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

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

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 -- ===

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 t

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

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

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

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

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

Re: [gmx-users] force field Parameters for DPG

Olaniyi Yusuff wrote: Hello, I am using molecular dynamics simulation to monitor the conformational transition of human adult hemoglobin from the deoxy- to the oxy-state and the effect of 2,3-DPG on the binding of oxygen to the hemoglobin molecule using gromos force field G43a1 in gromacs. P

Re: [gmx-users] Force Field Charge Parameters

Nancy wrote: The OPLS-AA force field is used for glucose and trehalose in conjunction with other force fields in the article by Sukit Leekumjorn and Amadeu K. Sum: "Molecular Dynamics Study on the Stabilization of Dehydrated Lipid Bilayers with Glucose and Trehalose". J. Phys. Chem. B, 2008

Re: [gmx-users] Force Field Charge Parameters

The OPLS-AA force field is used for glucose and trehalose in conjunction with other force fields in the article by Sukit Leekumjorn and Amadeu K. Sum: "Molecular Dynamics Study on the Stabilization of Dehydrated Lipid Bilayers with Glucose and Trehalose". J. Phys. Chem. B, 2008, 112 (34), pp 10732

Re: [gmx-users] Force Field Charge Parameters

Nancy wrote: Hello, I have successfully minimised and equilibrated two systems, one consisting of a single molecule of ethylene glycol (1,2-ethanediol) in a water box, and the other is one molecule of glycerol, also in a water box. I am planning to proceed to simulate other sugar alcohols

Re: [gmx-users] Force field problems

Michael McGovern wrote: Hello everyone, I'm working with a peptide-like molecule that is covalently bonded to a linker. For the peptide-like part I am using a modified version of the ffG53a6 force field files. The linker section contains an alkyl section, an oligo-ethylene glycol section

Re: [gmx-users] force field parameter for ligands

Zhanglin Ni wrote: Dear all, where do you usually get topolgy for small molecule ligand or do it manually? Dundee PRODRG Server seems to be capable of making .top for ffgmx only but not new ones like ffG53a6,etc. Thanks Search. There's a million posts on this mailing list pointing out that t

Re: [gmx-users] Force Field - Gromos96

On Mar 13, 2009, at 3:09 AM, tree wrote: Dear All: I appreciate it if it would be possible for me to have an answer related to Gromos96 force field. I am hoping to know if the Gromos96 force field can support All-Atom calculation? (Or does it 'only' support Unified Atom simulation?) O

Re: [gmx-users] Force field selection

Lucio Montero wrote: Hello! What is the best force field to use for a MD of a compley of three proteins and an organic molecule. And what are the best temperature and pressure coupling methods. "Best" is completely subjective, based on what you read about different force fields and which o

Re: [gmx-users] force field for boron-nitride nanotube

jj beh wrote: Dear all user How can I have a force field for simulation of boron-nitride nanotube? Has anything like that ever been simulated? If it hasn't, there may not be paramteers for such a species. I don't believe boron exists as an atom type in any of the force fields provided b

Re: [gmx-users] Force Field Parameters Nitrogen and Oxygen

Andy Shelley wrote: I am trying to simulate air and have not been able to find force field parameters for a Nitrogen Nitrogen bond or Oxygen Oxygen bond. If you could please direct me to where these could be found I would appreciate it. I believe these values typically come from spectrosc

Re: [gmx-users] Force Field: A new chemical compound

Chih-Ying Lin wrote: Hi Honestly, I don't know how to do the quantum chemistry calculation. I have the one azobenzene derivative force field parameters(from QM/MM paper) in hand. This azobenzene derivative is quite similar with the azotab compound, which I need. For the rest parts of the azota

Re: [gmx-users] Force field parameters in water or in vacuum?

[EMAIL PROTECTED] wrote: Please don't post to the users list and the developers list simultaneously with the same question. I think this is more appropriately a users list question. I guess if you also get a reply on the developers list then it pays to post to both, but the idea is to put it o

Re: [gmx-users] Force field parameters in water or in vacuum?

