Re: [gmx-users] virtual sites

On Tue, Oct 29, 2013 at 2:21 AM, Neha Gandhi wrote: > Dear Users, > > I have a system consisting of peptides and a linear carbohydrate. > Initially I tried to simulate these peptides using virtual sites and > it worked. I can use pdb2gmx for building virtual sites on protein > whereas I have an i

Re: [gmx-users] virtual sites

On 10/29/13 2:21 AM, Neha Gandhi wrote: Dear Users, I have a system consisting of peptides and a linear carbohydrate. Initially I tried to simulate these peptides using virtual sites and it worked. I can use pdb2gmx for building virtual sites on protein whereas I have an itp file for the carbo

[gmx-users] virtual sites

Dear Users, I have a system consisting of peptides and a linear carbohydrate. Initially I tried to simulate these peptides using virtual sites and it worked. I can use pdb2gmx for building virtual sites on protein whereas I have an itp file for the carbohydrate. Is it possible to apply virtual sit

Re: [gmx-users] virtual sites in gromacs

Hi Neha, Yes. The MN* particles are the virtual sites. Cheers, Tsjerk On Wed, Sep 18, 2013 at 7:13 AM, Neha Gandhi wrote: > Dear Users, > > I am trying to prepare file using pdb2gmx using Gomos 43a1 ff. I am > using following command. > pdb2gmx -f input.gro -o input1.gro -vsite hydrogens -i

[gmx-users] virtual sites in gromacs

Dear Users, I am trying to prepare file using pdb2gmx using Gomos 43a1 ff. I am using following command. pdb2gmx -f input.gro -o input1.gro -vsite hydrogens -ignh Upon visualisation I could see triangle like sites. Does the output seem right? 75 1VALMN11 2.913 3.551 3.288

Re: [gmx-users] Virtual sites parameters

On 6/18/13 12:20 PM, Bastien Loubet wrote: Dear GROMACS user, I have been trying to define parameters for virtual sites in CHARMM lipid, and I would like to know if there is something simillar to the [ bondtypes ] for virtual sites. Specifically the way I specify the parameters now is by havin

[gmx-users] Virtual sites parameters

Dear GROMACS user, I have been trying to define parameters for virtual sites in CHARMM lipid, and I would like to know if there is something simillar to the [ bondtypes ] for virtual sites. Specifically the way I specify the parameters now is by having lines in the topology such as (for a 3fout vi

Re: [gmx-users] Virtual sites setting

Dear Rajiv, Without a clear explanation of what you are doing and the specific error message from grompp it is impossible to offer any sensible advice. Other pieces of information which might be useful would be, the topology file, the actual grompp line, and the gro file for a single CO molecule

[gmx-users] Virtual sites setting

Dear gmx, I would like to set virtual sites for CO molecules with some specific charge. As per GROMACS manual, I've created virtual site2 in topology file for CO. Also, given the information in .rtp file as well as added the COM(center of mass) atom in .gro file. However, when I use gromp, it

Re: [gmx-users] virtual sites in reference structure

Hi Ahmet, What is an incorrect RMSD? What is a correct RMSD? If you want to calculate a backbone RMSD and you include side chain atoms, that's wrong. Likewise, if you want to calculate a heavy atom, or protein-all-atom RMSD and include virtual sites, that's wrong. If you want to calculate an all-p

Re: [gmx-users] virtual sites in reference structure

Dear Tsjerk, Do the virtual sites cause incorrect calculations of SASA, RMSD or something else? Regards 2013/2/21 Tsjerk Wassenaar > Hi Ahmet, > > You can always use suitable index groups for analysis. > > Cheers, > > Tsjerk > > On Thu, Feb 21, 2013 at 7:08 AM, Ahmet yıldırım > wrote: > > I th

Re: [gmx-users] virtual sites in reference structure

Hi Ahmet, You can always use suitable index groups for analysis. Cheers, Tsjerk On Thu, Feb 21, 2013 at 7:08 AM, Ahmet yıldırım wrote: > I thought the virtual sites can affect analysis.For example, dont they cause > incorrect calculations of SASA, RMSD or something else? > > Thanks in advance

Re: [gmx-users] virtual sites in reference structure

I thought the virtual sites can affect analysis.For example, dont they cause incorrect calculations of SASA, RMSD or something else? Thanks in advance 2013/2/20 Justin Lemkul > > > On 2/20/13 9:18 AM, Ahmet yıldırım wrote: > >> Dear users, >> >> I have the virtual sites in reference structure a

Re: [gmx-users] virtual sites in reference structure

On 2/20/13 9:18 AM, Ahmet yıldırım wrote: Dear users, I have the virtual sites in reference structure and all trajectory. When analyzing simulation, do I have to get rid of those(virtual sites)? If yes/no, why? Why do you think you need to remove them? -Justin -- =

