[gmx-users] g_hbond (v 3.14) vs g_hbond (3.3)

Dear Users, I have done clustering of equilibrium ensemble of octa-alanine model system, and when i was trying to find the no. of hydrogen bonds for each cluster, i found different result with different versions. Is there some bug to version 3.3 in comparison of version 3.14 or am i doing the wro

Re: [gmx-users] non-zero total charge for water

JMandumpal wrote: It says, System has non-zero total charge: -2.58e-01. [ molecules ] SOL 258 There's a pattern here. tip5P.itp file --- [ moleculetype ] ; molname nrexcl SOL2

[gmx-users] non-zero total charge for water

Dear Gromacs users, I built .tpr file prior to energy minimisation of box of tip5p water molecule. I received the output like this: calling /lib/cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 33252

Re: [gmx-users] Gel Phase in DMPC using Berger force field ??

What topology are you using? If you're using one based on the Kartunnen's group POPG (the only publicly available one I know of), then be aware that I think they saw gel phase too. Oh, and read the email you replied to, particularly the bit about 18 angstroms. - Original Message From:

[gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1

Dear users, I performed NPT simulations of few different systems using both gromacs v3.2.1 and v3.3.1. I use exactly the same parameters, starting files, topology files etc for both the versions. The systems are pure water system (10684 water molecules) and a protein-water system. However, the

Re: [gmx-users] Gel Phase in DMPC using Berger force field ??

I'm running MD at 300 K. I want fluid phase. On 12/13/07, Myunggi Yi <[EMAIL PROTECTED]> wrote: > > Dear Eric, > > I'm using Berger force field for DOPG (anionic head group). > Is is true for DOPG also? > > The following is my MD input. > I'm getting smaller area per lipid (~52 A^2) than expected

Re: [gmx-users] Gel Phase in DMPC using Berger force field ??

Dear Eric, I'm using Berger force field for DOPG (anionic head group). Is is true for DOPG also? The following is my MD input. I'm getting smaller area per lipid (~52 A^2) than expected (~62). What should I change? ** ; nblist cut-off rlist=

Re: [gmx-users] How to choose lipid molecules?

That depends entirely on the system you be simulating. In general you look at the type of membrane your system sits in and you try to match it with the lipids available. You also should look at the parameters that are available. Not all lipids are as good as they should. On Thu, 13 Dec 2007 22:4

Re: [gmx-users] How to choose lipid molecules?

liang wrote: > Dear all, > I am a freshman to membrane protein simulation, and i was wondering > how to choose lipid molecules for my system. > As we know, there are lots of lipid molecules: DMPC, DPPC, POPE. > but how do people decide that which type of lipid to use? and what > kinds of criter

[gmx-users] How to choose lipid molecules?

Dear all, I am a freshman to membrane protein simulation, and i was wondering how to choose lipid molecules for my system. As we know, there are lots of lipid molecules: DMPC, DPPC, POPE. but how do people decide that which type of lipid to use? and what kinds of criteria should we follow?

RE: [gmx-users] Re: Density Deferences between spc216 and tip4p

In TIP4P there is a fourth center (called M) close to the O atom. It reveals from the output that gromacs considers four atoms with this model but only three with SPC. If (this is a question) a mass is assigned to M in TIP4P, the density calculated by the PROGRAM must be larger than upon manual

Re: [gmx-users] Re: Density Deferences between spc216 and tip4p

[EMAIL PROTECTED] wrote: Dear Jochen, Sorry to bother you. I did not calculate the densities it is the program output!. Is this a bug?. Sorry to say that, but I don't have the feeling that it's my job to find the error in your calcuation... Regards Chandu Message: 8 Date: Thu, 13 Dec 2

Re: [gmx-users] trajectory concatenation

> Hi all, > I am doing some analysis with a 30 ns simulation of a 16 subunits > protein. > However, this simulation has two index files because of a stop in the > middle of simulation, index file 1 for 0ns-20ns and index file 2 for > 20ns-30ns. The same atoms in the two index files have differen

Re: [gmx-users] Re: Density Deferences between spc216 and tip4p

Chandu, It's clear you didn't do the calculations. Please do them yourself and see what answer you get for the density of 32885 water molecules in a box with volume 10^3 nm^3. Note also that there may be implicit assumptions underlying the value of the density provided by genbox, but it's the numb

[gmx-users] Re: Density Deferences between spc216 and tip4p

Dear Jochen, Sorry to bother you. I did not calculate the densities it is the program output!. Is this a bug?. Regards Chandu > Message: 8 > Date: Thu, 13 Dec 2007 10:28:02 +0100 > From: Jochen Hub <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Density Deferences between spc216 and tip4p > w

[gmx-users] trajectory concatenation

Hi all, I am doing some analysis with a 30 ns simulation of a 16 subunits protein. However, this simulation has two index files because of a stop in the middle of simulation, index file 1 for 0ns-20ns and index file 2 for 20ns-30ns. The same atoms in the two index files have different numbers. N

Re: [gmx-users] Density Deferences between spc216 and tip4p water models

[EMAIL PROTECTED] wrote: Dear All, I was trying create a box (cubic 10 10 10) of water. I am a bit surprised by looking at the density deferences between spc216 and tip4p water models. I am giving the brief output below. genbox -cs tip4p.gro -box 10 10 10 Output configuration contains 131540