Re: [gmx-users] isopeptide bond

Dear Mark, Thank you for your help! Now it works! I made MD without errors. I changed N3 to N, add one additional [angletype] to .itp (HP CT N) and removed one of HZ1 from Lys that participate in isopeptide bond; made appropriate changes in .atp, .hdp, .rtp and specbond.dat. 2011/3/14 Mark Abra

Re: [gmx-users] isopeptide bond

On 15/03/11, Yulian Gavrilov wrote: > Dear Mark, > Thank you for your help! Now it works! I made MD without errors. > I  changed N3 to N, add one additional [angletype] to .itp (HP  CT  N) and > removed one of HZ1 from Lys that participate in isopeptide bond; made > appropriate changes in .at

Re: [gmx-users] isopeptide bond

Thanks! I understand it, but I had several errors about it. Without adding of (HP CT N) [angletype] it does not work. How to force it to take its type from its current environment, not its historical one? 2011/3/15 Mark Abraham > > > On 15/03/11, *Yulian Gavrilov * wrote: > > Dear Mark, > Tha

Re: [gmx-users] isopeptide bond

On 15/03/11, Yulian Gavrilov wrote: > Thanks! I understand it, but I had several errors about it. Without adding of > (HP  CT  N) [angletype] it does not work. How to force it to take its type > from its current environment, not its historical one? > > Your .rtp and .hdp specify the atom t

Re: [gmx-users] Re: installation of gromacs (Dommert Florian)

On Tue, 2011-03-15 at 05:53 +0100, Thomas Koller wrote: > > I have installed Gromacs but if I want to open another terminal and > run another simulation it does not work. You have to make sure, that the binaries and libraries installed in $GROMACS/bin and $GROMACS/lib are found by the terminal,

[gmx-users] Failure to preserve simulation temperature

Hi all, I have something here which I am would like to pick your brains. Thank you in advance. In my trial-and-error attempt to equilibrate my membrane protein system, I encountered this problem. I was playing with 2 different mdp files (in succession), first by using the Nose Hoover then v

Re: [gmx-users] Failure to preserve simulation temperature

NG HUI WEN wrote: Hi all, I have something here which I am would like to pick your brains. Thank you in advance. In my trial-and-error attempt to equilibrate my membrane protein system, I encountered this problem. I was playing with 2 different mdp files (in succession), first by usi

[gmx-users] Grandcanonical Ensemble

Dear All 1-Does Gromacs support Grandcanonical ensemble too? 2-I want to increase the length of my simulation box during simulation,Is it possible? 3-As a result.I want to do my simulation in grandcanonical in the following way: As the length of my simulation box is increasing,I want to full the

[gmx-users] Umberella sampling

Dear All afew question in umberella sampling tutorial: 1-We do umberella sampling for each of 25 simulation windows,while using a spring(harmonic potential),Are these springs 1 or 3 dimensional? 2-Suppose the length of one windows is X nm,what is the approperiate K (spring constant) for this wind

Re: [gmx-users] Grandcanonical Ensemble

On 16/03/11, mohsen ramezanpour wrote: > Dear All > > 1-Does Gromacs support Grandcanonical ensemble too? > No. The number of particles is fixed at grompp time. > 2-I want to increase the length of my simulation box during simulation,Is it > possible? > Only via pressure-coupling. > 3

[gmx-users] Pulling

Dear All Afew question about Pulling in Umberella Sampling 1-the goal of pulling is making some primary structures (in different distances) to do umberella sampling for each one of them. I can make these states by transporting my ligands along a vector to prepare these primary structures.Is this

[gmx-users] pull forces

Dear all, does anybody know what the forces that are saved in the f*xvg files from the pull-code actually are? are these: 1) the (sum of the) forces due to the normal non-bonded interactions in the system acting on the ref and the the full groups. 2) only the forces from the harmonic restrain

