[gmx-users] (no subject)

Dear Gromacs users! I want to simulate membrane receptor in the Gromos 56 force field in the vacuu and I have some methodological questions. 1- I need to edit topology of my structure by adding one DOUBLE covalent bond between desires atoms ( they have been already placed in the desired adjacen

[gmx-users] Simulation of membrane protein in vacuu

Dear Gromacs users! I want to simulate membrane receptor in the Gromos 56 force field in the vacuu and I have some methodological questions. 1- I need to edit topology of my structure by adding one DOUBLE covalent bond between desires atoms ( they have been already placed in the desired adjacen

[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 for Vacuum simulation

n itself) ? I've done all steps in accordance to Justins tutorial but on the minimisation step my chromphore dissuse out of the protein interior because of absent of backbone group. Thanks again, James 2012/1/28, David van der Spoel : > On 2012-01-29 07:20, James Starlight wrote: >> D

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

n via pdb2gmx) Than I've done minimisation and chromophore have been diffused from my protein :) It seems that I must add covalent bond between CRO and protein into the topology. But how I could do it for my multi topology file ? James 2012/1/29 Justin A. Lemkul > > > James Starlight

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

y charges in TM helices and keep residues in LOOP intact. Might this aproache be correct? James 2012/1/29 David van der Spoel > 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 &

[gmx-users] Application of external forces during MD run

Dear Gromacs Users! I'm looking for some tutorial for the example of the biased MD driven by appication of the external forces. For example I have simple system wich consist of the peptide (small membrane chanell) in vacum where I study effect of some point mutations on the tight packing (primari

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

he bilayer, you might be able to get away > with using strong i,i+4 distance constraints within your TMs to preserve > helical stability while the entire protein is solvated. > > > On 2012-01-30 10:50:35AM +0400, James Starlight wrote: > > David, Justin > > > >

[gmx-users] Charge distribution in the topology file

Dear Gromacs Users! I want to perform in vacuum simulation for the simple peptid parametrised by Amber 99SB and Gromos 43.1 force fields. As I understoon the primary foal of in vacum simulation in the turn of all charges in the residues wich are not exposed to the solvent. >From topology file

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 rece

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

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

[gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Dear Gromacs Users! I have problems during npt equilibration of my solvent box with the CCl4 solvent (I'm preparing this hydrophobic layer for further membrane-mimicking system). As the result I want to obtain density value ~ 1.5 for such box but between 2 and 3 ns ( where the desity was 1.3) o

[gmx-users] Steered MD simulation

Dear Gromacs Users! I'm investigating activation of the GPCRs receptor in the membrane Because of potentialy long time required for the activation of such receptors I want to perform some sort of steered MD simulation. For example I I want to change rotameric dihedrals of some important swith resi

[gmx-users] Extract Gro coordinate from trr trajectory

Dear Gromacs Users! I want to extract Gro coordinate file from the unclompleated MD simulation. I have big trr file and I'd like to obtain GRO coordinates wich correspond to the last simulation step on the current moment. How I could do it? James -- gmx-users mailing listgmx-users@gromacs

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Justin, Larger cutoffs would not only make the problem worse (read the error > message carefully and consider the minimum image convention), but it would > also potentially break the validity of the force field model. The vdW > cutoff for Gromos96 should be 1.4 nm, not 0.9 nm, in any case. Thi

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

ound Cutoff = 1.2. Why in that case you've used such uncommon values ? James 2012/2/5 Justin A. Lemkul > > > James Starlight wrote: > >> Justin, >> >> >>Larger cutoffs would not only make the problem worse (read the error >>message

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Justin, 2012/2/6 Justin A. Lemkul > > Some simple calculations using the desired density and the box dimensions > (to get the volume) will tell you exactly how many molecules you need. If > you only "suppose" you've got a reasonable number, there are better ways to > be sure ;) > > In accordan

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Justin, Firstly I've created the box of desired size with only 500 molecules ( I need 1000) Than I've tried to add extra 200 molecules by means of Genbox genbox -cp super_box.gro -ci Ccl4.gro -nmol 200 -o new_solv.gro but no molecules have been added Added 0 molecules (out of 200 requested) of