[gmx-users] virtual sites in reference structure

Dear users, I have the virtual sites in reference structure and all trajectory. When analyzing simulation, do I have to get rid of those(virtual sites)? If yes/no, why? Regards -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-user

[gmx-users] Virtual sites LJ/mass

Dear Gromacs-Experts, for my simulations of pure hexane (united atom model) I would like to separate the mass and the interaction parameters of the CH3. So far I tried several different setups by using virtual sites but none of them is working. I hope somebody can help. Here is some background in

[gmx-users] virtual sites with CHARMM lipids

Dear GROMACS users, I have been working on a CHARMM36 POPC bilayer and in order to accelerate the simulation we want to use virtual sites for the hydrogen atoms in the lipid. We mainly want to do it for the carbon tails of the lipids. I have checked the different type of virtual sites in the GROM

Re: [gmx-users] Virtual Sites - remove from GRO

On Mon, May 14, 2012 at 1:51 PM, Mark Abraham wrote: > On 14/05/2012 10:42 PM, Steven Neumann wrote: > >> Dear Gmx Users, >> >> i run the implicit simulation with virtual sites on the hydrogen of my >> protein. Now I want to extract coordinates and run another simulation (in >> explicit solvent).

Re: [gmx-users] Virtual Sites - remove from GRO

On 14/05/2012 10:42 PM, Steven Neumann wrote: Dear Gmx Users, i run the implicit simulation with virtual sites on the hydrogen of my protein. Now I want to extract coordinates and run another simulation (in explicit solvent). Is there any way to remove those virtual sites from my gro file as

Re: [gmx-users] Virtual Sites - remove from GRO

On 5/14/12 8:42 AM, Steven Neumann wrote: Dear Gmx Users, i run the implicit simulation with virtual sites on the hydrogen of my protein. Now I want to extract coordinates and run another simulation (in explicit solvent). Is there any way to remove those virtual sites from my gro file as VMD w

[gmx-users] Virtual Sites - remove from GRO

Dear Gmx Users, i run the implicit simulation with virtual sites on the hydrogen of my protein. Now I want to extract coordinates and run another simulation (in explicit solvent). Is there any way to remove those virtual sites from my gro file as VMD write the file using atoms not recognized by pd

Re: [gmx-users] Virtual Sites in a polymer backbone

> > Any particular reason why improper dihedrals would not be suitable? They are > significantly easier to implement. Yes the force field parameters for the molecule are not known and I am therefore fitting the parameters to Density Functional Theory. If I allow the units to move out of plane eve

Re: [gmx-users] Virtual Sites in a polymer backbone

Broadbent, Richard wrote: I wish to keep certain parts of the backbone of my polymer rigid and planar, as my primary interest is in the long length and timescale motion of the polymer. I am attempting to utilise virtual sites as a means to keep aromatic groups rigid and planar. My intention

[gmx-users] Virtual Sites in a polymer backbone

I wish to keep certain parts of the backbone of my polymer rigid and planar, as my primary interest is in the long length and timescale motion of the polymer. I am attempting to utilise virtual sites as a means to keep aromatic groups rigid and planar. My intention is to replace groups such as p

Re: [gmx-users] virtual sites set up for topology file

yes it will... On Fri, May 6, 2011 at 11:02 AM, Gavin Melaugh wrote: > Cheers Sikandar > > I take it that because combination rule 3 (provide sigma and epsilon) is > stated gromacs assumes that all values in nonbonding parameters are > sigma and epsilon. I know this tp be tru for the atomtypes b

Re: [gmx-users] virtual sites set up for topology file

Cheers Sikandar I take it that because combination rule 3 (provide sigma and epsilon) is stated gromacs assumes that all values in nonbonding parameters are sigma and epsilon. I know this tp be tru for the atomtypes but does it filter down to all intermolecular interactions. Cheers Gavin Sikand

Re: [gmx-users] virtual sites set up for topology file

Yes, since sigma and epsilon are zero for VS then interactions between and VS-VS and VS-(any other atom) would result in zero force. Since you explicitly define the interaction between VS-C3, combination rule won't be used and C6(VS_C3) and C12(VS_C3) will be computed as per sigma(VS_C3) epsilon(VS

Re: [gmx-users] virtual sites set up for topology file

Am I correct in saying now, from the following topology (exerpts), that the virtual site VS will only interact with C3? I guess I don't have to give the atom indices of this interaction in the pair list which I use only for 1_4 interactions? Can I use sigma and epsilon in the nonbond_params directi

