[gmx-users] Umbrella Sampling - Changing force constant values between samples

Hello, I am wondering if it is valid to use different force constant (k) values between samples for umbrella sampling. It seems that gmx_wham accepts different k values in a set, but I wanted to make sure this is OK. Should I be wary of any artifacts with these simulations? Best Regards, Dan

Re: [gmx-users] gmx select with coordinates

> 45 and x < 90 and y > 90 > and y. What could be the reason for this? Appreciate, if you can reply me. > > Thank you. > > On Fri, Sep 28, 2018 at 12:00 AM Dan Gil wrote: > > > Hi, > > > > I believe you are trying to select atoms/particles that are in a

Re: [gmx-users] Buckingham parameters to Lennard Jones Parameters

Doesn't gmx sigeps do what you need? Dan On Wed, Sep 26, 2018 at 10:44 AM Sam David wrote: > What is your system? > Try to do a fitting and check. I have the same problem and still trying > > Good luck > Sam > > On Wed, Sep 26, 2018 at 9:08 AM sanjeet kumar singh ch16d012 < >

Re: [gmx-users] gmx select with coordinates

Hi, I believe you are trying to select atoms/particles that are in an infinitely tall box with the vertices (45, 90), (45, 125), (90, 90) and (90, 125)? Gmx select uses commands that are similar in syntax to a software called VMD. So I like to use VMD to figure out what I need to give to gmx

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 172, Issue 89

pics: > > > >1. free energy of complex system (abhisek Mondal) > >2. restrain ligand in free energy. (T?ng Ho?ng) > >3. Re: rotation of atoms by more than 90 degrees & LINCS > > Warnings (Dan Gil) > >4. Re: rotation of atoms by more than

Re: [gmx-users] rotation of atoms by more than 90 degrees & LINCS Warnings

Hi Sagar, At which time step do you get LINCS warnings? Also, please see: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings Dan On Tue, Aug 28, 2018 at 3:19 AM sagar bathla wrote: > Dear all, > > My system consists of 2 orthorhombic parallel graphene sheets in a big

Re: [gmx-users] No default Ryckaert-Bell. types

Hello, This is telling you that the OPLS-AA force field does not have the dihedral force-field parameters for your molecule (topol_Other_chain_C.itp) of the Ryckaert-Bell type. Your exact problem might be: (1) There is something wrong with the molecule topology. (2) OPLS-AA really doesn't have

Re: [gmx-users] ndx file with frames

Hi, I have used gmx select to create groups of atoms for each time frame - the indices of the atoms in each group changed with each step. Then I used this output in other gromacs utilities such as gmx rdf. I haven't used plumed, but from your question I believe gmx select might be a good start

Re: [gmx-users] zig-zag stacking

Hi, I haven't tried it, but I wonder if the gmx editconf utility can be used to translate groups of atoms, where the group is defined with an index file (make_ndx). Dan On Tue, Jul 31, 2018 at 1:21 PM, Nagasree Garapati < nagasree.garap...@mail.wvu.edu> wrote: > Hi All > > > I am trying to

Re: [gmx-users] gmx select and gmx trjconv or gmx density

useful way to use that index file is by matching it with the correct > single frame from the trajectory, which you might get from e.g. gmx trjconv > split > > Mark > > On Fri, Apr 6, 2018, 21:37 Dan Gil <dan.gil9...@gmail.com> wrote: > > > Hi, > > > > I am tryi

[gmx-users] gmx select and gmx trjconv or gmx density

. Does anybody have some advice? Thanks in advance. Best Regards, Dan Gil PhD Student Case Western Reserve University Department of Chemical and Biomolecular Engineering -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List befor

Re: [gmx-users] Parmbsc1 force-field

uite similar. I emailed with parmbsc1 developers and > their experience was the same. Together with parmbsc0, other authors have > used Dang 1995, so that's how our choice came about. To follow the parmbsc1 > authors you should indeed use the paper they cite. > > > > -- > V