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

mollecules :( In other words I wounder to know if there is any way to add some extra molecules to the pre defined box to make my system more tighly packed ( to short distance between existing molecules and place new ones in the new space ) ? James 2012/2/14 Mark Abraham > On 14/02/2012 4

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

nt_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy How I could solve it? James 2012/2/14 James Starlight > Mark, > >

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

essibility = 4.5e-5 i'm using this compressibility value because I'm modelling the lipid-like environment so I think that I must increase pressure. Could you remind me the dependence of pressure from density and volume for liquids ? :) James 2012/2/14 James Starlight > It see

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

am > On 14/02/2012 11:01 PM, James Starlight wrote: > > This also was solved by the some extra minimisation steps. > > > I've forced with another problem :D > > During npt equilibration my system have slightly expanded so my desired > volume and density were pertur

Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

equilibration of the membrane-mimicking CCl4 layer To: Discussion list for GROMACS users On 15/02/2012 4:45 PM, James Starlight wrote: Mark, due to hight density the volume of my system have been slightly increased and during NPT phase I've obtained error Fatal error: One of the box v

[gmx-users] Placing ions in the specified positions

Dear Gromacs users! I've constructed my biphastic system with the water-ccl4-water layers where in the ccl4 layer I've placed my membrane protein. Now I'd like to place addition 5 Cl ions to the bottow leafleat of water to mimick the 'positive-inside rule' (my protein consist of 5 Lys) of the me

Re: Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

lue in the vdwradii.dat file. James 2012/2/16 Mark Abraham > On 16/02/2012 1:45 AM, James Starlight wrote: > > Mark, > > I've used that dimensions in accordance to some literature where the same > membrane-mimicking simulation were performed. > > I've tried t

Re: Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

pure Ccl4 and allow only change in 2 other dimensions ? 2) I have not found radius for Cl for Gromos56 ff. Is this possible to decrease that value during npt phase to obtain system with desired hight density? What value should I use? James 2012/2/16 James Starlight > Mark, > >

Re: Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Mark, The pure Ccl4 cube was expanded in X dimension during npt phase. By the way I've been able to prevent it by increasing the ref_p of X up to 5 ussing semiisotropic pcoupltype By when I've inserted peptide on the npt of that system my Ccl4 box was expanded on Z rapidly. Might this way to

Re: Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

By the way I also wounder to know how I could keep my system after equilibration. E.g I've equilibrated CCl4+water system and obtain stabile system on desired timescale. Than I've used genbox to merge my pre-oriented peptide with the pre-equilibrated system. genbox -cp peptide_newbox.gro -cs CC

Re: [gmx-users] Re: Placing ions in the specified positions

Dear all :) I have one extra question about Genion. I want to neitralise my system with the qtot - 1.550002e by placing some Na and Cl ions under the physiological concetrantion 100 mmol/l I've performed genion -s ions.tpr -o b2ar_ions.gro -p topol.top -pname NA -nname CL -conc 0.1 -neutral bu

[gmx-users] Protonation state of the ionisable residues

Dear Gromacs Users! I'd like to change default protonation state of some specified Glu and Asp residues im my protein. By defaylt pdb2gmx -ignh create unprotonated state of the negatively charged residues but I want to make 2 of such residues protonated to mimick some intermollecular interactio

Re: [gmx-users] Protonation state of the ionisable residues

ing of the termi as well as changing of protonated state of that fragments. What advantages might have such capping of the termni of that protein? James 2012/2/22 Justin A. Lemkul > > > James Starlight wrote: > >> Dear Gromacs Users! >> >> >> >> I'd l

[gmx-users] Internal water in the membrane receptor

Dear Gromacs Users! I want to perform simulation of the membrane receptor in the membtane environment. There are some evidence about precense of the functional-relevant internal water mollecules in the transmembrane alpha-helix bundle of the receptor. I want to take into account that internal wa

[gmx-users] Re: Internal water in the membrane receptor

Up! :) Please provide me with the best sollution of my problem! I just want to copy some water mollecules from X-ray structure to my model and place it in the identical possitions inside the TM budle of my protein. What are the most trivial way to solve this task? James 2012/2/22 James

