Re: [gmx-users] force field for Titanium

Thank you very much from your answer. Best Regards Sara From: Justin Lemkul To: mohammad agha ; Discussion list for GROMACS users Sent: Wednesday, September 25, 2013 3:07 PM Subject: Re: [gmx-users] force field for Titanium On 9/25/13 4:54 AM

Re: [gmx-users] force field for Titanium

On 9/25/13 4:54 AM, mohammad agha wrote: Dear Gromacs Specialists, I am searched force field for Titanium (Ti) element. Parameters consist of sigma and epsilon. Can you help me, Please? http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species I sincerely doubt that a t

[gmx-users] force field for Titanium

Dear Gromacs Specialists, I am searched force field for Titanium (Ti) element. Parameters consist of sigma and epsilon. Can you help me, Please? Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive a

Aw: [gmx-users] Force Field for peptides and proteins

.  In addition, difference in simply looking at domain changes in proteins or affinites, etc...   Gesendet: Montag, 12. August 2013 um 14:19 Uhr Von: "Maria Astón Serrano" An: gmx-users@gromacs.org Betreff: [gmx-users] Force Field for peptides and proteins Dear Gromacs users, We would like t

Re: [gmx-users] Force Field for peptides and proteins

On this note, I wanted to ask about simulated unfolding of proteins. I have a primarily alpha-helical-protein ( about 300 amino acids, 5 alpha helices, no beta strands) and 3 of its single point mutants. Now, to answer the question of relative stability, I want to place them in a water bath and hea

Re: [gmx-users] Force Field for peptides and proteins

On 8/12/13 8:19 AM, Maria Astón Serrano wrote: Dear Gromacs users, We would like to know which is the Force Field which is customarily preferred for simulations of peptides and proteins. Interestingly, this same question was just asked on the development list, although the discussion indee

Re: [gmx-users] Force Field for peptides and proteins

I like CHARMM. Dr. Vitaly V. Chaban On Mon, Aug 12, 2013 at 2:19 PM, Maria Astón Serrano < m.aston.serr...@gmail.com> wrote: > Dear Gromacs users, > > We would like to know which is the Force Field which is customarily > preferred for simulations of peptides and proteins. > > Thank you very muc

Re: [gmx-users] Force Field for peptides and proteins

It depends on what properties of peptides and proteins that you want to explore. ~Thu On Mon, Aug 12, 2013 at 7:19 PM, Maria Astón Serrano < m.aston.serr...@gmail.com> wrote: > Dear Gromacs users, > > We would like to know which is the Force Field which is customarily > preferred for simulation

[gmx-users] Force Field for peptides and proteins

Dear Gromacs users, We would like to know which is the Force Field which is customarily preferred for simulations of peptides and proteins. Thank you very much. Best regards, Maria -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please s

Re: [gmx-users] force field for GPI ligands which has lipid and carbohydrates ?

On 1/9/13 2:48 AM, 라지브간디 wrote: Could you tell me which force field recognizes the GPI ligand which posses lipid and mannose which interacts with protein? Probably none do by default, but suitable parameters may exist within the literature or with a Google search. -Justin -- ===

[gmx-users] force field for GPI ligands which has lipid and carbohydrates ?

Could you tell me which force field recognizes the GPI ligand which posses lipid and mannose which interacts with protein? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_

Re: [gmx-users] force field

Dear Justin, with alcohols I can find their force field in AMBER or others. However, I have just got a paper regarding CTAB ( http://pubs.acs.org/doi/abs/10.1021/la302998k). They use Gromos force field. I am attempting to find the other better one. Best regards, Van On 6 December 2012 09:35, Jus

Re: [gmx-users] force field

On 12/5/12 8:29 PM, cuong nguyen wrote: Thanks for your email Justin. I remember you answered an email that there is a PRODRG server working with higher version of Gromos87. Could you show me the link please? The server has changed and is now managed by a company. I have not used it in mo

Re: [gmx-users] force field

Thanks for your email Justin. I remember you answered an email that there is a PRODRG server working with higher version of Gromos87. Could you show me the link please? Also could you please give me the advice about other force field for my simulation? I am working with surfactants like alcohols,

Re: [gmx-users] force field

On 12/4/12 10:22 PM, cuong nguyen wrote: Dear gmx users, i have got the coordinate and topol files of nonanol from the server: http://davapc1.bioch.dundee.ac.uk/prodrg/submit.html the .gro file was download from option GROMOS87/GROMACS polar H's only

