.5 or 4.6???

Hello Elham, I don't think this is a problem if you set the install location manually. With gromacs 4.5 try ./configure --prefix=/path/to/install/dir With gromacs 4.6 try cmake /path/to/gromacs-4.6/ -DCMAKE_INSTALL_PREFIX=/path/to/install/dir Best, Eric On Fri, Aug 14, 2015 at 11:32 PM, elham

[gmx-users] Question

Hello gromacs users, I am running a set of MD simulations where we are only interested in logging the coordinates and kinetic energy of a specific group in the system. I want to write the coordinates and energy of this group to file at every timestep. Supplying an index file with the group of

[gmx-users] Question about pdb2gmx

Hello gromacs users, As far as I understand, pdb2gmx only works for the residues/molecules defined in aminoacids.rtp. It cannot read coordinate data and infer the atomtype, charge, and connectivity from the structure file atomnames, correct? Best, Eric -- Gromacs Users mailing list * Please

[gmx-users] Questions about GROMACS capabilities

Hello GROMACS users, I have a few questions about what is possible in GROMACS: 1.) Is it possible reset the velocity of a subset of molecules in a MD simulation to an arbitrary, non-thermal distribution? I am particularly interested in the situation where all molecules of a certain type are

Re: [gmx-users] MD exit condition

, Aug 28, 2014 at 6:58 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, Aug 28, 2014 at 3:32 PM, Eric Smoll ericsm...@gmail.com wrote: Hello Gromacs users, I am using Gromacs 4.6.5 Is there a way to set an exit condition during a simulation? I am interested in terminating

[gmx-users] Bond rotation freedom or mobility

Hello GROMACS users, I am interested in quantifying the freedom or mobility of specific carbon-carbon single bonds in a organic molecule. Does anyone know the most appropriate method to do this? Can I make use of gmx chi? Best, Eric -- Gromacs Users mailing list * Please search the archive at

[gmx-users] GROMACS OPLS-AA question

Hello GROMACS users, I am interested in using the OPLS-AA as implemented in GROMACS. The OPLS-AA forcefield omits all nonbonded (Coulomb and LJ) interactions 1 and 2 bonds away. Nonbonded interactions 3 bonds are away are scaled by 1/2. Nonbonded interactions are applied without modification for

[gmx-users] GPU suggestions

Hello Gromacs users, We are running GROMACS molecular dynamics simulations on a cluster with the following specs: supermicro hardware, sandy bridge and haswell intel Xeons, 4 GB per core, Mellanox 10 GbE (w/RDMA) switching (no IB). We were thinking of adding GPU's to this system. Does anyone

[gmx-users] oplsaa.ff parameters

Hello GROMACS users, oplsaa.ff/ffbonded.itp contains the following line: CT CT CT CT 3 2.92880 -1.46440 0.20920 -1.67360 0.0 0.0 ; hydrocarbon all-atom These values are at odds with those used provided in two publications listed in

Re: [gmx-users] oplsaa.ff parameters

Hello James, Thank you for taking the time to respond to both of my OPLS-AA questions. Your help is much appreciated. Best, Eric On Sat, Sep 12, 2015 at 8:35 AM, Barnett, James W <jbarn...@tulane.edu> wrote: > On Thu, 2015-09-10 at 15:04 -0600, Eric Smoll wrote: > > Hell

[gmx-users] periodic improper dihedral

Hello GROMACS users, I have a question about specifying periodic improper dihedrals in GROMACS. In the GROMACS manual (chapter 5, table 5.5), the parameters of the periodic improper dihedral are listed as follows: phi_s ( deg ); k_phi (kJ mol^-1); multiplicity In the GROMACS manual (chapter 4,

Re: [gmx-users] periodic improper dihedral

unction type 2). Do you have any idea how I could trouble shoot this problem? Best, Eric On Wed, Dec 16, 2015 at 4:54 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Yes > > On Thu, 17 Dec 2015 05:39 Eric Smoll <ericsm...@gmail.com> wrote: > > > Hello GROMA

[gmx-users] gmx gangle selections help

Hello gromacs users, I want to map the angle between a specific bond vector (defined by the atoms A and B) and the z axis using gmx gangle. I am only interested in bond vectors that have a center-of-mass z-coordinate greater than C. Is there a way to make this selection using the 'gmx