Re: [gmx-users] virtual sites set up for topology file

Hi Mark Many thanks to you and all your colleagues for replying. This has worked, at least there are now no errors. Where the manual is incorrect is that it leads you to believe that you state; [virtual _siten] ;index of VS index of atoms for COG func 229 8 11 15

Re: [gmx-users] virtual sites set up for topology file

Mark Abraham wrote: On 6/05/2011 10:39 PM, Gavin Melaugh wrote: Hi Mark Cheers.Could you perhaps shed some insight into format of [virtual_siten] when trying to define the VS at the COG of three atoms. It is not obvious from the manual Indeed, it's undocumented - but I think Sikander's expe

Re: [gmx-users] virtual sites set up for topology file

On 6/05/2011 10:39 PM, Gavin Melaugh wrote: Hi Mark Cheers.Could you perhaps shed some insight into format of [virtual_siten] when trying to define the VS at the COG of three atoms. It is not obvious from the manual Indeed, it's undocumented - but I think Sikander's experience from my discuss

Re: [gmx-users] virtual sites set up for topology file

Hi Mark Cheers.Could you perhaps shed some insight into format of [virtual_siten] when trying to define the VS at the COG of three atoms. It is not obvious from the manual Cheers Gavin Mark Abraham wrote: > On 6/05/2011 10:17 PM, Gavin Melaugh wrote: >> Yeah I see your point about the types. Wi

Re: [gmx-users] virtual sites set up for topology file

On 6/05/2011 10:17 PM, Gavin Melaugh wrote: Yeah I see your point about the types. With regard to the initial configuration state I would have assumed that gromacs knew the initial position of the virtual site when I stated that it was to be at the COG of the 3 atoms in the [virtual_sitesn] d

Re: [gmx-users] virtual sites set up for topology file

O.k Cheers Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Yeah I see your point about the types. With regard to the initial >> configuration state I would have assumed that gromacs knew the initial >> position of the virtual site when I stated that it was to be at the >> COG of the 3 atom

Re: [gmx-users] virtual sites set up for topology file

Gavin Melaugh wrote: Yeah I see your point about the types. With regard to the initial configuration state I would have assumed that gromacs knew the initial position of the virtual site when I stated that it was to be at the COG of the 3 atoms in the [virtual_sitesn] directive. I believ

Re: [gmx-users] virtual sites set up for topology file

Yeah I see your point about the types. With regard to the initial configuration state I would have assumed that gromacs knew the initial position of the virtual site when I stated that it was to be at the COG of the 3 atoms in the [virtual_sitesn] directive. Justin A. Lemkul wrote: > > > Gavin

Re: [gmx-users] virtual sites set up for topology file

Gavin Melaugh wrote: Justin I have tried this but I am now getting different errors. I take it that: I specify the virtual sites in the atomtypes directive as I have seen from examples? Virtual sites are included in all the force fields already, but if you want some custom name, then yes, i

Re: [gmx-users] virtual sites set up for topology file

Justin I have tried this but I am now getting different errors. I take it that: I specify the virtual sites in the atomtypes directive as I have seen from examples? I index the virtual sites in the atoms directive in accordance with the rest of the molecule. atom numbers go from 1-228, therefore I

Re: [gmx-users] virtual sites set up for topology file

Gavin Melaugh wrote: Hi Justin Thanks for the reply. To create a virtual site at the centre of geometry of 3 atoms, according to the manual, do you not say: [virtual_sitesn], the index of the site, the index of the three atoms and then the function type 1 which determines that it is COG. OK,

Re: [gmx-users] virtual sites set up for topology file

Hi Justin Thanks for the reply. To create a virtual site at the centre of geometry of 3 atoms, according to the manual, do you not say: [virtual_sitesn], the index of the site, the index of the three atoms and then the function type 1 which determines that it is COG. Or as I now realise. State [vi

Re: [gmx-users] virtual sites set up for topology file

Gavin Melaugh wrote: Hi Having tried to run grompp using the data below I keep getting the following error Fatal error: Unknown vsiten type 7 Does anyone know why this might be? Your [virtual_sites] directive is not correct, either in its name (no such thing as "virtual_sitesn" - the "n" sh

Re: [gmx-users] virtual sites set up for topology file

Hi Having tried to run grompp using the data below I keep getting the following error Fatal error: Unknown vsiten type 7 Does anyone know why this might be? Gavin Gavin Melaugh wrote: > Hi > > I am trying to alter a topology to include 3 virtual sites and I have a > few queries, the answers to wh

Re: [gmx-users] virtual sites set up for topology file

Hi I am trying to alter a topology to include 3 virtual sites and I have a few queries, the answers to which are not obvious form the manual. Do I declare the virtual sites in the atomtypes directive like so ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 1