[gmx-users] Force field for ions

Dear all: Does anyone know the optimal force field in GROMACS for treating divalent ions in explicit solvent? Would appreciate any recommendations. Thanks, Lili -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

FW: [gmx-users] force field parameters

-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Saturday, September 22, 2012 10:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] force field parameters On 9/22/12 2:13 PM, Asaf Farhi wrote: > Dear Justin > > Thank you very much for the reply. >

Re: [gmx-users] force field parameters

gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Saturday, September 22, 2012 10:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] force field parameters On 9/22/12 2:13 PM, Asaf Farhi wrote: Dear Justin Thank yo

Re: [gmx-users] force field parameters

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Saturday, September 22, 2012 3:53 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] force field parameters On 9/22/12 8:48 AM

RE: [gmx-users] force field parameters

, September 22, 2012 3:53 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] force field parameters On 9/22/12 8:48 AM, Asaf Farhi wrote: > Dear Users > > Hi. I'm looking for a a list of bond stretching parameters for the potential > 0.5k(r-r_eq)^2 that has units (k

Re: [gmx-users] force field parameters

On 9/22/12 8:48 AM, Asaf Farhi wrote: Dear Users Hi. I'm looking for a a list of bond stretching parameters for the potential 0.5k(r-r_eq)^2 that has units (k and r_eq). Can anyone help me with that (article will be good)? All of that information is in the ffbonded.itp file for whatever fo

[gmx-users] force field parameters

Dear Users Hi. I'm looking for a a list of bond stretching parameters for the potential 0.5k(r-r_eq)^2 that has units (k and r_eq). Can anyone help me with that (article will be good)? Thanks in advance, Best regards, Asaf p.s it can be of any force field as long as there's list. -- gmx-users m

Re: [gmx-users] Force Field Choice

On 8/27/12 1:32 PM, Marcelo Depolo wrote: Dear all, Is there a consensus on force field choice? I read in this group, people suggesting compare experimental data and simulation data. But in case of there's none experimental data about structural data, what to do? There was a discussion abo

[gmx-users] Force Field Choice

Dear all, Is there a consensus on force field choice? I read in this group, people suggesting compare experimental data and simulation data. But in case of there's none experimental data about structural data, what to do? I apologize previously the silly doubt. Best regards! -- Marcelo Depólo P

Re: [gmx-users] force field parametrs for Mn2+

sorry it's my mistake . thanks a lot for the reply. On Mon, Jul 9, 2012 at 10:55 PM, Justin A. Lemkul wrote: > > > On 7/9/12 1:21 PM, tarak karmakar wrote: >> >> Oh !! nice work >> Thanks a lot for the quick reply. But I'm very sorry to inform you >> that whichever table [supplementary ta

Re: [gmx-users] force field parametrs for Mn2+

On 7/9/12 1:21 PM, tarak karmakar wrote: Oh !! nice work Thanks a lot for the quick reply. But I'm very sorry to inform you that whichever table [supplementary table S4] you are specifying in the supporting info, I couldn't find anywhere. So, may be I'm finding my way in wrong track. Can you pl

Re: [gmx-users] force field parametrs for Mn2+

Oh !! nice work Thanks a lot for the quick reply. But I'm very sorry to inform you that whichever table [supplementary table S4] you are specifying in the supporting info, I couldn't find anywhere. So, may be I'm finding my way in wrong track. Can you please provide me the link and / the table cont

Re: [gmx-users] force field parametrs for Mn2+

Hi, we published recently a paper where we determined the oplsaa parameters for Mn2+; have look to (supp mat): http://onlinelibrary.wiley.com/doi/10.1002/anie.201202032/abstract hope it helps On 07/09/2012 12:21 PM, tarak karmakar wrote: Dear All, Please suggest me any paper/article that

[gmx-users] force field parametrs for Mn2+

Dear All, Please suggest me any paper/article that contains force field parameters for Mn 2+ . Thanks -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA P

[gmx-users] Force field for graphene sheet: deformation at the boundaries

Dear colleagues, I came across a puzzling behaviour when simulating graphene sheets (periodic in xy). When running a simulation of just one position restrained graphene sheet in a large vacuum slab with periodic_molecules=yes and pbc=xyz, I found a static deformation of the boundaries of th