[gmx-users] gmx traj

Hello Gromacs users, 'gmx traj' can return the COM trajectory of any group specified in an index file. If many groups are specified in the index file, 'gmx traj' will prompt you to select one group for analysis. Is there anyway to return COM data on multiple user-defined groups at the same time

[gmx-users] gmx density question

Hello gromacs users, Gromacs 5.1.2 gmx density does not appear to have 'gmx select'-style selections yet. Is there a way to compute the number density distribution of a multiple-atom center-of-mass position along every frame of an xtc trajectory? Best, Eric -- Gromacs Users mailing list *

[gmx-users] 'gmx rdf' and 'gmx select' questions

Hello Gromacs users, I have a few syntax questions: (1) What is the difference between 'res' and 'mol' position specifiers? I assume 'res' refers the set of all atoms that have the same gro-file residue-number *and* residue name. Is this correct? What does 'mol' indicate? (2) 'gmx rdf' in

[gmx-users] gmx sasa

Hello Gromacs Users, "gmx sasa" in Gromacs 5.0.6 returns a message stating that all atom radii are obtained from the following reference: "A. Bondi, van der Waals Volumes and Radii, J. Phys. Chem. 68 (1964) pp. 441-451" Can the user still control the radii used by editing a local copy of the

[gmx-users] Question

Hello Gromacs users, When running pdb2gmx, what determines the function number used for each type of potential (bonds, angles, dihedrals, etc.). When I run pdb2gmx, my dihedrals section is built with function number 3. I would like to change this to function number 5. It is easy to edit the file

[gmx-users] gmx bar histogram data

Hello GROMACS users, I am using the "gmx bar" tool in GROMACS 5.1.2 and am interested in understanding the relevance of the histogram data output by the -oh flag. Dr. Lemkul provides a very helpful reference and a

Re: [gmx-users] Error at FEP lambda = 1; seg. fault. with "larger than the table limit" message

PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > > Hi, > >> On Fri, Apr 14, 2017 at 1:49 AM Eric Smoll <ericsm...@gmail.com> wrote: >> >> Hi Mark, >> >> Thanks for the rapid reply! I am using version 5.1.2. I can reproduce the >> error

Re: [gmx-users] Error at FEP lambda = 1; seg. fault. with "larger than the table limit" message

ere should be no particle overlap issue. That being said, I am using VDW and coulomb soft-core settings. Best, Eric On Thu, Apr 13, 2017 at 5:40 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Fri, Apr 14, 2017 at 1:30 AM Eric Smoll <ericsm...@gmail.com> wrote: > >

Re: [gmx-users] Error at FEP lambda = 1; seg. fault. with "larger than the table limit" message

lambda=0.9 with the same topology/input-structure/mdp settings. Best, Eric On Thu, Apr 13, 2017 at 6:04 PM, Eric Smoll <ericsm...@gmail.com> wrote: > Good point. I only mutate one solute to a different solute. I do not have > separate coulomb and vdw stages. If I examine the initial fra

[gmx-users] Error at FEP lambda = 1; seg. fault. with "larger than the table limit" message

Hello GROMACS users, I am running NVT alchemical free energy simulations (change in atom number, bonding, etc.). These simulations appear to go well at all lambda values below 1.0. At lambda=1.0, the system returns an error before or during the first step: WARNING: Listed nonbonded interaction

Re: [gmx-users] Error at FEP lambda = 1; seg. fault. with "larger than the table limit" message

, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/13/17 9:12 PM, Eric Smoll wrote: > >> Hello Mark, >> >> I did not answer one of your questions. You asked "what is the alchemical >> state at 1.0?" The transformation involves lengthening t

[gmx-users] Error at FEP lambda = 1; seg. fault. with "larger than the table limit" message

Hello GROMACS users, I am running NVT alchemical free energy simulations (change in atom number, bonding, etc.). These simulations appear to go well at all lambda values below 1.0 (no errors and the resulting trajectories show no unusual behaviour). At lambda=1.0, the system returns an error