[gmx-users] Re: surface tension

Dear Elisabeth, PBC are still there when you increase the box length in one direction, but that increase creates an empty region between the periodic images. provided the empty region is large enough (larger than cutoff values, for instance), periodicity no longer affects the system during a typic

[gmx-users] Pulling

1. yes. it is acceptable. It is different, but neither method is de facto better. 2. to enhance convergence by limiting the amount of phase space that must be sampled. Changing the restraints can change the profile, but if you care only about the integrated standard binding free energy th

[gmx-users] Umberella sampling

1. Depends on how you set them in your .mdp file. It could be either. 2. There is no general method. Use trial and error. Also, your question is flawed, K defines X. Unless by "length of one windows" you meant the distance between neighbouring centers of restraint (umbrellas). 3. you need

[gmx-users] LINCS and number of nodes

Dear experts, I am trying to build up a polymer in hexane system by increasing the density. After PR step, my NVT and NPT trailes failed. Initially I used to get LINCS and 1-4 warnings (even for NVT) which were not because of flawed topology file. It turned out that simulations crashed just becaus

Re: [gmx-users] LINCS and number of nodes

Moeed wrote: Dear experts, I am trying to build up a polymer in hexane system by increasing the density. After PR step, my NVT and NPT trailes failed. Initially I used to get LINCS and 1-4 warnings (even for NVT) which were not because of flawed topology file. It turned out that simulations

[gmx-users] Re: pull forces

Message: 5 Date: Tue, 15 Mar 2011 07:17:28 -0700 (PDT) From: Michael Brunsteiner Subject: [gmx-users] pull forces To: gmx users Message-ID:<613152.30411...@web120517.mail.ne1.yahoo.com> Content-Type: text/plain; charset=us-ascii Dear all, does anybody know what the forces that are saved in the

Re: [gmx-users] g_order for DPC alkyl chain in the micelle

Hi very recently I faced the same problem with a system that gives micelles of different geometries and, as far as I saw, g_order don't do that. Then I decided to compute a kind of local order parameters defined as: S_i=(3 cos(\theta)-1)/2 where theta is the angle between the segments joining th

[gmx-users] Forces with Constraints

Hello GROMACS users, I am trying to compute PMF profile for water by integrating the force profile along a given direction. I take the forces directly from MD. I am using SETTLE for constraining the geometry of water molecules (SPC/E model). My question is that do these forces include the constrai

[gmx-users] OPLS forcefield for Alkane and ethers?

Hi, I was wondering whether OPLS supports force-field for alkane chain or ethers . One of the molecule I am looking forward to using is ethylene glycol ( CH2-O-CH2-O-CH2 ). But, I was wondering whether it is available in OPLS forcefield . Any help will be appreciated . Sanku -- gmx-

Re: [gmx-users] OPLS forcefield for Alkane and ethers?

On 2011-03-15 21.30, Sanku M wrote: Hi, I was wondering whether OPLS supports force-field for alkane chain or ethers . One of the molecule I am looking forward to using is ethylene glycol ( CH2-O-CH2-O-CH2 ). But, I was wondering whether it is available in OPLS forcefield . Any help will be appre

Re: [gmx-users] OPLS forcefield for Alkane and ethers?

Sanku M wrote: Hi, I was wondering whether OPLS supports force-field for alkane chain or ethers . One of the molecule I am looking forward to using is ethylene glycol ( CH2-O-CH2-O-CH2 ). But, I was wondering whether it is available in OPLS forcefield . Practically speaking, if you can d

[gmx-users] Replacing a residue and continuing a simulation run

Hello all, I was wondering, is it possible to replace a residue and then continue a simulation using the new parameters/geometry of the new residue? The reason I ask is that I am interested in performing simulations of proteins with tryptophan in its excited state following a lengthy equilibration