Re: [gmx-users] Re: Internal water in the membrane receptor

e chains of the residues wich are in contact with the new waters Might this aproach be usefull? Commonly I use it to prepare protein-ligand complexes. James 2012/2/24 Mark Abraham > On 24/02/2012 6:31 PM, James Starlight wrote: > > Up! :) > > Please provide me with the best s

Re: [gmx-users] Re: Internal water in the membrane receptor

Mark, So as I understood the ussage of X-ray structure as the starting model where the internal water is already present might be good in case to avoid those sterric issues doesn't it ? What are additional options should I use for preparation of such system with pdb2gmx ? Should I use posres on

Re: [gmx-users] Re: Internal water in the membrane receptor

s in the GRO file. Why this error might occur? my topology ; Include X-ray water topology #include "XW.itp" ; Include Position restraint for XW #ifdef POSRES_XW #include "posre_XW.itp" #endif my mdp define= -DPOSRES_XW integrator= steep James 2012/2/25 Ma

Re: [gmx-users] Re: Internal water in the membrane receptor

Justin, 2012/2/25 Justin A. Lemkul > > > > You likely have a [settles] directive applied the the XW molecules > (crystal waters, yes?) and SOL. You can't do that. The block of molecules > to which [settles] are applied must be continuous. You'll have to replace > the [settles] directive in XW

Re: [gmx-users] Re: Internal water in the membrane receptor

Mark, I've found a possible sollution to restrict oxygens of my X-ray water by possible plasing the below string in the TOPOLOGY.top of my system ; Include X-ray water topology #include "XW.itp" ; Include Position restraint file #ifdef POSRES_XW [ position_restraints ] ; i funct fcx

[gmx-users] Distance between selected atoms during simulation

Dear Gromacs Users! I want to perform measurements of the distances between backbone as well as side-chain atoms of the selected residues using gro and trajectory files. What Gromacs program should I use for such measurements? James -- gmx-users mailing listgmx-users@gromacs.org http://li

[gmx-users] Generation of the Distance Restraints

Dear Gromacs users! I want to perform constrained MD simulation of my protein with inclusion of some experimental restraints. 1) I found that genrest cpmmand could be usefull for the generation of the distance restrictions wich I could use in my constrined simulation. Also in manual I've found

Re: [gmx-users] Generation of the Distance Restraints

ou can make an index file using make_ndx where you specify > the atoms you want to restraint. > Hope this can help. > Francesca > > 2012/3/12 James Starlight : > > Dear Gromacs users! > > > > > > I want to perform constrained MD simulation of my protein

Re: [gmx-users] Generation of the Distance Restraints

ble ? Should I obtain value for the initial Ca-Ca distance between my residues from the initial structure? How I could do it? James 12 марта 2012 г. 18:38 пользователь Justin A. Lemkul написал: > > > James Starlight wrote: > >> Francesca, >> >> Yes

Re: [gmx-users] Generation of the Distance Restraints

Justin, 1) I've already tried to examine this graphs but have not understood the meaning of the Ro value. E.g I have known distance restrains for the pair of residue wich are 1написал: > > > James Starlight wrote: > >> Mark, Justin, >> >> Thanks for advis

Re: [gmx-users] Generation of the Distance Restraints

Mark, > Anything else you've known and understood about distance restraints in > some unknown context doesn't matter. What's written in the GROMACS > manual matters for using them in GROMACS :-) > So because I'm not quite understood those equations I could not properly define my restrains (wich

Re: [gmx-users] Generation of the Distance Restraints

Mark, thanks for explanation. So if I understood that graph correctly I must define R1=1 and R2=2 values from my example 1написал: > > > I can't think of a clearer way to explain the functional form of the > distance restraint than the given equation with an example graph of it > nearby. You have

Re: [gmx-users] Generation of the Distance Restraints

to define restraines based on the BONDS enty in the topology file. Could you provide me with the more information about this simpler way ? Thanks for help again, James 14 марта 2012 г. 10:50 пользователь James Starlight написал: > Mark, thanks for explanation. > > So if I understoo

Fwd: [gmx-users] Generation of the Distance Restraints

but in the absence of a command > line and your .top file fragment, we can't possibly know. > > > Mark > > > > Thanks for help again, > > > James > > 14 марта 2012 г. 10:50 пользователь James Starlight < > jmsstarli...@gmail.com> написал: &g

