Re: [gmx-users] creating representative structures

Le 16/03/2016 16:54, Shyno Mathew a écrit : I wrote a tcl script to do cluster analysis, using gromos method. My results are slightly different from the g_cluster results. I see the difference is coming from RMSD values. For example, with g_cluster, “The RMSD ranges from 0.149614 to 0.220387 nm”

[gmx-users] Infinite DNA periodic boundary conditions

Dear Gmx's,  I am trying to get an infinite DNA chain to work. I was following an earlier discussion: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096970.html I got pdb2gmx to accept my lose ends and also added bonds, angles and dihedrals to the topology file connecti

Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

As James said, if you are using Discovery Studio it can model missing atoms and residues. But why are you deleting a residue? What do you hope to learn from this? And don't just ignore missing atoms. I also don't understand the genion error, but I don't think you reported it exactly. Didn't

[gmx-users] umberlla sampling

Dear Justin, In the tutorial of "umbrella sampling ", what happens if we set the pull_coord1_rate to zero value? Does it work like a harmonic force (spring) between two groups with a constant distance avera

Re: [gmx-users] Temperature dependence of virial of an initial configuration

On 3/17/16 11:50 AM, rakesh sharan wrote: Dear all, I have a question regarding computation of different components of virial of my starting initial configuration using Gromacs. When I am running job by setting nstep = 0 (system is bulk spce water) to get potential energy and Note that doin

[gmx-users] You are applying a switch function to vdw forces or potentials from 0 to 1.2 nm

Hello: i'm running the grompp of NVT but during the run i have the following:NOTE: You are applying a switch function to vdw forces or potentials from 0 to 1.2 nm, which is more than half the interaction ranges whereas switch functions are intended to act only close to the cut-offWhat does it m

Re: [gmx-users] You are applying a switch function to vdw forces or potentials from 0 to 1.2 nm

The problem is you have not set rvdw-switch and the default value is 0. You should instead set this to something closer to rvdw such as 1.0 It looks like vdw-modifier: potential shift would be a better choice and then rdw-switch isn't used. See http://manual.gromacs.org/documentation/5.1.1/user-gu

[gmx-users] Volume and boundary Questions

Hello, I have two questions about setting up my box for simulation. Thank you for any and all input in advance. 1. Is the simulation box dimensions and volume fixed throughout the simulation (or are they allowed to fluctuate around the set dimensions)? 2. Is it possible to make custom box shapes

Re: [gmx-users] Reconstruction of atomistic details from coarse-grained-structures

btwh dont understand clearly the whole methodology for instance If I have coarse'grained system obtained from the martinize tool consisted of the 1) many proteins embedded within big bilayer and at the same time 2) FG full atomistic topology for one protein (without lipids etc) parametrized via ff

[gmx-users] pull code for Gromacs 5

Hi all, I¹m very unfamiliar with the pull code as of Gromacs 5. Unfortunately my system is not experiencing any noticeable Œpull¹. From the options below, which is the group experiencing the pull and which is the reference group? Would applying a set of position restraints on the reference group

Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

actually i m not getting how to proceed futher i m beginner to GROMACS it would be helpful if you can elaborate the process On 17 March 2016 at 21:54, Pradip Kaur wrote: > so should i go for sol molecules :1612 > Na :11 > > On 17 March 2016 at 21:44, Peter Stern wro

Re: [gmx-users] Potential energy of each atom

Potential energy for one atom is not well defined physical quantity as far as I know, you can only calculate potential energy for at least two body (atoms). You need to give more details about what you want and I do not know what LAMMPS do. Josip 2016-03-18 11:03 GMT+01:00 张正财 : > > Subject: Re:

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 80

Dear Justin, Thanks for your reply. I meant, that the PRODRG server gave error in giving the topology file since my inhibitor contains a metal which the server doesn't process. If PRODRG is meant for GROMOS, should I use CGENFF for CHARMM? In that case, how do we include the topology of the inhibi

Re: [gmx-users] Domain decomposition error tied to free energy perturbation

On Fri, Mar 18, 2016 at 7:47 AM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > > Message: 4 > Date: Fri, 18 Mar 2016 07:46:48 -0400 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Domain decomposition error tied to free > energy perturbation > M

Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

Missing atoms in GLU 474 is because the coordinates for the GLU side chain weren't resolved in the crystallographic data and aren't included in the pdb file. Long bonds are probably because of missing residues. Check the pdb file for MISSING residues and atoms (listed in the header records).

