Re: [gmx-users] How to construct user specified bond potential

2010-12-07 Thread Jia Haitao
Manual section 4.2.13 maybe not enough. My potential functional shape is much more complex. I need at least two different force constants as C6 and C12 in LJ potential function in section 6.7.2. I use this for block copolymer system. There is only two types of monomer(e.g. A, B) and two types of bo

Re: [gmx-users] pdb2gmx and atomtype.atp

2010-12-07 Thread Justin A. Lemkul
Justin A. Lemkul wrote: Please file a bugzilla, uploading all of the input files needed to reproduce the problem. It appears that you can cause LP2 to be assigned an LP type if it is the first line in atomtypes.atp, but the mass and charge are still nonsense. Certainly you can manually mod

Re: [gmx-users] neutral plasma

2010-12-07 Thread Mark Abraham
On 8/12/2010 4:52 AM, Igor Marques wrote: Hello everybody, I've digging around the user manual, the website and the mailing list archives and I'm afraid I might be missing something: does GROMACS have some kind of /neutral plasma /as AMBER does? You're probably referring to some descriptions

Re: [gmx-users] NVE simulation and pressure scaling in one dimension and constant size simulation in another.

2010-12-07 Thread Justin A. Lemkul
zhongjin wrote: Hi all, I want to know how to set a NVE simulation ? Now I can do a NVT or NPT simulation. tcoupl = no pcoupl = no http://www.gromacs.org/Documentation/Terminology/NVE How to realize pressure scaling in one dimension and constant size simulation in another? For ex

Re: [gmx-users] NVE simulation and pressure scaling in one dimension and constant size simulation in another.

2010-12-07 Thread Mark Abraham
On 8/12/2010 1:30 PM, zhongjin wrote: Hi all, I want to know how to set a NVE simulation ? Now I can do a NVT or NPT simulation. It's the default, simply use neither T nor P coupling. How to realize pressure scaling in one dimension and constant size simulation in another? For exa

[gmx-users] NVE simulation and pressure scaling in one dimension and constant size simulation in another.

2010-12-07 Thread zhongjin
Hi all, I want to know how to set a NVE simulation ? Now I can do a NVT or NPT simulation. How to realize pressure scaling in one dimension and constant size simulation in another? For example,the simulation box size in the z-direction was adjusted to maintain the constant pressure, whil

Re: [gmx-users] Calculate ion disasociation constant

2010-12-07 Thread Mark Abraham
On 7/12/2010 6:34 PM, גדעון לפידות wrote: Hi all, Does anyone know of way I can use Gromacs to calculate the disasociation constant of a calcium ion held by two loops in a protein in water simulation? my starting point was a pdb file of the protein with the bound ions in place. Eventually I wo

Re: [gmx-users] Replacing charges of a residue, pdb2gmx -rtpo alternative?

2010-12-07 Thread Mark Abraham
On 8/12/2010 4:07 AM, J. Nathan Scott wrote: Hello all! I spent some time searching the archive and can't find an answer to this question. Is there a replacement for the -rtpo option for pdb2gmx? This option is mentioned in the v 4.5.3 (the version I am using) manual (pg 115) but does not seem to

Re: [gmx-users] what is the "nicelevel" ?

2010-12-07 Thread Linus Östberg
The nicelevel is simply the priority of the process, where 19 is the lowest priority (ie most other programs will use the cpu before the gromacs process does) and -20 the highest. See man nice. // Linus On Tue, Dec 7, 2010 at 10:13 PM, GZ Zhang wrote: > Hi, ALL >      I'm using "genbox" to crea

Re: [gmx-users] what is the "nicelevel" ?

2010-12-07 Thread Justin A. Lemkul
GZ Zhang wrote: Hi, ALL I'm using "genbox" to create a water box. There is a flag called "-nice" which is described to be used to set the nicelevel. What is nicelevel ? What does the default value "19" mean ? What if I Google is your friend here. would like to increase the decimal pl

[gmx-users] what is the "nicelevel" ?

2010-12-07 Thread GZ Zhang
Hi, ALL I'm using "genbox" to create a water box. There is a flag called "-nice" which is described to be used to set the nicelevel. What is nicelevel ? What does the default value "19" mean ? What if I would like to increase the decimal places (the default is 3) of all numbers. Thanks.