Re: [gmx-users] Parmbsc1 force-field

ers > providing the parameters on the website, but as Mark said, it's up to you > to double-check it. If you do find actual errors, I'm interested in hearing > about it :) > > -- > Viveca > > > On Fri, Mar 2, 2018 at 5:19 PM, Dan Gil <dan.gil9...@gmail.com>

Re: [gmx-users] Parmbsc1 force-field

s.org/doi/abs/10.1021/ja00131a018. Does that cover the > question? > > Mark > > On Fri, Mar 2, 2018 at 5:20 PM Dan Gil <dan.gil9...@gmail.com> wrote: > > > Hello, update here. > > > > I think there is a possibility that the parmbsc1 force-field

Re: [gmx-users] Parmbsc1 force-field

, Dan On Thu, Mar 1, 2018 at 7:00 PM, Dan Gil <dan.gil9...@gmail.com> wrote: > Hi, > > I am using the parmbsc1 force-field (http://www.gromacs.org/@api/d > eki/files/260/=amber99bsc1.ff.tgz) in GROMACS. I am looking for the > original paper where the Na+ and Cl- ion 12-6 Len

[gmx-users] Parmbsc1 force-field

important to me, but I have apparently hit a dead end. Best Regards, Dan Gil PhD Student Department of Chemical and Biomolecular Engineering Case Western Reserve University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] How can I check external electric field was applied?

Hi, You guessed correctly - gmx potential only calculates the electric field and potential of the system. It does not take into account the applied field. Are you using walls in your system? If so, are you using the 3DC correction along with PME for Ewald summation? If you answered yes to both

Re: [gmx-users] Using xy periodic boundary and 3dc Ewald summation

sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Dan Gil < > dan.gil9...@gmail.com> > Sent: Tuesday, February 6, 2018 03:49 > To: gmx-us...@gromacs.org > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Using xy pe

Re: [gmx-users] Using xy periodic boundary and 3dc Ewald summation

I believe that the 3DC method still applies summations over Z. From the abstract of the paper: "The proposed method adds a correction term to the standard Ewald summation formula." What the 3DC method does is add a correction term so that unrealistic electrostatic interactions between periodic

Re: [gmx-users] Installing gromacs on the windows 10 linux subsystem

Yes! I have gromacs installed and running on my machine. Dan On Sat, Dec 9, 2017 at 4:02 AM A. Alamir wrote: > Dear all, > > I would like to know if using gromacs on the Windows 10 ubuntu Linux > subsystem (WLS) is supported. On WLS the gromacs package can be directly >

Re: [gmx-users] Ewald summation in 2 dimensions with correction

F9FDF2> On Mon, Nov 13, 2017 at 10:22 AM, Dan Gil <dan.gil9...@gmail.com> wrote: > Hi, > > I am using gmx potential to measure the electric field. I've reported the > values from field.xvg in my previous email. The field at the edges of the > ionic liquid near the walls

Re: [gmx-users] Ewald summation in 2 dimensions with correction

, 2017 at 2:23 AM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > On 11/11/17 16:44, Dan Gil wrote: > >> Hi, >> >> Just wanted to see if anyone had any thoughts... >> >> For more information, if I use: >> wall-ewald-zfac = 3 >> E-z

Re: [gmx-users] Ewald summation in 2 dimensions with correction

ail> Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email_source=link_campaign=sig-email_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Wed, Nov 8, 2017 at 11:37 AM, Dan Gil <dan.gil9...@gmail.com> wrote: > Hello, > > I am studyi

Re: [gmx-users] walls and E-z

>>> understood and the threshold depends on the ionic strength, but > >>> 0.4-0.5V/nm > >>> is generally where the fun begins. MD modelers working with solvated > >>> systems casually ignore this, unless they have the great misfortune of > >>> get