Re: Fwd: [gmx-users] Generation of the Distance Restraints

der ? I've recieved errors about wrong PME order when tried to lauch my simulations on big ammoun of the nodes but could not find possible way to fix it :( James 14 марта 2012 г. 19:43 пользователь Justin A. Lemkul написал: > > > James Starlight wrote: > >> Mark, >>

[gmx-users] Problems with simulation on multi-nodes cluster

Dear Gromacs Users! I have some problems with running my simulation on multi-modes station wich use open_MPI I've launch my jobs by means of that script. The below example of running work on 1 node ( 12 cpu). #!/bin/sh #PBS -N gromacs #PBS -l nodes=1:red:ppn=12 #PBS -V #PBS -o gromacs.out #PBS

Re: [gmx-users] Generation of the Distance Restraints

Mark, thanks again for explanation > The force is the negative of the derivative of the potential with respect > to the distance. So the force is also zero between r_0 and r_1. So if you > want a distance to be restrained between 1 and 2 nm, set r_0=1 and r_1=2. > That way the force is zero if

Re: [gmx-users] Problems with simulation on multi-nodes cluster

the scheduler run it). >> > > grompp is running successfully, as you can see from the output > > I think "mpiexec -np 12" is being interpreted as "mpiexec -n 12 -p", and > the process of separating the grompp stage from the mdrun stage would help > make that

Re: [gmx-users] Generation of the Distance Restraints

> 2) Also I've found that there is more simple way to define restraines > based on the BONDS enty in the topology file. Could you provide me with the > more information about this simpler way ? > > > Simpler, but not a restraint to within a region. The manual section we are > discussing links you t

Re: [gmx-users] Problems with simulation on multi-nodes cluster

hing wrong with parameters of my simulation? JAmes 15 марта 2012 г. 15:25 пользователь James Starlight написал: > Mark, Peter, > > > I've tried to do .tpr file on my local CPU and launch only > > mpiexec -np 24 mdrun_mpi_d.openmpi -v -deffnm MD_100 > > on the cluster wi

Re: [gmx-users] Generation of the Distance Restraints

This days I tested some distance restrains applied on my protein. I had some literature data from wich I've used such restrains as well as similar wirk where authors applied this data on the same protein to view some biological-relevant event :) I've applied my restrains gradually to rise force f

[gmx-users] Principal Components Analysis in Gromacs

Dear Gromacs Users! I have some questions about PCA implemented in Gromacs. 1- I want to increase amplitude of the motions seen on the selected PCs but I can't found scalling factor option for that. 2- I have calculated MD trajectory for my protein. From this trajectory I want to find some r

Re: [gmx-users] Generation of the Distance Restraints

Mark, This sounds like I use very small forces but expect reasonable effect. But I've applied different forces with step-by-step increasing of force constants ( from very softest comparable with the thermal motion ( 0.1 kj mol nm-2) to relatively hight (10). As the consequence I've observed effec

Re: [gmx-users] Principal Components Analysis in Gromacs

Hi Tsjerk! First, I'd like also thanks you for your help. Today I tried to make PCA of my X-ray data as well as comparison between results of such PCA and EDA ( PCA wich is based on the MD trajectory of the same protein). In generaly I have no any problems with the X-ray PCA but I've forced wi

Re: [gmx-users] Generation of the Distance Restraints

Mark, thanks for explanation again. 28 марта 2012 г. 16:04 пользователь Mark Abraham написал: That can mean big restraint forces and tiny integration steps and lots of > tweaking and praying. > Yes I think this aproach could be usefull in my case. Actually I want to move some parts of the he

[gmx-users] Editing of the existing system

Dear Gromacs Users! I have some system wich consist of protein in membrane-mimicking layer surrounded by water. I want to modify my existing system by adding small peptide fragment to this system. I want to dock this peptide to the some part of my protein wich is situated in the bottom water lay

Re: [gmx-users] Editing of the existing system

Mark, Also I'd like to know some more about most correct parametrisation of such new edited system. My new system consist of two proteins ( one- wich was initially and the second small peptide wich I've docked to the first protein). So now I need to define 2 separate groups for the below enties o