Re: [gmx-users] Reconstruction of atomistic details from coarse-grained-structures

Hi James, From the tutorial I sent you: To run the script we need the following: The CG structure to backmapp, provided in CG_posre.gro - The CG structure you want to back map. A complete fine-grained force field corresponding to all the CG molecules in  CG_posre.gro. Here we use CHARMM36, see a

[gmx-users] The bond in molecular type DPPC between atoms 31 C21 y 32 022 has an estimated oscillational period of 2.1e-02 ps, which is less than 5 times the time step of 1.0e-01 ps

Hello. I' ḿ simulating a DPPC membrane with TIP3 water model and charmm36 forcefield and in the grompp of NVT equilibration i have this warning: (Warning 1: file topol.top line 24) The bond in molecular type DPPC between atoms 31 C21 y 32 022 has an estimated oscillational period of 2.1e-02 ps,

Re: [gmx-users] Hydrogen bonding pair selection (Erik Marklund)

Dear Eric, You are right, it doesn’t cause any problems with the results! Thanks a lot! Binwu > On Mar 17, 2016, at 5:18 PM, > gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: > > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se

[gmx-users] LINCS warnings for some lambdas.

hii am performing protein ligand (pdb:4HBV)binding free energy calculations, i am done with complex simulation , now stuck in ligand simulation since last 2 weeks. first i was getting zero energy, and when i changed some of parameters and position restraint my ligand , now i am getting LINCS war

Re: [gmx-users] Volume and boundary Questions

On 3/17/16 3:01 PM, ANAND AMITKUMAR DHARIA wrote: Hello, I have two questions about setting up my box for simulation. Thank you for any and all input in advance. 1. Is the simulation box dimensions and volume fixed throughout the simulation (or are they allowed to fluctuate around the set dim

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 80

On 3/17/16 8:04 PM, Soumya Lipsa Rath wrote: Dear Justin, Thanks for your reply. I meant, that the PRODRG server gave error in giving the topology file since my inhibitor contains a metal which the server doesn't process. If PRODRG is meant for GROMOS, should I use CGENFF for CHARMM? In that c

Re: [gmx-users] You are applying a switch function to vdw forces or potentials from 0 to 1.2 nm

Hi, Like it says, you've somehow chosen for a switching radius to start at 0 nm, which you likely did not intend nor should do. Consider your recent changes. Mark On Thu, 17 Mar 2016 17:46 Poncho Arvayo Zatarain wrote: > > Hello: i'm running the grompp of NVT but during the run i have the > fo

[gmx-users] simulation a box of water

Dear all I want to simulate a box of water (2*2*2 nm with 1401 molecules). Is there difference between using a model for water molecules and importing this molecule from other programs(such as nwchem)? I want to do a small simulation and it is not important to treat water molecules explicitly. I u

Re: [gmx-users] simulation a box of water

On 3/16/16 12:00 PM, Saeed Nasiri wrote: thanks so much for all the comments. as far as I know the water molecules created by models have solid bods and angles. I want to extract thermodynamical parameters from the simulation, for this purpose I used this method. Is this a trick to used water

Re: [gmx-users] creating representative structures

Hi Shyno, Is there a difference in mass-weighting? Can you try on C- alphas only? Cheers, Tsjerk On Mar 16, 2016 15:55, "Shyno Mathew" wrote: > Dear all, > > > I wrote a tcl script to do cluster analysis, using gromos method. My > results are slightly different from the g_cluster results. I se

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 78

I am sending my message again because my mdp options were looking a little weird: hi I am performing protein ligand (pdb:4HBV)binding free energy calculations, I am done with complex simulation , now stuck in ligand simulation since last 2 weeks. first i was getting zero energy, and when I ch

Re: [gmx-users] Reconstruction of atomistic details from coarse-grained-structures

Is it better than http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Reverse-transformation 7 PArticularly for my case I need to convert from CG to FG the structure of GPCR simulated within CG lipids excluding lipids in the final FG model. 2016-03-17 15:49 GMT+01:00 : > Hi J