Re: [gmx-users] walls and E-z

d is already quite high (0.1 V/nm) and of course I could > go completely nuts and exceed the experimental dielectric breakdown > threshold values for water, but the question remains, no? > > Thanks, > > Alex > > > > On 11/8/2017 9:58 AM, Dan Gil wrote: > >> Hi Alex, >

[gmx-users] Ewald summation in 2 dimensions with correction

Hello, I am studying room-temperature ionic liquids in slab geometry and I am experiencing that I cannot get rid of the interactions between periodic images in the z-direction. Is there something wrong with what I am doing or is this inevitable? The reason I think this is because when I change

Re: [gmx-users] Software for PDB input for GROMACS

c.edu/make-na/ > > Cheers > > Tom > > > On 03/11/17 19:54, Dan Gil wrote: > >> Hi, >> >> I would like to use the parmbsc1 force field to simulate DNA. I installed >> the force-field and am now actually running a simulation with a Drew >> Dickerson

[gmx-users] Software for PDB input for GROMACS

Hi, I would like to use the parmbsc1 force field to simulate DNA. I installed the force-field and am now actually running a simulation with a Drew Dickerson Dodecamer structure I downloaded from the RCSB database. Now I would like to generate my own structures and simulate them. I tried using

Re: [gmx-users] Surface tension for water

Iman, You get the error message in the terminal if you are running it on your own machine. If you are running on a supercomputer, the error messages will be directed to a file. How do you know the simulation is crashing without the software telling you? Please find the message (check all

Re: [gmx-users] Surface Tension Calculation

Hi Lei, 1. In the Gromacs manual you can find the formula that the software uses to calculate surface tension. It is just based on a few components of the pressure tensor, so I imagine you can just use gmx energy (or g_energy depending on the version of Gromacs you are using). 2. Freezing doesn't

Re: [gmx-users] Surface tension for water

What is the error message? What version of Gromacs are you using? Can you post the entire .mdp file? On Tue, Aug 29, 2017 at 9:34 AM, Iman Ahmadabadi wrote: > Dear All Users, > > I'm calculating the surface tension of the water, my box contains almost > 5000 water

Re: [gmx-users] RDF

H <drrahulsur...@gmail.com> wrote: > Hi Dan > > Thank you so much for you descriptive answers. I have few clarifications > that I have posted here. I will go through the papers here. > > On Fri, Aug 18, 2017 at 5:01 PM, Dan Gil <dan.gil9...@gmail.com> wrote: > &g

Re: [gmx-users] RDF

Hi Rahul, I can't find the exact papers right now, but I remember seeing some inconsistency in how people name these functions especially the radial distribution function and pair correlation functions. If we go far back into literature, we can see JG Kirkwood using pair correlation functions as

Re: [gmx-users] non zero free energy values in mass transformation

free energy calculations I got non zero value. (~ +6.2 > kJ/mol). So I am still worried about this non zero behavior. > > Thanks and regards > > Deepak > > > > > > > > > > > > On Sat, Aug 12, 2017 at 10:11 AM, deepak bapat <duba...@gmail.com

Re: [gmx-users] Non bonded interaction mapping

Hi Sameer, There is a quick and easy way to visualize hydrogen bonds. Convert your traj.trr file to .gro and open it in VMD software. You can then manipulate VMD options to show hydrogen bonds. Dan On Sun, Aug 6, 2017 at 10:57 AM, Sameer Edirisinghe wrote: > Dear all, > > I

Re: [gmx-users] (no subject)

Hi Iman, If I understand, you are planning on calculating the surface tension of water? To me, it seems odd that you would try to apply a surface-tension couple to your system, and then calculate the surface tension. Dan On Thu, Aug 10, 2017 at 5:42 AM, Iman Ahmadabadi