Re: [gmx-users] Force field

Dialing Pretty wrote: Dear All, Is the following force field still practical or not? GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) Is there some reason to suggest otherwise? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Sch

[gmx-users] Force field

Dear All,   Is the following force field still practical or not?   GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)   Cheers,   Dialing-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Sup

Re: [gmx-users] Force Field for Vacuum simulation

On 2012-02-03 08:46:25AM +0300, James Starlight wrote: > Peter, > > 1- Yes I've also found that the umbrella simulation is exactly that I need. > Now I'm studing this tutorial more carefully. > > > 2- In other words my second question was: in what exactly situations ( e.g > some kind of point mu

Re: [gmx-users] Force Field for Vacuum simulation

Peter, 1- Yes I've also found that the umbrella simulation is exactly that I need. Now I'm studing this tutorial more carefully. 2- In other words my second question was: in what exactly situations ( e.g some kind of point mutation) the unbiassed MD may be enought to detect unstability of the sy

Re: [gmx-users] Force Field for Vacuum simulation

On 2012-02-02 04:46:03PM +0300, James Starlight wrote: > Peter, > > thank you it's very intresting survey. I'll try to investigate it > carefully. I've looking for the same issue for along time it's also would > be good to find more recent review on the same topic. > > By the way today I've found

Re: [gmx-users] Force Field for Vacuum simulation

Peter, thank you it's very intresting survey. I'll try to investigate it carefully. I've looking for the same issue for along time it's also would be good to find more recent review on the same topic. By the way today I've found that the testing on the receptor stability in the case of some point

Re: [gmx-users] Force Field for Vacuum simulation

I don't know if using small molecules in place of lipid chains will save or use more computer time. On one hand, bond constraints applied to the lipids will reduce the calculation with respect to degrees of freedom compared to the same volume of interacting smaller non-polar molecules. Then again,

Re: [gmx-users] Force Field for Vacuum simulation

Peter, firstly- thanks for the so detailed discussion. The negative aspects of water-vacum-water sandwich system wich you provided indeed keep me from the modelling of such system. Indeed I found some information about influence of the specific lipids on the stability of the protein by the regul

Re: [gmx-users] Force Field for Vacuum simulation

On 2012-02-02 11:57:22AM +0300, James Starlight wrote: > Peter, > > Yes the main reason is the CPU economy for such experiment. My current > experiment consist of investigation of the tight paking forces (primarily > vdv effect) in the membrane receptor by inclusion of some point mutations. > >

Re: [gmx-users] Force Field for Vacuum simulation

Peter, Yes the main reason is the CPU economy for such experiment. My current experiment consist of investigation of the tight paking forces (primarily vdv effect) in the membrane receptor by inclusion of some point mutations. Actyally I think that simple biphastic system ( like in the Justin tu

Re: [gmx-users] Force Field for Vacuum simulation

I am not sure of the actual interpretive value of such a methodology. Are you just trying to save computational time by not having to simulate an all atom bilayer? The solvent layer is going to contribute to the majority of the computation cost in the first place. As an example, the bilayer we

Re: [gmx-users] Force Field for Vacuum simulation

David, Justin Thanks again for help! I have just few questions about in vacum sumulation of membrane proteins. I want to simulate GPCR receptor wich have big transmembrane ( helix) domain and some connecting loop regions wich are exposed to the solvent. As I understood in classical vacum simu

Re: [gmx-users] Force Field for Vacuum simulation

On 2012-01-29 17:09, James Starlight wrote: Hi, Justin. Yes. The GFP chromophore is a part of backbone. It's formed from Ser Tyr Gly by cyclisation of the Ser with Gly and subsequent dehydrotation. As the consequence the mature chromophore has cyclised structure wich named as the CRO residue in

Re: [gmx-users] Force Field for Vacuum simulation

James Starlight wrote: Hi, Justin. Yes. The GFP chromophore is a part of backbone. It's formed from Ser Tyr Gly by cyclisation of the Ser with Gly and subsequent dehydrotation. As the consequence the mature chromophore has cyclised structure wich named as the CRO residue in PDB structure.