Re: [gmx-users] Distance between two specific residues

On 3/17/16 12:01 AM, Abid Channa wrote: Dear Gromacs users, I am trying to calculate distance between two specific residues of active site of my protein in MD. I have made separate .index file of two specific groups. Then I am trying this command " gmx distance -f md_0_1.xtc -s md_0_1.tpr -oav

Re: [gmx-users] Volume and boundary Questions

Hey :) You can define any box 'shape', expressed in terms of the corresponding lattice vectors, compliant with the rules stated in chapter 3 of the manual. You can set a hexagonal prism cell using editconf, using the -box and -angles options. In your case, the long edge should be along x, and has

Re: [gmx-users] Hydrogen bonding pair selection

Dear Binwu, Is there really a problem? With your selections you will not register any hbonds with N_H_&GLY as the acceptor, since the other group contains no donors. Kind regards, Erik > On 17 Mar 2016, at 20:10, Binwu Zhao wrote: > > Dear Gromacs Users, > > I was trying to calculate the num

[gmx-users] Distance between two specific residues

Dear Gromacs users, I am trying to calculate distance between two specific residues of active site of my protein in MD. I have made separate .index file of  two specific groups. Then I am trying this command " gmx distance -f md_0_1.xtc -s md_0_1.tpr -oav distance.xvg -select -n index.ndx -tu n

Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

You need to use a tool outside GROMACS to model in missing residues. Discovery studio has capabilities to do this using MODELLER so you could do that if you're comfortable with that software already (see http://accelrys.com/services/training/life-science/protein-homology-modeling.html which I just

[gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

i am currently working with 2bbo.pdb protein ,i have edited this protein in Discovery studio 4.5 and deleted phenylalanine at 508 position , now i m running molecular dynamics simulation in GROMACS 5.0.2 bt after running pdb2gmx with GROMOS96 53a6 force field Water model :spc216 ,it is showing

[gmx-users] Potential energy of each atom

Dear all, Could anyone tell me how can I output potential energy of each atom from a trajectory file? All the best, Zhengcai Iggcas, CAS -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before pos

[gmx-users] Temperature dependence of virial of an initial configuration

Dear all, I have a question regarding computation of different components of virial of my starting initial configuration using Gromacs. When I am running job by setting nstep = 0 (system is bulk spce water) to get potential energy and components of virial of my starting configuration, I am ob

Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

Thank you for all your suggestion ,ya I did some mistake after adding Na ions I selected system option (0) As per your suggestion when I selected Sol (13) my problem solved ...Do I need to go for modeller now or should I continue with this ... On 18-Mar-2016 12:41 pm, wrote: > I'd suggest creat

[gmx-users] About The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element

Hello, due to one of my last question and about the error: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. How can do large the box? My .gro files vectors are 8.9 8.90 and 7.90

Re: [gmx-users] Potential energy of each atom

> Subject: Re: [gmx-users] Potential energy of each atom > Message-ID: <56eba4a9.8020...@xray.bmc.uu.se> > Content-Type: text/plain; charset=UTF-8; format=flowed > > On 18/03/16 03:40, ??? wrote: > > Dear all, > > > >Could anyone tell me how can I output potential energy of each atom > >

Re: [gmx-users] Reconstruction of atomistic details from coarse-grained-structures

what I have found from the ./initram.sh -h -f Input coarse grained structure *FILE: None -p Input atomistic target topology *FILE: None does it means that -p should be full atomic topology of the system (not coarse grained) ? Is so whether is possible to make such CG

Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

My project is on cystic fibrosis 508 del mutation ,what I m trying to do is that I have taken nuclear binding domain with 508phenylalanine (2bbo.pdb) and I deleted that 508 phenylalanine to create a similar situation as what occurs in body in case of cystic fibrosis ...after minimization of this pr

Re: [gmx-users] Using FFTK generated parameter file for Protein-Ligand simulations

On 3/16/16 10:18 PM, Soumya Lipsa Rath wrote: Dear Gromacs Users, I have to run a protein-ligand system. I am using CHARMM36 ff for the simulation. For generating the parameters for the ligand molecule I used the forcefield development toolkit of vmd, which gives CHARMM compatible parameters.