Re: [gmx-users] non zero free energy values in mass transformation

Hi Deepak, I am battling the same problem too. I am doing free energy calculation for heptane -> perfluoro-heptane in water. Also SPC/E water, Gromacs 5.1. Like Andre said, there is expected to be a free energy change when you change the mass of a particle. But if you do the same transformation

Re: [gmx-users] Perturbation Thermodynamic Integration

2 0.000 76.649 0.711 0.9 128.781 1.370 36.130 7231.535 0.000 74.006 0.000 0.000 0.155 1.0 On Tue, May 16, 2017 at 3:50 PM, Hannes Loeffler <hannes.loeff...@stfc.ac.uk > wrote: > On Tue, 16 May 2017 15:13:10 -0400 > Dan Gil <dan.gil9...@gmail.com> wrote: > > > &

Re: [gmx-users] Perturbation Thermodynamic Integration

oeffler < hannes.loeff...@stfc.ac.uk> wrote: > On Tue, 16 May 2017 10:28:08 -0400 > Dan Gil <dan.gil9...@gmail.com> wrote: > > > Thank you for the advice on the cut-off schemes and PME methods. > > > > What is the physical meaning of a non-interacting final st

Re: [gmx-users] Perturbation Thermodynamic Integration

e initial state? I believe the mass > contributions are supposed to cancel in a closed thermodynamic cycle > but what is the cycle you are simulating? > > > On Tue, 16 May 2017 09:30:08 -0400 > Dan Gil <dan.gil9...@gmail.com> wrote: > > > Sorry, here is the mdp fil

Re: [gmx-users] Perturbation Thermodynamic Integration

t method immediately unless there was evidence that it worked > well for a range of observables, and was consistent with other practice for > that force field. If there is such evidence, for my information, what model > / force field does it like that?) > > Mark > > O

Re: [gmx-users] Perturbation Thermodynamic Integration

nts for moieties like > -CH2Cl, and latest grompp now detects this. > > Mark > > On Tue, 16 May 2017 01:16 Dan Gil <dan.gil9...@gmail.com> wrote: > > > Hello, > > > > The last thread was getting too big, and the conversation evolved to a > > topic differ

[gmx-users] Perturbation Thermodynamic Integration

Hello, The last thread was getting too big, and the conversation evolved to a topic different from my original question, so I decided to start a new thread. We were discussing thermodynamic integration, and why the mass_lambdas would have any contribution to the derivative of the Hamiltonian. I

Re: [gmx-users] Using the md integrator for calculating free energy of solvation

HEPT H 7 0.060 1.008 opls_965 -0.12018.998 ... [ bonds ] ... [ angles ] ... etc... On Thu, May 11, 2017 at 11:33 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/11/17 9:49 AM, Dan Gil wrote: > >> Thank you Dr. Lemkul, >> >>

Re: [gmx-users] Using the md integrator for calculating free energy of solvation

Regards, Dan On Wed, May 3, 2017 at 10:46 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/3/17 10:43 AM, Dan Gil wrote: > >> Hi Dr. Kausar, >> >> If I want the molecule to have all of its nonbonded interactions with the >> rest of the system (sol

Re: [gmx-users] Using the md integrator for calculating free energy of solvation

dentical states. > > You can also see the alchemistry.org for detail information about the free > energy calculations. > > On Wed, May 3, 2017 at 2:14 AM, Dan Gil <dan.gil9...@gmail.com> wrote: > > > Thank you Dr. Lemkul, > > > > Following your advice, I was

Re: [gmx-users] Using the md integrator for calculating free energy of solvation

= vdwq couple-lambda1 = vdwq On Mon, Apr 3, 2017 at 2:05 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/3/17 2:01 PM, Dan Gil wrote: > >> Thank you Dr. Lemkul, >> >> I am trying to run grompp with the md integrator, but I am getting th