Re: [gmx-users] precision of input gro file

Hello Yu, Read this carefully. http://manual.gromacs.org/online/gro.html As far as I know, Gromacs will accept gro files with high precision if the input file follows this format. Best, Eric > On Jun 15, 2017, at 4:33 AM, Yu Ogawa wrote: > > Hello gmx users, > Can we

[gmx-users] Dihedral parameters from QM and MM relaxed surface scans

Hello Gromacs Users, I am trying to reproduce some published forcefield development work. In this paper, dihedral parameters are derived from QM and MM relaxed surface scan data collected on individual small molecules in vacuum. My replication workflow is as follows. The MM relaxed surface scan

[gmx-users] REMD

Hello Gromacs Users, I am interested in calculating the equilibrium distribution of molecular structures at the vacuum-liquid interface of several different low vapor pressure liquids. All of these liquids are very viscous at or near room-temperature and I suspect that conformational barriers may

[gmx-users] REMD

Hello GROMACS users, As far as I understand, increasing the number of random exchanges to a large number (mdrun suggests N^3 where N is the number of replicas) moves a REMD simulation from a neighbor exchange procedure to a Gibbs exchange procedure. Can anyone provide some practical advice or

Re: [gmx-users] Shell (Drude) model for polarization in GROMACS

utable on a single node for shell MD, correct? Thread parallelization is still permitted, correct? Thanks again, Justin. I hope my questions are clear and easy to answer. Best, Eric On Mon, Jun 18, 2018 at 12:07 PM, Justin Lemkul wrote: > > > On 6/18/18 3:00 PM, Eric Smoll wrote: > >&g

[gmx-users] Shell (Drude) model for polarization in GROMACS

Hello GROMACS users, I am looking over the shell (Drude) model for polarization in GROMACS. There isn't much information available in the manual (probably because this feature is rarely used). I was hoping someone knowledgeable about polarizable simulations in GROMACS could help answer a few of

[gmx-users] Surface Tension: equation and tail corrections?

Hello GROMACS users, I am using gromacs 2018.1 The manual and the gmx energy help page does not explicitly explain how the "(surface tension) x (surface number)" is calculated. I assume it is equation 3.69: L_{z} ( P_{zz}(t) - ( 0.5*P_{xx}(t) + 0.5*P_{yy}(t) ) ) Has anyone implemented a tool

Re: [gmx-users] Shell (Drude) model for polarization in GROMACS

_polarization directive). Sorry for the additional questions. I suspect this conversation will drag on for a long time. Best, Eric On Sun, Jul 1, 2018 at 1:27 PM, Justin Lemkul wrote: > > > On 7/1/18 3:13 PM, Eric Smoll wrote: > >> Thank you, >> >> I have comp

Re: [gmx-users] Shell (Drude) model for polarization in GROMACS

On 6/18/18 4:05 PM, Eric Smoll wrote: > >> Justin, >> >> Thank you so much for the rapid and clear reply! Sorry to ask for a bit >> more clarification. >> >> The thole_polarization isn't in the manual at all. Is it structured the >> same way as the [ po

Re: [gmx-users] Shell (Drude) model for polarization in GROMACS

e still diminished by 0.5. Am I correct? Best, Eric On Tue, Jun 26, 2018 at 8:40 AM, Justin Lemkul wrote: > > > On 6/26/18 10:37 AM, Eric Smoll wrote: > >> Justin, >> >> In a previous thread on core/shell optimization ( >> https://mailman-1.sys.kth.

[gmx-users] custom topology questions

Hello Gromacs Users, I have a few custom topology questions. Input on any of these questions would be greatly appreciated. 1.) What gromacs tools use the information in atomtypes.atp? 2.) Table 5.4 claims the atomtypes directive consists of lines with the format: atom-type, mass, charge,

Re: [gmx-users] Dihedral parameters from QM and MM relaxed surface scans

rvations of quantities that depend on the FES is > less clear. > > Mark > > On Sat, Apr 28, 2018 at 9:30 AM Eric Smoll <ericsm...@gmail.com> wrote: > > > Hello Gromacs Users, > > > > I am trying to reproduce some published forcefield development work. In

Re: [gmx-users] Dihedral parameters from QM and MM relaxed surface scans

. Thank you for the guidance. Best, Eric On Sun, Apr 29, 2018 at 4:05 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/29/18 5:48 PM, Eric Smoll wrote: > >> Mark, >> >> *Thank you for the reply! * >> >> I understand your conclusion but I am try

