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 autocorrelation

1. Run mdrun with nstfout set appropriately 2. g_traj -h 3. g_analyze -h 4. Profit! Mark On Tue, Dec 11, 2012 at 3:31 PM, khuws wrote: > Hi > Does anyone know if, and if so how, GROMACS can generate a force > autocorrelation function? > If this is not possible then can I extract the force exter

[gmx-users] force autocorrelation

Hi Does anyone know if, and if so how, GROMACS can generate a force autocorrelation function? If this is not possible then can I extract the force exterted by each atom on a single labelled atom? Regards Ted -- View this message in context: http://gromacs.5086.n6.nabble.com/force-autocorrelati

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 vs time plot

On 11/24/12 7:09 AM, Paula Andrea Delgado Pinzon wrote: Hi to all gromacs users, I am trying to run an umbrella sampling and i am getting the initial conformations by pulling simulations but i want to check the simulation through the force vs time plot to see if my complex did or did not sep

[gmx-users] force vs time plot

Hi to all gromacs users, I am trying to run an umbrella sampling and i am getting the initial conformations by pulling simulations but i want to check the simulation through the force vs time plot to see if my complex did or did not separate, so how can i get this plot? Thank you for your time

[gmx-users] Force vs distance plot in pulling simulation?

But be aware that the force depends on the pulling velocity. If you perform the simulation with two different pulling velocities you'll get two different forces for each distance. The easiest way to get the force as a function of the distance (without the bias of the pulling velocity) would be t

Re: [gmx-users] Force vs distance plot in pulling simulation?

16 nov 2012 kl. 22.42 skrev Justin Lemkul: > > > On 11/16/12 10:45 AM, Gmx QA wrote: >> Hello gmx-users, >> >> I've performed a pulling simulation and obtained a force-vs-time plot and a >> distance-vs-time plot (xvg-files). >> Is it common to somehow combine these to get a force-vs-distance-p

Re: [gmx-users] Force vs distance plot in pulling simulation?

On 11/16/12 10:45 AM, Gmx QA wrote: Hello gmx-users, I've performed a pulling simulation and obtained a force-vs-time plot and a distance-vs-time plot (xvg-files). Is it common to somehow combine these to get a force-vs-distance-plot using a hacked-together script, or how do people that have e

Re: [gmx-users] Force calculations were truncated at a distance of 1.2 nm

On 10/15/12 9:04 AM, Ali Alizadeh wrote: Dear All users I want to specify this statement in my input files but Where does it specify?( i don't know!) I know but i do not certain, Force calculations were truncated at a distance of 1.2 nm That likely refers to cutoff values. -Justin -- ===

[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 fields, is there a review article?

On 2012-08-25 13:07, Luca Mollica wrote: I have read a variation on this advice many. many times here: "The ultimate choice of force field should be based on your reading and understanding of their derivation and known applications/limitations, all of which comes from the literature. Choose

Re: [gmx-users] Force fields, is there a review article?

I have read a variation on this advice many. many times here: "The ultimate choice of force field should be based on your reading and understanding of their derivation and known applications/limitations, all of which comes from the literature. Choose the one that you think is most sound :)"

[gmx-users] Force fields, is there a review article?

I have read a variation on this advice many. many times here: "The ultimate choice of force field should be based on your reading and understanding of their derivation and known applications/limitations, all of which comes from the literature. Choose the one that you think is most sound :)" I am

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

Re: [gmx-users] Force constant - units

1 pN/A = 10^-23 kJ/nm2 So 1pN/A = 6,02214129 kJ/mol nm2 Thank you All, Steven On Tue, Jul 3, 2012 at 6:20 PM, Thomas Schlesier wrote: > You have 1mol of your system. > > conversition factor for > kJ/(mol*nm) -> pN is approx 1.661 > > > Am 29.06.2012 10:33, schrieb gmx-users-requ...@gromac

[gmx-users] Force constant - units

You have 1mol of your system. conversition factor for kJ/(mol*nm) -> pN is approx 1.661 Am 29.06.2012 10:33, schrieb gmx-users-requ...@gromacs.org: Dear Gmx Users, How to recalculate the force constant from the harmonic potential: 1 [pN/A] into [kJ/mol nm2] ? Where is the [mol] here? T