Re: [gmx-users] Editing of the existing system

ition of the second protein to my system I've resolvated my system again). Might my system be not properly minimized or does something wrong else in addition? James 31 марта 2012 г. 2:20 пользователь Mark Abraham написал: > On 31/03/2012 1:00 AM, James Starlight wrote: > > Mark,

Re: [gmx-users] Editing of the existing system

Justin, I've minimised my system to emtool=1.0 but the error still occurs 31 марта 2012 г. 16:27 пользователь Justin A. Lemkul написал: > > Separate COM motion removal groups are tricky. I'm still not completely > clear on what your system looks like, but if you've got two proteins in two > la

Re: [gmx-users] Editing of the existing system

Justin, 31 марта 2012 г. 18:18 пользователь Justin A. Lemkul написал: > > Start by inspecting the initial configuration in the vicinity of these > atoms. Something is likely clashing here. Yes, I've checked both of the proteins and found that the problem atoms were situated exactly in the docke

Re: [gmx-users] Editing of the existing system

eck this results too and attach all logs here. Many thanks again for help James 31 марта 2012 г. 21:57 пользователь Justin A. Lemkul написал: > > > James Starlight wrote: > >> Justin, >> >> 31 марта 2012 г. 18:18 пользователь Justin A. Lemkul > jalem...@vt.

Fwd: [gmx-users] Editing of the existing system

un minimisation in vacuum as you've told me but this results would be aviable tomorrow. Could you tell me whats exactly wrong with that system and is there possible ways to fix the problem? Thanks for help James 31 марта 2012 г. 22:05 пользователь James Starlight написал: Justin, > &

Re: [gmx-users] Editing of the existing system

could not to resolve such crushes. Thanks again James 1 апреля 2012 г. 21:37 пользователь Justin A. Lemkul написал: > > > James Starlight wrote: > >> Justin, >> >> Sorry again for the delay. >> >> I've finished minimise my system with the CG

Re: [gmx-users] Problems with simulation on multi-nodes cluster

льзователь Mark Abraham написал: > On 20/03/2012 10:35 PM, James Starlight wrote: > >> Could someone tell me what tell the below error >> >> Getting Loaded... >> Reading file MD_100.tpr, VERSION 4.5.4 (single precision) >> Loaded with Money >> >> >

Re: [gmx-users] Editing of the existing system

gestions or should I start with another conformation of first protein ? James 2 апреля 2012 г. 9:56 пользователь James Starlight написал: > Justin, > > Thanks again for attention to my problem. > > > I've checked my system and found that the problem was exactly in the 1

[gmx-users] Simulation in the high temperature conditions

Dear Gromacs users! I want to perform simulation of the membrane protein in the Ccl4-membrane-mimicking interiour in the increaced ( up to 600 K) temperature on the nvt ensemble. As the consequence I'd like to protect the temperature caused destabilisation of my protein and simulate native-like

[gmx-users] Re: Simulation in the high temperature conditions

methodology require several mdp files with slightly different ref_t as well as gen_temp options ? Finally what exactly is tau_t time constant? James 3 апреля 2012 г. 13:14 пользователь James Starlight написал: > Dear Gromacs users! > > > I want to perform simulation of the membrane protein i

Re: [gmx-users] Re: Simulation in the high temperature conditions

Justin,thanks! 1) For example for the situation presented in manual for 2 groups with 3 and 4 points the time enty should be annealing_time = 0 3 6 0 2 4 6 from this I've understood that 0 value is the start of timer for each group and subsequent values are the actual time in the ps, havennt it

Re: [gmx-users] Re: Simulation in the high temperature conditions

annealing equilibration I want to simulate my system on the high temperature condition for efficient conformation sampling. Might it be that initial high velocities could be usefull for such sampling efficacy? James 4 апреля 2012 г. 17:25 пользователь Justin A. Lemkul написал: > > > Ja

[gmx-users] Monitoring of Salt bridges during simulation Run

Dear Gromacs Users! I'd like to monitor origin and destabilisation of salt-bridges during simulation time. In particular I want to define some charged residues within selection groups to monitor both of intra-protein as well as protein-protein interactions. In past I've used only g_hbond