Re: [gmx-users] Replacing a residue and continuing a simulation run

J. Nathan Scott wrote: Hello all, I was wondering, is it possible to replace a residue and then continue a simulation using the new parameters/geometry of the new residue? The reason I ask is that I am interested in performing simulations of proteins with tryptophan in its excited state follow

Re: [gmx-users] g_wham PMF profile

The reliability of the PMF curve depends on the reliability of sampling. If you're over-sampling in some regions along the reaction coordinate and under-sampling in others, then the weighting is probably wrong and the result inaccurate. I can't tell exactly from your description what's go

Re: [gmx-users] Zero Potential of Mean Force with g_wham

Hi, please use g_wham 4.5.2 or later. We largely updated g_wham recently. If you get a flat PMF, check the warnings that g_wham gives you and --very important-- look at the histograms. That usually gives you a clue where the histograms to not overlap. In case you find a bug, please let me kn

[gmx-users] (no subject)

Hi, I have got a situation and I don't know how to cope with it. I carried out a simulation in gromacs 4.5.3 and the objects are protein, rna, water...The idea is that one atom part of rna has to create an h-bond with a water molecule, which at the same time makes h-bonds with aminoacids of the bin

[gmx-users] Pull Error message

Hi, I'm running MD on a 30x30x7,5nm system in which I pull two proteins away from each other. I have successfully pulled them apart to 9.4nm. But when I now use a pull_init1 = 9.59 pull_start = no pull_rate1 = 0 pull_dim = Y Y Y At one point, I get the following error message

Re: [gmx-users] (no subject)

Алексей Раевский wrote: Hi, I have got a situation and I don't know how to cope with it. I carried out a simulation in gromacs 4.5.3 and the objects are protein, rna, water...The idea is that one atom part of rna has to create an h-bond with a water molecule, which at the same time makes h-bo

Re: [gmx-users] LINCS and number of nodes

On 16/03/11, Moeed wrote: > Dear experts, > > I am trying to build up a polymer in hexane system by increasing the density. > This seems to have been taking months. Why aren't you using genbox on your polymer starting configuration and an equilibrated box of hexane of the right density? M

[gmx-users] g_membed tool

Dear all.. I am using g_membed tools to embed the protein into lipid membrane. I read that before doing g_membed we need to run a short run with some options in .mdp files. what are the steps do we need to do before g_membed. It is given that box size should be taken from the membrane strucutu

[gmx-users] Pressure Fluctuations

Dear users, Upon was trying to simulate an npt ensemble (protein in water), pressure was coupled using parinello rahman system with tau_p = 2, tau_t = 1; compressibility 4.5e-5, type = isotropic. (cut off scheme (vdw_type = switch; rvdw = 1.0; rvdw_switch = 0.9; rcoulomb = 1.2; rlist = 1.2). No

Re: [gmx-users] Replacing a residue and continuing a simulation run

Hi :) I'd say that if the changes are small you should be able to get away with it. You might want to start off the second part of the run with a smaller time step to relax, though. If the change is from TRP to TRP*, you only need to have a modified topology, without touching the coordinates. You

[gmx-users] g_hbond output

@ legend length 2 @ s0 legend "Hydrogen bonds" @ s1 legend "Pairs within 0.35 nm" 0 0 0 200 0 0 400 2 1 600 0 3 800 0 2 1000 1 0

[gmx-users] Re: g_hbond output

@ legend length 2 @ s0 legend "Hydrogen bonds" @ s1 legend "Pairs within 0.35 nm" 0 0 0 200 0 0 400 2 1 600 0 3 800 0 2 1000 1 0

Re: [gmx-users] Pressure Fluctuations

On 16/03/11, Kavyashree M wrote: > Dear users, > > Upon was trying to simulate an npt ensemble (protein in water), > pressure was coupled using  parinello rahman system with tau_p = 2, > tau_t = 1; compressibility 4.5e-5, type = isotropic. > > (cut off scheme (vdw_type = switch; rvdw = 1.0; r