Re: [gmx-users] Force constant - units

Hi Steven, How much is 1 [pN/A] in [kJ/nm2] (without the mol)? And why would anyone want to use force-constants in the 10^-23 ? So why not define a force-constant for 1 mol of bonds instead of a sole bond? I think you can see where I'm going. Oliver On Fri, Jun 29, 2012 at 2:32 AM, Steven Neu

[gmx-users] Force constant - units

Dear Gmx Users, How to recalculate the force constant from the harmonic potential: 1 [pN/A] into [kJ/mol nm2] ? Where is the [mol] here? Thanks, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed

Re: [gmx-users] Force constant in g_wham

Hi, the umbrella potential is 0.5*k*(z-z0)^2 Jochen Am 6/14/12 11:41 PM, schrieb rainy908: Dear gmx-users, I am writing to clarify that the force constant kappa for g_wham corresponds to K_i itself, and not the quantity (1/2)*K_i in the umbrella potential W_i(ξ) = (K_i/2)*(ξ-ξ_i)^2. I rec

[gmx-users] Force constant in g_wham

Dear gmx-users, I am writing to clarify that the force constant kappa for g_wham corresponds to K_i itself, and not the quantity (1/2)*K_i in the umbrella potential W_i(ξ) = (K_i/2)*(ξ-ξ_i)^2. I recall reading somewhere that the force constant sometimes includes the (1/2) term in front of K_i,

Re: [gmx-users] Force Constants and Unit Systems

That helps a lot. Thank you, I guess I got it now :-) Greetings Lara - Ursprüngliche Message - Von: Richard Broadbent An: Lara Bunte ; Discussion list for GROMACS users CC: "jalem...@vt.edu" Gesendet: 11:21 Freitag, 18.Mai 2012 Betreff: Re: [gmx-users] Force Constant

Re: [gmx-users] Force Constants and Unit Systems

gt; Greetings > Lara > > > > > > - Ursprüngliche Message - > Von: Justin A. Lemkul > An: Lara Bunte ; Discussion list for GROMACS users > > CC: > Gesendet: 20:37 Donnerstag, 17.Mai 2012 > Betreff: Re: [gmx-users] Force Constants and Unit Systems

Re: [gmx-users] Force Constants and Unit Systems

s CC: Gesendet: 20:37 Donnerstag, 17.Mai 2012 Betreff: Re: [gmx-users] Force Constants and Unit Systems On 5/17/12 1:33 PM, Lara Bunte wrote: > Hi > >> Therefore either they have a potential of the form 1/[Length] or they >> weren't using the term correctly. > > But

Re: [gmx-users] Force Constants and Unit Systems

On 5/17/12 3:32 PM, Lara Bunte wrote: Hi what I meant was, that if a force constant would have the unit kcal/mol, the corresponding potential will be a coulomb potential and I said that this makes no sense. Springs has a quadratic potential, not a Coulomb Potential, like V(r) = 1/r. Please

Re: [gmx-users] Force Constants and Unit Systems

g=AFQjCNFOxi8Cf2eUshmA9rzPfLPra5u-gw&sig2=79QqmWk3b8LSFlVjey4FFg Do you think it is a typo? Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul An: Lara Bunte ; Discussion list for GROMACS users CC: Gesendet: 20:37 Donnerstag, 17.Mai 2012 Betreff: Re: [gmx-users] Force Con

Re: [gmx-users] Force Constants and Unit Systems

On 5/17/12 1:33 PM, Lara Bunte wrote: Hi Therefore either they have a potential of the form 1/[Length] or they weren't using the term correctly. But a 1/[lenght] potential, which is a coulomb potential makes no sense for springs, that have a quadratic potential, like V(x) = 1/2 * k * x^2 of

Re: [gmx-users] Force Constants and Unit Systems

on list for GROMACS users CC: Gesendet: 19:18 Donnerstag, 17.Mai 2012 Betreff: Re: [gmx-users] Force Constants and Unit Systems Hi Lara, On Thu, 2012-05-17 at 17:58 +0100, Lara Bunte wrote: > Hi > > > >One cannot convert between these units, since kcal/mol is an energy term,

Re: [gmx-users] Force Constants and Unit Systems

please explain this? > > Greetings and really thanks for your help > > Lara > > > > > > - Ursprüngliche Message - > Von: Justin A. Lemkul > An: Lara Bunte ; Discussion list for GROMACS users > > CC: > Gesendet: 18:52 Donnerstag, 17.Mai