Re: [gmx-users] Monitoring of Salt bridges during simulation Run

only Rmin but could I define Rmax cutoff as well? James * 5 апреля 2012 г. 12:36 пользователь Peter C. Lai написал: > g_saltbr? > > If you have salt bridges you already know about and want to look at, you > can always go with g_dist per pair manually. > > On 2012-04-05 12:23:02PM

[gmx-users] MD after equilibration phase

Dear Gromacs users! I have small question about order of the runs and input data. Ussually I do 2 equilibration phases and subsequent productive phase in the conditions wich are equal to the last equilibration phase ( e.g often this is npt ). In the second equil.mdp and md.mdp there is option

Re: [gmx-users] Re: Simulation in the high temperature conditions

_CCl4 SOL_NA_CL_XW where XW is the water observed in the X-ray structure of that protein ( I've defined that mollecules in separate layer) Thanks for help James 4 апреля 2012 г. 18:14 пользователь Justin A. Lemkul написал: > > > James Starlight wrote: > >> Justin, >&g

Re: [gmx-users] Re: Simulation in the high temperature conditions

Mark, > If you make your layer boundaries perpendicular to some axis then you can > use position restraints on water oxygens that have non-zero force constants > only with respect to that axis. Then relax the water position restraints > before any others. > > Yes, I've thought about this to appl

Re: [gmx-users] Re: Simulation in the high temperature conditions

Mark, > Assuming you're raising your temperature during equilibration and then > running at high temperature, then you don't want water moving into the > receptor interior during equilibration for the same reason you didn't want > water moving into the CCl4. And you're going to run further equ

Re: [gmx-users] Re: Simulation in the high temperature conditions

Lemkul написал: > > > James Starlight wrote: > >> Mark, >> >> >> >> >> >>Assuming you're raising your temperature during equilibration and >>then running at high temperature, then you don't want water moving >>into

Re: [gmx-users] Re: Simulation in the high temperature conditions

Justin, 10 апреля 2012 г. 16:21 пользователь Justin A. Lemkul написал: > > I have never used the bd integrator so I cannot offer any help here. I > don't see any magical reason why you should expect it to enhance sampling > though. I've found in the literature that this integrator could rise

Re: [gmx-users] Re: Simulation in the high temperature conditions

Justin, I have not quite sure about methodology of aplication of such harmonic distance restrains yet. E.g I want to constraint distancec of the backbone atoms of my protein within 7 A ( to allow deviation of all backnones up to 7 A) I've tried genrestr -f start.gro -n index.ndx -disre -disre_

Re: [gmx-users] Re: Simulation in the high temperature conditions

Tsjerk, Thank you for suggestions! Indeed the hight temperature ( I'm using 700K) which I use for enhansing sampling rate resulted in destabilisation of the secondary structure. To prevent this I've used two slightly different aproaches based on the restraint. But in both cases I've used sligh

Re: [gmx-users] Re: Simulation in the high temperature conditions

evance of your results? > > Cheers, > > Tsjerk > > On Wed, Apr 11, 2012 at 12:01 PM, James Starlight > wrote: > > Tsjerk, > > > > Thank you for suggestions! > > > > > > Indeed the hight temperature ( I'm using 700K) which I use for enhansi

Re: [gmx-users] Re: Simulation in the high temperature conditions

tried :p Nonetheless, applying local restraints to > maintain integrity and use an elevated temperature to enhance > conformational sampling, might actually also be a valuable approach. > Good luck :) > > Tsjerk > > On Wed, Apr 11, 2012 at 8:27 PM, James Starlight > wrote: &

[gmx-users] Simulation of the pure lipid bilayer

Dear Gromacs Users! I want to perform simulation of the pure bilayer surrounded by water. I'm using already pre-equilibrated bilayers as the initial structure. During conversion pdb-> gro -> pdb the velocities from initial equilibration runs of the structure were lost. Should I start generating t

Re: [gmx-users] Re: Simulation in the high temperature conditions

Dear Gromacs Users! By that moments I've completed 2 sets of simulation in high temperature 1- With applied posres on the backbone atoms ( fc= 200 ). The result was- that the posres prevented motion of the helixes as the rigid bodies so I've not noticed any conformation sampling. Question : Cou