Re: [gmx-users] virtual sites

Hi Sikandar A couple of questions regarding the virtual sites. 1) Do I have to number the virtual site in accordance with the atom indices of the rest of the molecule? 2) Is the parameters for the virtual site declared in the atomtypes directive? Cheers Gavin Sikandar Mashayak wrote: > in doin

Re: [gmx-users] virtual sites

in doing so .. by default all pair interactions with virtual sites would result in zero forces except those between atoms defined in [nonbond_params] On Thu, May 5, 2011 at 11:57 AM, Sikandar Mashayak wrote: > hey > > another approach to do this without using energy group exclusion is to > defin

Re: [gmx-users] virtual sites

hey another approach to do this without using energy group exclusion is to define non-bonded interactions parameter explicitly between atoms in ffnonbonded.itp file. You can specify sigma and epsilon to be zero in virtual sites atoms definition and specify individual pair interactions parameters u

Re: [gmx-users] virtual sites

Hi Justin I do not intend to have charges on the sites. All I want is; when a CH3 group gets close to the site it feels a repulsive force. I have calculated a sigma and epsilon value for this interaction. Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi Justin >> >> I am reading th

Re: [gmx-users] virtual sites

Gavin Melaugh wrote: Hi Justin I am reading the manual at the moment. I want to include some virtual sites in my molecule so that only surrounding CH3s atom type C3 interact with then. All other atoms I don't want to interact with them. Do I create energy groups in the index file called say "v

Re: [gmx-users] virtual sites

Hi Sikandar Many Thanks for the reply. When you define energygrps in the mdp file, does that mean that only these groups are written to the energy file. I take it that all iother information regarding the energy is written as well i.e if you left this section blank Cheers Gavin Sikandar Mashaya

Re: [gmx-users] virtual sites

Hi Justin I am reading the manual at the moment. I want to include some virtual sites in my molecule so that only surrounding CH3s atom type C3 interact with then. All other atoms I don't want to interact with them. Do I create energy groups in the index file called say "virtual sites" and "exclus

Re: [gmx-users] virtual sites

you can do it as following 1. create index file make_indx -f conf.gro -n index.ndx ( select VS and any other atoms you want lets say OTHERS) 2. in .mdp define energygrps "VS OTHERS" 3. exclude interactions by specifying energygrp_excl VS OTHERS in .mdp file for more you can refer to manual.. I h

Re: [gmx-users] virtual sites

Gavin Melaugh wrote: Hi Sikandar Cheers. How do you actually define the energy groups? Read in the manual about the .mdp option "energygrps" and apply custom index groups as necessary. -Justin Gavin Sikandar Mashayak wrote: yes, you can make virtual sites interact with only specific

Re: [gmx-users] virtual sites

Hi Sikandar Cheers. How do you actually define the energy groups? Gavin Sikandar Mashayak wrote: > yes, you can make virtual sites interact with only specific sites by > using Energy Exclusion between energy groups. This can be done by > defining energy groups for virtual sites and other atoms,

Re: [gmx-users] virtual sites

yes, you can make virtual sites interact with only specific sites by using Energy Exclusion between energy groups. This can be done by defining energy groups for virtual sites and other atoms, then exclude or include the non-bonded interactions between them accordingly... On Thu, May 5, 2011 at 7:

[gmx-users] virtual sites

Hi All Is it possible to have a virtual site interact with only specific atoms and not interact at all with everything else? Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/

Re: [gmx-users] virtual sites and heavy atoms for longer time steps

On 2/12/2010 11:13 AM, Hassan Shallal wrote: I have some issues to discuss with the mailing list users, 1- Is using virtual sites alone enough to allow me to lengthen the time step from 2 fs to 4 fs, or I have also to use heavy hydrogens when creating topology files in order to use 4 fs time s

[gmx-users] virtual sites and heavy atoms for longer time steps

I have some issues to discuss with the mailing list users, 1- Is using virtual sites alone enough to allow me to lengthen the time step from 2 fs to 4 fs, or I have also to use heavy hydrogens when creating topology files in order to use 4 fs time step? 2- Another question, does vitual sites

Re: [gmx-users] virtual sites

zhang wrote: Dear users, I use the Cationic Dummy Atom methods by Pang to simulate a protein containing Zn2+. How to get the parameters in [ virtual_sites? ] section? I use the model 4fd. In the following example, how to get the value of parameters a, b and d? [ virtual sit

[gmx-users] virtual sites

Dear users, I use the Cationic Dummy Atom methods by Pang to simulate a protein containing Zn2+. How to get the parameters in [ virtual_sites? ] section? I use the model 4fd. In the following example, how to get the value of parameters a, b and d? [ virtual sites4 ] ;