Re: [gmx-users] Force Constants and Unit Systems

7.Mai 2012 Betreff: Re: [gmx-users] Force Constants and Unit Systems On 5/17/12 12:25 PM, Lara Bunte wrote: Hello I never had contact with such units. Could you please help me and explain me how to transform following units: 1.) kcal / mol --> kJ / (mol * nm^2) One cannot convert

Re: [gmx-users] Force Constants and Unit Systems

trization I have this values. Could you please explain this? Greetings and really thanks for your help Lara - Ursprüngliche Message - Von: Justin A. Lemkul An: Lara Bunte ; Discussion list for GROMACS users CC: Gesendet: 18:52 Donnerstag, 17.Mai 2012 Betreff: Re: [gmx-users] For

Re: [gmx-users] Force Constants and Unit Systems

On 5/17/12 12:25 PM, Lara Bunte wrote: Hello I never had contact with such units. Could you please help me and explain me how to transform following units: 1.) kcal / mol --> kJ / (mol * nm^2) One cannot convert between these units, since kcal/mol is an energy term, and kJ/(mol nm^2) is a

[gmx-users] Force Constants and Unit Systems

Hello I never had contact with such units. Could you please help me and explain me how to transform following units:   1.) kcal / mol --> kJ / (mol * nm^2) 2.) kcal / (mol * rad^2) --> kJ / (mol * rad^2) I have additionally some question to that:  Both should be units of a force constant. From

[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 constant - Umbrella Sampling

al-Nachricht > Datum: Mon, 19 Mar 2012 08:48:15 + > Von: Steven Neumann > An: Discussion list for GROMACS users , jalem...@vt.edu > Betreff: [gmx-users] Force constant - Umbrella Sampling > Dear Gmx Users, Dear Justin, > > As I saw in your tutorial you used the

[gmx-users] Force constant - Umbrella Sampling

Dear Gmx Users, Dear Justin, As I saw in your tutorial you used the force of 1000 kJ/mol nm2 for the harmonic potential. You pulled the whole chain which is quite heavy. Would you decrease the force constant for a small molecule (app. 500 Da) during the umbrella sampling (e.g. 500 kJ/mol nm2) ? Is

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

Re: [gmx-users] Force equations of virtual site type 4fdn

On 22/11/2011 7:27 PM, xuji wrote: Hi all-gmxers The force equations of old virtual site type 4fd were shown in GROMACS manual. But the ones of corresponding new type 4fdn are not shown in new GROMACS manual. Can someone do me a favor to give the force equations? You will have seen that the

[gmx-users] Force equations of virtual site type 4fdn

Hi all-gmxers The force equations of old virtual site type 4fd were shown in GROMACS manual. But the ones of corresponding new type 4fdn are not shown in new GROMACS manual. Can someone do me a favor to give the force equations? Appreciate any help and thanks in advance! 2011-11-22 Best

Re: [gmx-users] force vs displacement

ibi2010...@iiita.ac.in wrote: hello Justin, For afm simulation,I have obtained force vs time and displacemnet vs time plot.how to get force vs displacement plot? please tell. You have all the data you need in the output files already. You can write a simple script to parse out the inform

[gmx-users] force vs displacement

hello Justin, For afm simulation,I have obtained force vs time and displacemnet vs time plot.how to get force vs displacement plot? please tell. Thanx - This email has been sent using ArithMail at "Indian Institute of Information Technology, Allahabad,

[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 a gromacs tool to write step-by-step a result in a xvg file

Hi, I would suggest you extract the single snapshot from your xtc file and then run the analysis tool on the single snapshot file. /Flo On Tue, 2011-09-06 at 12:12 +0200, intra\sa175950 wrote: > Dear All > > > > I use the g_clustersize to examine the cluster decay vs. time during > the ag

[gmx-users] Force a gromacs tool to write step-by-step a result in a xvg file

Dear All I use the g_clustersize to examine the cluster decay vs. time during the aggregation process of glycolipids into a micelle with the following command: $WORKDIR/gromacs-4.5.3/bin/g_clustsize_mpi -f *.xtc -s run_1.tpr -mc bDM-AMBER99SB-ILDN-Self_b_cluster.xvg -nc bDM-AMBER99SB-ILDN-

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

[gmx-users] Force evaluation in umbrella pulling with nonzero pull_rate

Hi, I'm trying to use umbrella pulling to do a targeted MD and I have the following pull code: pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = no pull_ngroups = 1 pull_group0 = REF pull_group1 = PULL pull_init1

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

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