Chih-Ying Lin wrote: Hi For one molecule, will Gromacs give the same set of force field parameters to this molecule no matter this molecule is put in water or in vacuum? The bond length, the bond angle, and the dihedral angles of the same molecule will be different in water and in vacuum. So, wil

Re: [gmx-users] Force field parameters in water or in vacuum?

Quoting Chih-Ying Lin <[EMAIL PROTECTED]>: > Hi > For one molecule, will Gromacs give the same set of force field > parameters to this molecule no matter this molecule is put in water or > in vacuum? Depending on what's defined within the specific force field, yes. For example, ffG43b1 is a "vac

Re: [gmx-users] force field parameters for hydronium

Yes, that's exactly the article I had in mind! There are also people studying stuff like dissociative hydration of, e.g., silica, they have some water models that can dissociate when needed, as well... http://pubs.acs.org/cgi-bin/abstract.cgi/nalefd/2003/3/i10/abs/nl034480e.html http://www.rsc.or

Re: [gmx-users] force field parameters for hydronium

Vasilii Artyukhov wrote: 2008/4/28 Mark Abraham <[EMAIL PROTECTED] >: Trying to model hydronium is a pretty flawed thing to do, since the hydrogens in real water are labile - so the molecule you'd label as "hydronium" moves much faster than any atoms do.

Re: [gmx-users] force field parameters for hydronium

2008/4/28 Mark Abraham <[EMAIL PROTECTED]>: > Trying to model hydronium is a pretty flawed thing to do, since the > hydrogens in real water are labile - so the molecule you'd label as > "hydronium" moves much faster than any atoms do. I actually seem to remember reading something about some dis

Re: [gmx-users] force field parameters for hydronium

Bert wrote: Hi gmx-users, I wonder if I can add H3O+ (Eigen) and OH- combined with SPC/E water model into my system. I have not found any available force field parameters for them in gmx yet, does anyone has itps and gros file for modeling them? BTW, I do not care about the PH value, and I

RE: [gmx-users] Force field

Hi Nihar, unfortunately I can't help you with thioflavin parameterization and probably other people here will address you to general links. Our CDs were built on the base of topologies for smaller sugars already available in the gromos force field (pasting building blocks). I hope someone else can

RE: [gmx-users] Force field

Hi Ángel, Thanks a lot for coming forward. Regarding CD (\alpha, \beta and \gamma) I will contact you as soon as possible. For the moment I would like to get the same for Thioflavin-T. It is a fairly big molecules with I think 39 atoms. Can you tell me how go about (procedure in detail) to get t

RE: [gmx-users] Force field

Dear Nihar, if you contact me off the list I could send to you itp files for native alpha, beta, and gamma cyclodextrins compatible with the gromos forcefield (the ones we used in "jpcb (2007) 4383" and "jpcb (2007) 12625"). Unfortunately I do not have the thioflavin. Regards, Angel Piñeiro. --

Re: [gmx-users] force field

Hi, This is the kind of stuff OPLS excels at, although you'll have to hack the topology more or less manually. Look at OPLS-AA atom types #465-473 and #490-492. Cheers, Erik On Mar 22, 2007, at 7:50 PM, Ashish Gupta wrote: Hello gromacs users, Can anybody suggest me some reference

Re: [gmx-users] force field optimization

I published a program to do this type of things a few years ago... check it out and see if it matches your needs. It is available on the cpc web site. There is a version that works with amber and charmm, should be easy to adapt to Gromacs... or run it with amber and use the obtained forcefield in g

RE: [gmx-users] force field parameters/B state dihedrals

From: "David Mobley" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: "Discussion list for GROMACS users" Subject: [gmx-users] force field parameters/B state dihedrals Date: Thu, 20 Jul 2006 15:07:35 -0700 Dear all, I'm setting up some relative free energy calculations i

Re: [gmx-users] force field

hjbai wrote: > Hi, all > What's the difference between different force fields? such as gromos 87, > gromos 96 and opls/aa, I was confused -- How can I get some information > about this? I have looked through the manual, and cant get a clear > picture for this problem. > Thank you, any kinds of disc