Re: [gmx-users] Shell (Drude) model for polarization in GROMACS

On Sun, Jul 1, 2018 at 6:52 PM, Justin Lemkul wrote: > > > On 7/1/18 6:37 PM, Eric Smoll wrote: > >> Justin, >> >> Thank you for the response! I deeply appreciate the effort you put into >> this community. >> >> I am still very confused *but* I learn mo

Re: [gmx-users] nonbond_params directive

Hi Justin, No problem. Thanks for the clarification. I think I understand now. Best, Eric On Sat, Jul 28, 2018 at 6:39 PM, Justin Lemkul wrote: > > > On 7/28/18 8:35 PM, Eric Smoll wrote: > >> Justin, >> >> Thank you for the guidance. >> >> &quo

Re: [gmx-users] nonbond_params directive

ond_params directive. Since the directive takes atomtypes, there is no way to specify and scale the 1-4 CH2-CH2 LJ interactions. Am I missing something? Best, Eric On 7/28/18 7:19 PM, Eric Smoll wrote: > On Sat, Jul 28, 2018 at 2:17 PM, Justin Lemkul wrote: > > >> On 7/26/18

Re: [gmx-users] nonbond_params directive

On Sat, Jul 28, 2018 at 2:17 PM, Justin Lemkul wrote: > > > On 7/26/18 5:52 PM, Eric Smoll wrote: > >> Hello GROMACS users, >> >> I have a quick question about the nonbond_params directive. >> >> If I provide gen-pairs=yes and fudgeQQ=0.5 in the default

[gmx-users] Restart

Hello GROMACS users, I had a simulation terminate unexpectedly very close to completion and I would like to resume the simulation from a checkpoint file. my mdrun flags are -cpi, -s, -o, -x, -c, -e, -g, and -cpo. All of the associated files are present (except the -c file since there was a

[gmx-users] nonbond_params directive

Hello GROMACS users, I have a quick question about the nonbond_params directive. If I provide gen-pairs=yes and fudgeQQ=0.5 in the defaults directive, GROMACS will (1) compute VDW parameters for all atomtype-pairs and (2) scale all 1-4 interactions specified in the pairs directive by 0.5. Note

Re: [gmx-users] Restart

making sure the restart also has all the names > matching. Perhaps -noappend will let you get something done, but I strongly > suggest using directories for your project organization using the default > file names, rather than manually managing file names. > > Mark > > &g

[gmx-users] msd

Hello GROMACS Users, I am interested in calculating spatially resolved diffusion constants. Is this possible? In GROMACS 2018.1, gmx msd does not seem to support dynamic selection like gmx select. Best, Eric -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Shell (Drude) model for polarization in GROMACS

Justin, No problem. That makes sense. Can I send my atp, rtp, itp, and gro files used with the pdb2gmx from your drude branch off-list? Best, Eric On Fri, Jul 13, 2018 at 8:12 PM, Justin Lemkul wrote: > > > On 7/13/18 8:14 PM, Eric Smoll wrote: > >> Justin, >>

Re: [gmx-users] Shell (Drude) model for polarization in GROMACS

topology for my problem molecules. It should be easy to compare with the topology I have prepared with my own tools. They should be identical. Best, Eric On Fri, Jul 13, 2018 at 2:51 PM, Justin Lemkul wrote: > > > On 7/13/18 4:48 PM, Eric Smoll wrote: > >> Hello Justi

Re: [gmx-users] Shell (Drude) model for polarization in GROMACS

2 3...N" series. Is this expected? Shouldn't intramolecular nonbonded interactions be permitted at and beyond 1-4 interactions? Best, Eric On Fri, Jul 13, 2018 at 3:02 PM, Eric Smoll wrote: > Hi Justin, > > Very grateful for the rapid reply and warning. If you suggest that I &

Re: [gmx-users] Documentation on gmx densorder?

Hello Micholas and David, If possible, could this discussion be kept on the list. I was unaware of this tool and would like to know about "gmx densorder" input, output, and usage. If not, would it be OK if I sent my own followup questions to Micholas or David in an independent email? David,

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