Re: [gmx-users] Re: Simulation in the high temperature conditions

ively current confrmation ? James 16 апреля 2012 г. 15:05 пользователь Justin A. Lemkul написал: > > > James Starlight wrote: > >> Dear Gromacs Users! >> >> By that moments I've completed 2 sets of simulation in high temperature >> >> 1- With applied

Re: [gmx-users] Re: Simulation in the high temperature conditions

апреля 2012 г. 17:36 пользователь Justin A. Lemkul написал: > > > James Starlight wrote: > >> Justin, >> >> >> I've applied disres on each backbone atom of my potein within cutoff >> distance of 1nm ( Rc=1.0 nm). I've selected this value for cutoff to >

Re: [gmx-users] Re: Simulation in the high temperature conditions

lations. Thanks for help again, James 16 апреля 2012 г. 18:09 пользователь Justin A. Lemkul написал: > > > James Starlight wrote: > >> Justin, >> >> >> Thank you for explanation. Tomorrow I'll try to check results of >> simulation with the disre

[gmx-users] Making Disulfide Bonds

Dear Gromacs Users! I have a model of my protein wich has 4 S-S bounds in the loop regions. So I want to define in topology all those four S-S linkage. Unfortunatelly one of that S-S have not been recognised by Gromacs ( Also I've tried to check this bond in pymol and found that distance between

Re: [gmx-users] Making Disulfide Bonds

te the topology. > > Francesco > > 2012/4/28 James Starlight > >> Dear Gromacs Users! >> >> I have a model of my protein wich has 4 S-S bounds in the loop regions. >> So I want to define in topology all those four S-S linkage. >> >> Unfortunatelly

Re: [gmx-users] Making Disulfide Bonds

file ). As the result I have not noticed any perturbation in the distance between two S-S atoms the distance between wich I've constrained. 2012/4/28 James Starlight > Hi Francesco! > > So I must define in the current topology the disres bettwen two S atoms ( > in the below

Re: [gmx-users] Making Disulfide Bonds

ustin A. Lemkul > > > On 4/28/12 10:08 AM, James Starlight wrote: > >> .. and the main question- what should be in mdp file of such restrained >> minimisation ? >> >> Today I've done vry properly minimisation of such system in vacuum with >> the CG >

Re: [gmx-users] Coordinate file for lipid bilayer

t FFs > which means the atom naming would not be immediately be compatible with > your FF; for example mine are built for charmm36 and would require atom > renaming for another FF, even charmm27. > > On 2012-05-26 11:24:12AM +0400, James Starlight wrote: > > Dear Gromacs Users!

[gmx-users] Measure of density in homo- and heterogeneous systems

Dear Gromacs users! In this task I have two systems: First system consist of single layer of Ccl4 molecules. Second system consist of membrane-mimicking layer of Ccl4 surrounded by water and the protein embedded in that biphastic layer. I'd like to measure density in both of my systems to chec

Re: [gmx-users] Measure of density in homo- and heterogeneous systems

Justin, the main problem is the my simulation in nvt ensemble :) I understand that density is constant in that conditions but I'd like to find way to check this values for different components of my system. James 2012/5/28 Justin A. Lemkul > > > On 5/28/12 3:09 PM, James S

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

imicks adjacent residues) it's difficult recognize suitable dihedral types. Do you know any others attemps to simulate GFP with chromophore in charmm with proof parameters ? James 2012/12/12, Justin Lemkul : > > > On 12/12/12 3:11 PM, James Starlight wrote: >> Justin, >> >

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

acuum and didnt notice any inaccuracy in the conformation of chromophore. So the last that I should is the carefull assignment of the 9 missed dihedral terms with the rest of the protein. James 2012/12/14, Justin Lemkul : > > > On 12/14/12 2:28 PM, James Starlight wrote: >> Today I

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

y the way If you had had your rtp of the chromophore which you've done in accordance to that paper could you provide me with them for comparison with my model ? James 2012/12/14, Justin Lemkul : > > > On 12/14/12 3:20 PM, James Starlight wrote: >> Justin, >> >> in

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