Re: [gmx-users] Force Field for Vacuum simulation

Hi, Justin. Yes. The GFP chromophore is a part of backbone. It's formed from Ser Tyr Gly by cyclisation of the Ser with Gly and subsequent dehydrotation. As the consequence the mature chromophore has cyclised structure wich named as the CRO residue in PDB structure. I've made for this CRO residue

Re: [gmx-users] Force Field for Vacuum simulation

James Starlight wrote: Hi David! Thanks for reference I'll study it carefully. I have some general question about the vacuum simulation 1- I've found that common GROMOS fields are not suitable for the vacuum simulation because of its implementation for condensed phase . But In some referenc

Re: [gmx-users] Force Field for Vacuum simulation

Hi David! Thanks for reference I'll study it carefully. I have some general question about the vacuum simulation 1- I've found that common GROMOS fields are not suitable for the vacuum simulation because of its implementation for condensed phase . But In some referencces I've found that people

Re: [gmx-users] Force Field for Vacuum simulation

On 2012-01-29 07:20, James Starlight wrote: Dear Gromacs USers! I'm looking for good force field for the simulation of the protein-ligand complex in vacuum. In accordance to the Justin's tutorial I've found that GROMOS96 43b1 force field might be good choice for that task. But my version of G

[gmx-users] Force Field for Vacuum simulation

Dear Gromacs USers! I'm looking for good force field for the simulation of the protein-ligand complex in vacuum. In accordance to the Justin's tutorial I've found that GROMOS96 43b1 force field might be good choice for that task. But my version of GROMACS lack for that force field .rtps :( Cou

Re: [gmx-users] force field

On 24/01/2012 2:58 AM, lina wrote: Hi, which gromacs force field shares the high "quasi-compatibility" with the amber force field. Force fields are not designed for compatibility, and the exceptions to this are very rare. I checked the heme only exists in gromos and the charmn while gbsa

[gmx-users] force field

Hi, which gromacs force field shares the high "quasi-compatibility" with the amber force field. I checked the heme only exists in gromos and the charmn while gbsa only shows in amber and oplsaa, truth is that I don't know how to get the gbsa parameter for heme, Thanks for any suggestions, Bes

Re: [gmx-users] Force field for polymer molecule - tips

On 13/12/2011 5:06 PM, Jernej Zidar wrote: Hi. I would like to use a CHARMM (CGennFF based) of polymer molecule in Gromacs. The polymer is composed of three different monomer and two different terminal residues (one for each of the the two terminals) - five residues in total. The CHARMM gene

[gmx-users] Force field for polymer molecule - tips

Hi. I would like to use a CHARMM (CGennFF based) of polymer molecule in Gromacs. The polymer is composed of three different monomer and two different terminal residues (one for each of the the two terminals) - five residues in total. The CHARMM generalized FF has already been ported to Gromacs s

[gmx-users] force field for argon

Dear gmx'ers, Inspecting gromacs' OPLSAA files, I find here two atom types for argon. File ffoplsaa.atp includes: opls_097 39.94800 ; Argon from Verlet & Weis Mol.Phys.,24,1013 (1972) and Ar 39.948; Argon LJ parameters are (file ffoplsaanb.itp): [ atomtypes ] ; name bond_t

Re: [gmx-users] Force field for thiocyanate ions

On 18/08/2011 5:07 AM, Sanku M wrote: Hi, Does anyone know about availability of MM pair-wise additive forcefield for thiocyanate anion ( SCN- ) , either in CHARMM or OPLS format ? Sanku Google can suggest some possible leads. Mark -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Force field for thiocyanate ions

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

Re: Re: [gmx-users] Force-field checking options

Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Thursday, August 4, 2011. For all questions about CloudBroker and the CloudBroker Platfo

Re: [gmx-users] Force-field checking options

hanks! Cheers, Matt > > Forwarded Message ---- > > From: Mark Abraham > > Reply-to: Discussion list for GROMACS users > > To: Discussion list for GROMACS users > > Subject: Re: [gmx-users] Force-field checking options &

Re: [gmx-users] Force-field checking options

mx. Mark Mark Cheers, Matt Forwarded Message From: Justin A. Lemkul Reply-to: jalemkul at vt.edu, Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Force-field checking options Date: Wed, 03 Aug 2011 00

Re: [gmx-users] Force-field checking options

e of its energy contribution is available. ...and trivial to turn off in pdb2gmx. Mark Mark Cheers, Matt Forwarded Message From: Justin A. Lemkul Reply-to: jalemkul at vt.edu, Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re:

Re: [gmx-users] Force-field checking options

ing up. CP2K doesn't have CMAP implemented, but that only a >> small part according to GROMACS. > > ...and the magnitude of its energy contribution is available. ...and trivial to turn off in pdb2gmx. Mark > > Mark > >> >>Cheers, Matt >> >>&

Re: [gmx-users] Force-field checking options

...@vt.edu, Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Force-field checking options Date: Wed, 03 Aug 2011 00:12:35 -0400 mcgrath wrote: Hi. I'm fairly new to GROMACS, and I've been using it to run some classical MD simulations

Re: [gmx-users] Force-field checking options

cording to GROMACS. ...and the magnitude of its energy contribution is available. Mark Cheers, Matt Forwarded Message From: Justin A. Lemkul Reply-to: jalem...@vt.edu, Discussion list for GROMACS users To: Discussion list for GROMACS users

Re: [gmx-users] Force-field checking options

ROMACS users > > > > To: Discussion list for GROMACS users > > Subject: Re: [gmx-users] Force-field checking options > > Date: Wed, 03 Aug 2011 00:12:35 -0400 > > > > > > mcgrath wrote: > > > Hi. I'm fairly new to GROMACS, and I'

Re: [gmx-users] Force-field checking options

mcgrath wrote: Hi. I'm fairly new to GROMACS, and I've been using it to run some classical MD simulations. In order to be sure that I'm using the correct force field (I had to add a molecule to CHARMM27), I'm comparing it to another simulation code that I know well, CP2K (using GROMACS 4.5.4

[gmx-users] Force-field checking options

Hi. I'm fairly new to GROMACS, and I've been using it to run some classical MD simulations. In order to be sure that I'm using the correct force field (I had to add a molecule to CHARMM27), I'm comparing it to another simulation code that I know well, CP2K (using GROMACS 4.5.4 and a recent CVS ve

Re: [gmx-users] Force field parameters for phosphorylated tyrosine

On 2011-06-13 08:33:15AM -0500, bharat gupta wrote: > thanks for the reply... > > Actually I have found the amber parameters for p-TYR from the following links > : http://www.pharmacy.manchester.ac.uk/bryce/amber#pro > > I am not able to how build the residue topology .. shall I add the topolog

Re: [gmx-users] Force field parameters for phosphorylated tyrosine

bharat gupta wrote: thanks for the reply... Actually I have found the amber parameters for p-TYR from the following links : http://www.pharmacy.manchester.ac.uk/bryce/amber#pro I am not able to how build the residue topology .. shall I add the topology of phosphate only from this to norma

Re: [gmx-users] Force field parameters for phosphorylated tyrosine

thanks for the reply... Actually I have found the amber parameters for p-TYR from the following links : http://www.pharmacy.manchester.ac.uk/bryce/amber#pro I am not able to how build the residue topology .. shall I add the topology of phosphate only from this to normal tyrosine residue ?? !!

Re: [gmx-users] Force field parameters for phosphorylated tyrosine

On 13/06/2011 7:15 PM, bharat gupta wrote: Hi, Does gromacs and its associated FFs have parameters for phosphorylated tyrosine ?? Probably not. The best place to search is the literature. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] Force field parameters for phosphorylated tyrosine

Hi, Does gromacs and its associated FFs have parameters for phosphorylated tyrosine ?? -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before postin

Re: [gmx-users] force field for simulation of BCN

On 29/12/2010 11:06 PM, mina Madah wrote: dear all user How can I have a force field for simulation of boron-nitride-carbon (BCN) graphene? all force field in gromacs don't have boron as an atomtype . That's because those forcefields are primarily aimed at biochemistry simulations. You need

[gmx-users] force field for simulation of BCN

dear all user How can I have a force field for simulation of boron-nitride-carbon (BCN) graphene? all force field in gromacs don't have boron as an atomtype . -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive a

[gmx-users] force field changes in version 4.5.1

I am trying to figure out changes made in v 4.5.1 in share/gromacs/top. In earlier versions, there were some defined variables, e.g., hyp_prop_1 for hydroxyprolines and grep -r hyp_prop_1 ~/gromacs_4.0.5/share/gromacs/ top/ would show ~15 lines, including for example: ffamber99bon.itp:#define hy