[gmx-users] neutral plasma

2010-12-07 Thread Igor Marques
Hello everybody, I've digging around the user manual, the website and the mailing list archives and I'm afraid I might be missing something: does GROMACS have some kind of *neutral plasma *as AMBER does? Or every simulation must have a net charge of 0.000 ? Best regards, Igor Marques -- g

[gmx-users] Entropy by total atoms

2010-12-07 Thread nahren manuel
Dear Gromacs Users, I am calculating entropy from QHA and Schlitters formula to determine the entropy change in my proteinA-proteinB complex. Since proA and proB are quite different in terms of number of residues, I am little confused if I should divide the entropy value with the number of atoms

[gmx-users] Replacing charges of a residue, pdb2gmx -rtpo alternative?

2010-12-07 Thread J. Nathan Scott
Hello all! I spent some time searching the archive and can't find an answer to this question. Is there a replacement for the -rtpo option for pdb2gmx? This option is mentioned in the v 4.5.3 (the version I am using) manual (pg 115) but does not seem to work, and yields the error "Invalid command li

[gmx-users] profile

2010-12-07 Thread Gavin Melaugh
Hi all I have recently generated a PMF curve for pulling a guest molecule into a host. The curve for this process appears fine. Analysis of the histograms are also fine except that some histograms are not centred on their r0 values in the barrier region. To circumvent this I increased the force c

Re: [gmx-users] How to construct user specified bond potential

2010-12-07 Thread Justin A. Lemkul
Jia Haitao wrote: Hello, everyone In gromacs user manual 6.7, they form non-bond potentials using table files, What should I do if I want to use a new *Bond* potential? The new bond potential combines two harmonic bond potentials, Vb(r)=0.5K1(r-b1)^2+0.5K2(r-b2)^2. The first part is a sta

[gmx-users] How to construct user specified bond potential

2010-12-07 Thread Jia Haitao
Hello, everyone In gromacs user manual 6.7, they form non-bond potentials using table files, What should I do if I want to use a new *Bond* potential? The new bond potential combines two harmonic bond potentials, Vb(r)=0.5K1(r-b1)^2+0.5K2(r-b2)^2. The first part is a standard harmonic potential.

Re: [gmx-users] conversion of gromacs files to amber files

2010-12-07 Thread Oliver Grant
Hi Leila, I would try the other suggested options like catdcd or vmd. The script is a pain and you would have to adapt it to work with DNA. It cost me a lot of time. I used g_hbond for residence time like this: g_hbond -f 8_fullMD_CA.xtc -s 7_fullMD.tpr -n g_hbond.ndx -a 170 -num > g_hbond.log

[gmx-users] reg compilation error in mopac gromacs

2010-12-07 Thread vidhya sankar
Dear gerrit sir,     thank you for your reply Here I have got compilation  error as follows /root/gromacs-4.5.3/src/mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac_SH': qm_mopac.c:(.text+0x2a7): undefined reference to `domop_' /root/gromacs-4.5.3/src/mdlib/

[gmx-users] Re:6. QMMM, Segmentation fault (Olga Ivchenko)

2010-12-07 Thread Gerrit Groenhof
Dera gromacs users, I am trying to do QMMM in the latest gromacs version :gromacs-4.5-beta2. When I run DFT I got an error: number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 Segmentation fault Are you tryin

Re: [gmx-users] Reg: Surface tension of water

2010-12-07 Thread André Farias de Moura
no surface, no surface energy, just that simple... check any colloid & surfaces textbook before you try to calculate surface tension (and read the manual as well, specially the section dealing with surface coupling) best Andra On Tue, Dec 7, 2010 at 9:28 AM, vinothkumar mohanakrishnan wrote: > No

Re: [gmx-users] conversion of gromacs files to amber files

2010-12-07 Thread Francesco Oteri
You can try using vmd. It has a powerful language selection and it can be used remotely. There is one disadvantage: the trajectory MUST fit into memory since vmd loads the trajectory into memory. If this is not the case, you can use the script "bigdcd" that permits to load one frame in memory

Re: [gmx-users] LJ Plot

2010-12-07 Thread ms
On 07/12/10 03:06, nishap.pa...@utoronto.ca wrote: Quoting ms : I did two different simulation. One with van der Waals attractive term and one without van der Waals attractive term. And so to see the difference between the LJ potential between the two simulation I wanted to plot the LJ potential