Re: [gmx-users] simulation a box of water

On 3/16/16 8:30 AM, Saeed Nasiri wrote: Dear all I want to simulate a box of water (2*2*2 nm with 1401 molecules). Is there difference between using a model for water molecules and importing this molecule from other programs(such as nwchem)? I want to do a small simulation and it is not import

Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

On 3/18/16 6:31 AM, jkrie...@mrc-lmb.cam.ac.uk wrote: Definitely use modeller first. Then go through everything again. I'm happy you solved the problem with the multiple of 11. Perhaps Justin or Mark or someone could comment on why it said that. While it makes sense to replace solvent atoms wi

Re: [gmx-users] Potential energy of each atom

On 18/03/16 03:40, 张正财 wrote: Dear all, Could anyone tell me how can I output potential energy of each atom from a trajectory file? What does that mean? If you have a Na+ and a Cl- in the gas phase Gromacs can compute Coulomb energy and Lennard Jones energy. But how would you partiti

Re: [gmx-users] simulation a box of water

thanks so much for all the comments. as far as I know the water molecules created by models have solid bods and angles. I want to extract thermodynamical parameters from the simulation, for this purpose I used this method. Is this a trick to used water molecule explicitly? -- Gromacs Users mailin

Re: [gmx-users] The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element

On 3/15/16 12:23 PM, Poncho Arvayo Zatarain wrote: Hello, i ḿ working in a lipid bilayer using charmm36 forcefield and trying to do NVT equilibration but when i use grompp for nvt i receive the folowing error: The cut-off length is longer than half the shortest box vector or longer than the sm

Re: [gmx-users] Custom forcefield tutorial?

On 3/18/16 6:30 AM, Michał Kadlof wrote: Hello, I would like to perform some simulations with my own simple forcefield. Just a chain of beads, with Lenard-Jones, some harmonic and angle potential, and play with it's parameters. I don't want to write all the computing part from the scratch. I

Re: [gmx-users] umberlla sampling

On 3/18/16 5:21 AM, Ali Mohyeddin wrote: Dear Justin, In the tutorial of "umbrella sampling ", what happens if we set the pull_coord1_rate to zero value? Does it work like a harmonic force (spring) betw

[gmx-users] Building dimer system using MARTINI

Dear Gromacs Users! I wonder to ask suggestions regarding assembly of the oligomeric systems parametrized using martini ff. Briefly using only 1 type of protein the situation is very simple - 1) prepare box for the monomer using martinize, 2) equilibrate it and 3) make replicas vwithin one system

Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

Definitely use modeller first. Then go through everything again. I'm happy you solved the problem with the multiple of 11. Perhaps Justin or Mark or someone could comment on why it said that. While it makes sense to replace solvent atoms with ions in most cases, I would have thought any replacemen

Re: [gmx-users] creating representative structures

Hi Stephane, The difference is too large for rounding errors. I was not suggesting different selections, but rather mass-weighting versus non-mass-weighting. Cheers, Tsjerk On Mar 17, 2016 23:15, "Téletchéa Stéphane" < stephane.teletc...@univ-nantes.fr> wrote: > Le 16/03/2016 16:54, Shyno Mathe

Re: [gmx-users] Questions about parameters

Dear Justin, Thanks for your insightful replies. I decided that I will not use position restraints but rather all-bond constraints because I want to allow the molecules to move freely and reorient without getting disintegrated, although they did not look like disintegrating even without constraint

Re: [gmx-users] Reconstruction of atomistic details from coarse-grained-structures

Just tested the ./initram.sh script embedded within the Unfortunatelly for my case It didnt works 1- I firstly extract the gro file consisted of the protein CG representation only from my Cg.gro using below command and selecting protein group g_editconf -f system.gro -n -o protein.gro than I edi

[gmx-users] Thermostatting in non-equilibrium dynamics

Dear all, The question I have has been posted here by other user last year but with not satisfactory answer (if I have searched properly!), so I'd like to open this topic again. It concerns non-equilibrium dynamics and thermostating. For simulations of Poisseuille flow in explicit atomistic slabs

[gmx-users] Questions about parameters

Dear gmxers, After some basic simulations of a box of a non-aqueous solvent, I want to know your opinion about the meaning of some parameters, the values I have used for these, and how they affect the accuracy of simulations and their speed (which at this moment is rather unimportant for me). I s

Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

I'd suggest creating models with and without residue 508 in the target sequence. MODELLER should be able to rebuild the loop without residue 508 and then you won't have long bonds. A hole in a protein is not physically or biologically meaningful. Rather a deletion mutation will end up in the riboso

Re: [gmx-users] simulation a box of water

you have to select water molecule for running the simulation .choose water model SPC nd then run the command. I hope then it will work On 16 March 2016 at 18:51, Justin Lemkul wrote: > > > On 3/16/16 8:30 AM, Saeed Nasiri wrote: > >> Dear all >> >> I want to simulate a box of water (2*2*2 nm wit

Re: [gmx-users] Reconstruction of atomistic details from coarse-grained-structures

Hi James, Yes, that is possible too. If you need a hand, contact me off-list. Best, Tsjerk On Mar 17, 2016 16:32, "James Starlight" wrote: > btwh dont understand clearly the whole methodology > > for instance If I have coarse'grained system obtained from the > martinize tool consisted of the 1

[gmx-users] gmx order index option

Hi, I have a question of “gmx order” usage. I am studying a membrane system so I need calculate the deuterium order parameter. In some older tutorials, they said the “gmx order” can be used to do the job. The recommended command is like “gmx order -s xx.tpr -f xx.xtc -n xx.ndx -d z -nd deuter.xv

Re: [gmx-users] simulation a box of water

On 3/16/16 3:38 PM, Saeed Nasiri wrote: Thank you Justin I don't understand. Do I use the explicit water molecules or the model? You're going to have to explain what this means. Either you have water molecules or you don't. If you have water molecules, you have to represent them using a f

[gmx-users] Domain decomposition error tied to free energy perturbation

Hello, I have been attempting to carry out some free energy calculations, but to verify the sanity of my parameters, I decided to test them on a structure I knew to be stable -- the lysozyme from Lemkul's lysozyme in water tutorial. I chose the L75A mutation because it is out on the surface to mi

[gmx-users] Reconstruction of atomistic details from coarse-grained-structures

Dear Gromacs users! I wonder to ask for some suggestions about possibility of the CG to full atomistic conversion of sample pdb files extracted from the CG (Martini based) md trajectories. I will be especially thankful for any kind of the useful tutorial focused on the subject. Thanks for help in

Re: [gmx-users] Reconstruction of atomistic details from coarse-grained-structures

Hi James, Sadly I have no idea. I have never used that method/approximation before. Hope someone with more experience can answer your last question. Best, Carlos --  Carlos Navarro Retamal Ingeniero en Bioinformática Ph. D (c) en Ciencias Aplicadas. Centro de Bioinformática y Simulación Molecular

Re: [gmx-users] Questions about parameters

On 3/16/16 3:13 PM, abhishek khetan wrote: Dear gmxers, After some basic simulations of a box of a non-aqueous solvent, I want to know your opinion about the meaning of some parameters, the values I have used for these, and how they affect the accuracy of simulations and their speed (which at

[gmx-users] Using FFTK generated parameter file for Protein-Ligand simulations

Dear Gromacs Users, I have to run a protein-ligand system. I am using CHARMM36 ff for the simulation. For generating the parameters for the ligand molecule I used the forcefield development toolkit of vmd, which gives CHARMM compatible parameters. But, I am unable to understand how should I inclu

Re: [gmx-users] The bond in molecular type DPPC between atoms 31 C21 y 32 022 has an estimated oscillational period of 2.1e-02 ps, which is less than 5 times the time step of 1.0e-01 ps

On 3/16/16 1:10 PM, Poncho Arvayo Zatarain wrote: Hello. I' ḿ simulating a DPPC membrane with TIP3 water model and charmm36 forcefield and in the grompp of NVT equilibration i have this warning: (Warning 1: file topol.top line 24) The bond in molecular type DPPC between atoms 31 C21 y 32 022

Re: [gmx-users] Domain decomposition error tied to free energy perturbation

On 3/17/16 8:21 PM, Ryan Muraglia wrote: Hello, I have been attempting to carry out some free energy calculations, but to verify the sanity of my parameters, I decided to test them on a structure I knew to be stable -- the lysozyme from Lemkul's lysozyme in water tutorial. I chose the L75A mu