Re: [gmx-users] Force-field files location and order of reading in Gromacs 4.5.2

On Thu, Oct 21, 2010 at 14:28, Justin A. Lemkul wrote: > My guess is that this is a matter of how the force field was #included in > the .top file.  For instance: > > #include "my.ff/forcefield.itp" > > will match $GMXLIB first, but > > #include "./my.ff/forcefield.itp" > > will match the working

Re: [gmx-users] Force-field files location and order of reading in Gromacs 4.5.2

Thanks Justin, this explains everything. I've got #include "my.ff/forcefield.itp" line in my top file. > My guess is that this is a matter of how the force field was #included in > the > .top file. For instance: > > #include "my.ff/forcefield.itp" > > will match $GMXLIB first, but > > #include "

Re: [gmx-users] Force-field files location and order of reading in Gromacs 4.5.2

Karel Berka wrote: Karel Berka wrote: > Hi all, > > I have detected that preference in reading forcefield files in Gromacs > 4.5 has probably been changed from Gromacs 4.0.x and older. > In older gromacs, when there was forcefield with modification present

Re: [gmx-users] Force-field files location and order of reading in Gromacs 4.5.2

> > > Karel Berka wrote: > > Hi all, > > > > I have detected that preference in reading forcefield files in Gromacs > > 4.5 has probably been changed from Gromacs 4.0.x and older. > > In older gromacs, when there was forcefield with modification present in > > my working directory, then it was read

Re: [gmx-users] Force-field files location and order of reading in Gromacs 4.5.2

Karel Berka wrote: Hi all, I have detected that preference in reading forcefield files in Gromacs 4.5 has probably been changed from Gromacs 4.0.x and older. In older gromacs, when there was forcefield with modification present in my working directory, then it was read preferentially, but no

[gmx-users] Force-field files location and order of reading in Gromacs 4.5.2

Hi all, I have detected that preference in reading forcefield files in Gromacs 4.5 has probably been changed from Gromacs 4.0.x and older. In older gromacs, when there was forcefield with modification present in my working directory, then it was read preferentially, but now it seems that forcefiel

Re: [gmx-users] Force field definitions in 4.0 and 4.5

On 11/10/10 15:45, Justin A. Lemkul wrote: I am currently using GROMACS 4.0.7 with a custom force field I developed (coarse-grained model I am developing). I want to jump to 4.5 , but I wonder if something in the syntax of force fields has changed from 4.0.x to 4.5 :just to know in advance if I h

Re: [gmx-users] Force field definitions in 4.0 and 4.5

ms wrote: Dear users, I am currently using GROMACS 4.0.7 with a custom force field I developed (coarse-grained model I am developing). I want to jump to 4.5 , but I wonder if something in the syntax of force fields has changed from 4.0.x to 4.5 :just to know in advance if I have to change t

[gmx-users] Force field definitions in 4.0 and 4.5

Dear users, I am currently using GROMACS 4.0.7 with a custom force field I developed (coarse-grained model I am developing). I want to jump to 4.5 , but I wonder if something in the syntax of force fields has changed from 4.0.x to 4.5 :just to know in advance if I have to change the files or i

[gmx-users] force field parameters for lipids on lipidbook.bioch.ox.ac.uk

Hi, readers of this list who are interested in the simulation of membranes, membrane proteins, micelles etc. might be interested in a new web site we recently set up [1]: http://lipidbook.bioch.ox.ac.uk It is a public repository for force field parameters with a special emphasis on lipids

RE: [gmx-users] force field to freeze/evaporate

Hi, Of the "cheap" models I would think tip4p 2001 is the best. This has been parametrized to reproduce the phase diagram of water and does surprisingly well. Berk > From: vvcha...@gmail.com > Date: Fri, 17 Sep 2010 16:01:50 -0400 > To: gmx-users@gromacs.org > Subject: [

[gmx-users] force field to freeze/evaporate

Hi all, Sorry for my a bit off-top message. Does anybody know the force field model for water (polarizable/non-polarizable) that can reproduce the temperatures of liquid freezing/evaporation? For other common liquids, such models are also of interest. Thanks a lot. ~Vitaly -- Dr. Vitaly V. Chaban

Re: [gmx-users] Force Field => Residues PHE, TRP, TYR, HIS ?

Hi Chih-Ying Lin, There's no such thing as a pi bond in a classical force field, bonds are merely connections with a certain distance based potential. Gromacs doesn't deal with polarity, the distribution of charges, etc. is part of the force field. Better check the papers relating to the force fi

[gmx-users] Force Field => Residues PHE, TRP, TYR, HIS ?