[gmx-users] conversion of gromacs files to amber files

2010-12-07 Thread leila karami
Dear Oliver very thanks for your help. Justin's perl script is good for direct hydrogen bonds, while I want to study water mediated hydrogen bonds and residence time and occupation of them. Are youe sure g_hbond give you residence time of hydrogen bonds? before you said you used a script to cha

Re: [gmx-users] Reg: Surface tension of water

2010-12-07 Thread vinothkumar mohanakrishnan
No.. i didn't do that. I just filled the box with 865 water molecules based on my number density calculations and the box size is 3.255*3.255*2.545 and performed energy minimisation followed by NVT and NPT equilibration. what should i do now to get the correct surface tension? Regards Vinoth 2010

Re: [gmx-users] Reg: Surface tension of water

2010-12-07 Thread André Farias de Moura
did you increase the size of the box in one direction in order to create a water/vacuum interface on each side of the water slab? best, Andre On Tue, Dec 7, 2010 at 8:21 AM, vinothkumar mohanakrishnan wrote: > Hi all > > I want to calculate the surface tension of water using SPC model of water. I

Re: [gmx-users] conversion of gromacs files to amber files

2010-12-07 Thread Shozeb Haider
I have previously used catdcd software for trajectory conversions between gromacs-Amber. Best Wishes Shozeb On 7 Dec 2010, at 10:57, "leila karami" wrote: > Dear Oliver Grant > > thanks for your attention. > > I want to use amber tool for hydrogen bond analysis especially (water > mediate

Re: [gmx-users] conversion of gromacs files to amber files

2010-12-07 Thread Oliver Grant
Hi Leila, I've done this with g_hbond and g_bond. If you search the forums there is a perl script available from Justin Lemakul that will do this for you. You can do it manually too if you have only a few to look at. Its a little tricky but a lot easier than traj conversion. :) I was able to get %

[gmx-users] conversion of gromacs files to amber files

2010-12-07 Thread leila karami
Dear Oliver Grant thanks for your attention. I want to use amber tool for hydrogen bond analysis especially (water mediated hydrogen bonds and residence time and occupation of them). -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Ch

Re: [gmx-users] conversion of gromacs files to amber files

2010-12-07 Thread Oliver Grant
I suppose it depends on what kind of analysis you would like to do... I'm not aware of any scripts for converting back from gmx into amber trajectories but I have done this before when doing an mmpbsa calculation using ambertools. As I only needed "snaphots" of the trajectory and not energies or ve

[gmx-users] Reg: Surface tension of water

2010-12-07 Thread vinothkumar mohanakrishnan
Hi all I want to calculate the surface tension of water using SPC model of water. I searched the mailing list and there is no post on the surface tension of water.I performed md simulation of 482 molecules of water in a triclinic box. I got the average surface tension value of water (300K) as 38.3

[gmx-users] Re: QMMM, Segmentation fault

2010-12-07 Thread Olga Ivchenko
Dear gromacs users, > > I am trying to do QMMM in the latest gromacs version :gromacs-4.5-beta2. > When I run DFT I got an error: > > number of CPUs for gaussian = 1 > memory for gaussian = 5000 > accuracy in l510 = 8 > NOT using cp-mcscf in l1003 > Level of SA at start = 0 > Segmentation fault

[gmx-users] QMMM, Segmentation fault

2010-12-07 Thread Olga Ivchenko
Dera gromacs users, I am trying to do QMMM in the latest gromacs version :gromacs-4.5-beta2. When I run DFT I got an error: number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 Segmentation fault Please could you

[gmx-users] Inaccurate time frame

2010-12-07 Thread Hsin-Lin Chiang
Hi, Mark, I'll adopt your suggestion. Thank you for your reply again. Sincerely yours, Hsin-Lin On 7/12/2010 6:01 PM, Hsin-Lin Chiang wrote: >/ />>/ Ah, sorry, I didn't read you well enough. />>/ />>/ I've just seen that GROMACS 4.5 introduced trjconv -round to address />>/ this kind of iss

Re: [gmx-users] Inaccurate time frame

2010-12-07 Thread Mark Abraham
On 7/12/2010 6:01 PM, Hsin-Lin Chiang wrote: Ah, sorry, I didn't read you well enough. I've just seen that GROMACS 4.5 introduced trjconv -round to address this kind of issue. I suppose you will find trjconv -round -split works for you. Mark Hi, Mark Thank you for your suggestion. I'm so