Re: [gmx-users] Using the md integrator for calculating free energy of solvation

f I obtain comparable values for ethanol. Best Regards, Dan On Mon, Mar 27, 2017 at 12:51 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/26/17 9:40 PM, Dan Gil wrote: > >> Hi, >> >> I am following Dr. Sander Pronk's and Dr. Justin Lemkul's tutorial on >>

[gmx-users] Using the md integrator for calculating free energy of solvation

Hi, I am following Dr. Sander Pronk's and Dr. Justin Lemkul's tutorial on calculating free energy of solvation. Is it possible and theoretically sound to use the md integrator instead of the sd integrator for these calculations? I have already done a considerable amount of work using md

[gmx-users] Umbrella Sampling - LINCS error when pull group is in vapor phase

Hi, I am trying to calculate the adsorption free energy of a molecule onto water. I want to use umbrella sampling to obtain the free energy profile as a function of distance normal to a water surface. I am getting LINCS error when my molecule is in the vapor phase. The error messages indicate

Re: [gmx-users] trr file

Hi Rita, How long did your simulation run? If it happens to be very long and you do not want to run the simulation again, perhaps you can try analyzing it in pieces. Use trjconv with -b and -e options to extract small pieces of the .trr file at a time. Analyze the small pieces, delete the .xtc

Re: [gmx-users] How to make a program run on the trajectory

Hi Prasun, Does your question have to do with reading the .trr format? If you want, you could convert it into a friendlier format such as .gro. Use gromacs trjconv to convert from .trr to .gro format. Best Regards, Dan On Saturday, September 17, 2016, João Henriques <

[gmx-users] Force-Field for Ketals

Hi, I want to model a linear compound that has a ketal component. While building the OPLSAA topology (.itp) file for this molecule I ran into not having the C-C-C angle parameterized in -O-(CH3)2C-O-. I have spent some time looking for a different force field that may have this entire molecule,

Re: [gmx-users] Help with MD of water

Hi, There is a method in gromacs to insert water molecules into a box of size defined by you. Depending on the version of gromacs you have, it will be something like gmx insert-molecules. Dan On Tuesday, August 9, 2016, Omamuyovwi Akemu wrote: > Dear Gromacs Users,

Re: [gmx-users] (no subject)

Hi, On gromacs 4.6, the use of g_dist explicitly states "the molecule in the input trajectory should be whole (e.g. by preprocessing with trjconv -pbc) or a matching topology should be provided." If you want to calculate the distance

Re: [gmx-users] umbrella sampling for determining interfacial energy

Hi, this is a good coincidence, but I think I do something very similar to what you just described. I use umbrella sampling to estimate the free energy profile as a function of distance from a liquid-vapor interface. Then, the free energy cost of adsorption to the interface can be approximated. I

Re: [gmx-users] radial-density profile and radial distribution curve for water-CNT system

The manual for version 4.6 is available online. The analysis command you want is g_rdf, for version 4.6. g_rdf plots the radial distribution function, which is what I think you are calling radial distribution curve. The manual has a nice explanation of it so please check it out. The radial density

Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

I see. Now I understand what "pull-start" option means. Changing that option made it work! Thank you Justin. On Mon, Aug 8, 2016 at 6:04 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/7/16 1:21 PM, Dan Gil wrote: > >> In Gromacs/4.6, I used init to define

Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

, 2016 at 1:15 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/7/16 1:13 PM, Dan Gil wrote: > >> Hi, >> >> I've made the change you suggested. The output file pullx.xvg has changed >> from something like: >> >> @ s0 legend "1" &

Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

11:37 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/7/16 11:35 AM, Dan Gil wrote: > >> Hi, >> >> The pullx.xvg file is returning the coordinates of the solvent, and not >> the >> solute (a_Cooh) as I want. >> The solute is being pulled in

Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

doubt the entire process. > > Best regards, > > Billy > > On 7 August 2016 at 03:34, Dan Gil <dgil...@gmail.com> wrote: > > > Hi, > > > > I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of .mdp > > file that I am confused wi

[gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

Hi, I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of .mdp file that I am confused with. I am pulling an atom of solute, indexed a_Cooh, towards the COM of solvent. This is a slab geometry, with the plane normal to the z-axis direction. My output (pullx.xvg) should contain the

[gmx-users] Questions about OPLS force fields

Hi, I am creating a topology for a molecule that is not defined by OPLS. I have some questions that I want to ask: 1. What is bondtype and ptype in ffnonbonded.itp? 2. If I use the Buckingham potential to define nonbonded interactions between atom A and atom B, does this potential apply to all

Re: [gmx-users] Radial Distribution Function - is there symmetry?

t; single Cl replaced by Br (or half of them, or whatever) and assume all the > lattice dimensions remain the same. G(r)_ClNa is the same as before, but > G_(r)_NaCl cannot be the same as before. Or try it on your favourite > simulation trajectory :-) > > Mark > > On Wed, Jun 22, 2

[gmx-users] Radial Distribution Function - is there symmetry?

Hi, I am calculating the radial distribution function, and I am wondering if G(r)_jk = G(r)_kj. I always assumed that it was, and when I looked at the equation it seemed to be the case. But I am having trouble finding sources that state G(r)_jk = G(r)_kj, therefore I wanted to ask for your

Re: [gmx-users] Gromacs 5.1 insert-molecules - Generating bad contacts?

You are right! Thank you. On Mon, Jun 20, 2016 at 1:00 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/20/16 12:04 PM, Dan Gil wrote: > >> Hi Mark, >> >> I thought about your said, and tried to manage the VDW radi of atoms with >> the "-radiu

Re: [gmx-users] Gromacs 5.1 insert-molecules - Generating bad contacts?

Hi Mark, I thought about your said, and tried to manage the VDW radi of atoms with the "-radius" option. I believe it scales the known VDW radi values by the number specified by me. So I try: "gmx insert-molecules ... ... -radius 1.2" The result is still the same, I get segmentation errors

[gmx-users] Gromacs 5.1 - trouble with insert-molecules

Hi, I am upgrading from gromacs 4.6 to gromacs 5.1. Gromacs 4.6 had "genbox," which I was able to use without a problem. With gromacs 5.1, I am using insert-molecules to generate my initial configuration containing water, ethanol, and a lennard-jones particle which I defined. When I attempt to

[gmx-users] Gromacs 5.1 insert-molecules - Generating bad contacts?

Hi, I am upgrading from gromacs 4.6 to gromacs 5.1. Gromacs 4.6 had "genbox," which I was able to use without a problem. With gromacs 5.1, I am using insert-molecules to generate my initial configuration containing water, ethanol, and a lennard-jones particle which I defined. When I attempt to

Re: [gmx-users] Calculating hydrogen bonding density - issues with g_sas?

Is g_sas applicable to more than one molecule at a time? I have 4500 water molecules in the liquid state. I am using the command: g_sas -f traj.trr -s topol.tpr -tv volume.xvg On Tue, Jul 7, 2015 at 10:31 AM, Dan Gil dan.gil9...@gmail.com wrote: I am using the default radius of 0.14 nm

[gmx-users] Calculating hydrogen bonding density - issues with g_sas?

, T=300K) periodic in the x and y directions, volume was found to be about 60nm^3, whereas I expected 130nm^3. I would appreciate any advice! Best, -- Dan Gil Case Western Reserve University | Class of 2016 Researcher, Department of Chemical Engineering dan.gil9...@gmail.com -- Gromacs Users

Re: [gmx-users] Calculating hydrogen bonding density - issues with g_sas?

. On Tue, Jul 7, 2015 at 10:11 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Is the radius being used consistent with your assumption? Mark On Tue, Jul 7, 2015 at 3:58 PM Dan Gil dan.gil9...@gmail.com wrote: Hi, I am using g_hbond to count the number of h-bonds and then g_sas