HI Residues PHE, TRP, TYR, and HIS are carrying "Rings", or say pi bonds. How does the Gromacs deal with polarity for all this four residues? Is a single charge assigned for each atom on the center of atoms of the four residues ? Is pi bond given for the four residues in the force field? Tha

Re: [gmx-users] Force field parameters for the heme in ff53a6

It appears that the parameters in 53a6 are unchanged relative to 43a1, the reference for which is the GROMOS manual. Unfortunately, you have to pay the licensing fee to obtain the manual. There are certainly several literature references for various aspects of the GROMOS functional form and

[gmx-users] Force field parameters for the heme in ff53a6

Hi, All, Does anyone know where the force field parameters for the heme in the ff53a6 force field were obtained? Much appreciated, Art Art Roberts 7254 Shoreline Dr. #130 San Diego, CA 92122 cell: 206-850-7468 email: aroberts99...@yahoo.com skype=aroberts92122 -- gmx-users mailing list

Re: [gmx-users] force field parameters for FeCL4 anion

Nilesh Dhumal wrote: Hello, I am looking for force field paratmers of FeCL4 anion. I could not find which report the force field paraters for this anion. I am also trying to get lennard jones parameter for Fe (III). If any have have force field parameters for FeCl4 anion or lennard-jones parame

[gmx-users] force field parameters for FeCL4 anion

Hello, I am looking for force field paratmers of FeCL4 anion. I could not find which report the force field paraters for this anion. I am also trying to get lennard jones parameter for Fe (III). If any have have force field parameters for FeCl4 anion or lennard-jones parameter for Fe(III), let me k

Re: [gmx-users] force field: heme group

Matthew L. Danielson wrote: Ramachndran, If you are trying to use the AMBER force field ports for Gromacs (assuming you installed them correctly), I have defined the HEME group for Amber03. If this would help you let me know, and i can provide the files that you need to replace in your gr

Re: [gmx-users] force field: heme group

Ramachndran, If you are trying to use the AMBER force field ports for Gromacs (assuming you installed them correctly), I have defined the HEME group for Amber03. If this would help you let me know, and i can provide the files that you need to replace in your gromacs "top" folder -Matt Dani

Re: [gmx-users] force field: heme group

Ramachandran G wrote: Dear all, It is known that force field for the heme group doesn't exist in gromacs. So i tried to use amber force fields(AMBER94, AMBER99, That's not true; all of the Gromos variants have heme parameters. AMBER99p, AMBER03, AMBERGS, AMBERGSs) by patching with my

Re: [gmx-users] force field: heme group

No, you're wrong. There are parameters for HEME in several flavours of the GROMOS forcefields, which you can find in the share/gromacs/top/ directory. Ramachandran G skrev: Dear all, It is known that force field for the heme group doesn't exist in gromacs. So i tried to use amber force

[gmx-users] force field: heme group

Dear all, It is known that force field for the heme group doesn't exist in gromacs. So i tried to use amber force fields(AMBER94, AMBER99, AMBER99p, AMBER03, AMBERGS, AMBERGSs) by patching with my latest gromacs version 4.0.5 but still it gives the error message 'Residue 'HEME' not found in

Re: [gmx-users] force field

Hi, leila karami wrote: I want to do MD simulation by gromacs but there are following force fields in gromacs program: ffG43a1- ffG43a2 - ffG43a3 - ffG43a5 - ffG43a6 - ffOPLS-AA - ffgmx - ffgmx2 - ffencads - ffencadv. How can I use other force fields such as AMBER or CHARMM. For AMBER, downl

Re: [gmx-users] force field

leila karami wrote: I want to do MD simulation by gromacs but there are following force fields in gromacs program: ffG43a1- ffG43a2 - ffG43a3 - ffG43a5 - ffG43a6 - ffOPLS-AA - ffgmx - ffgmx2 - ffencads - ffencadv. How can I use other force fields such as AMBER or CHARMM. For AMBER, downlo

[gmx-users] force field

I want to do MD simulation by gromacs but there are following force fields in gromacs program: ffG43a1- ffG43a2 - ffG43a3 - ffG43a5 - ffG43a6 - ffOPLS-AA - ffgmx - ffgmx2 - ffencads - ffencadv. How can I use other force fields such as AMBER or CHARMM. ___

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