[gmx-users] resolved pdm2gmx

Hi, I've written the Gromacs Mail list before, but I did not get the answer that I wanted. I am new user Gromacs. *1. I installed fftw-3.2.2 as following* a...@ab-desktop:~/Masaüstü/ cd fftw-3.2.2 a...@ab-desktop:~/Masaüstü/fftw-3.2.2 a...@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure --enable-th

[gmx-users] charmm tip5p in Gmx 4.5.2

Dear Gmxers, Does anyone have an idea about what time the Gmx 4.5.2 will be released?And in 4.5.2, would the modified tip5p.itp in charmm27 force field be the same as that in current git version? Thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mai

RE: [gmx-users] Dispersion correction in a heterogeneous system

Hi, I think you are looking at the wrong issue. Unless your concentration is ridiculously high, the dispersion heterogeneity will be irrelevant. Furthermore, at distances were the correction works, the distribution will be close to homogenous. But you do have an issue with dispersion correction

Re: [gmx-users] numerical matrix from xpm file

No, there's no ability to do this. I think there should be, though, and seem to recall discussion of it on one or other mailing list or the web page. Mark - Original Message - From: Anupam Nath Jha Date: Saturday, October 2, 2010 21:32 Subject: [gmx-users] numerical matrix from xpm file

Re: [gmx-users] Reg: Putting molecules on one side of the box

Yes, giving you a set of commands would be the simplest thing for you :-) However I can't give you a set of commands for an arbitrary such operation, because there's a whole set of conditions you haven't stated. Moreover, figuring out the fine detail would take time that I don't have available.

Re: RE: [gmx-users] Dispersion correction in a heterogeneous

Berk, Thank you very much for the answer. It was not clear from my post (sorry for that) but my main concern was indeed related to the inhomogeneity near the surfaces. I am not targeting complete quantitative agreement, but I would like to be save from "hidden" undesired qualitative effects. As

[gmx-users] Fw: last frame in trr

sorry for the incomplete post before, believe it or not my cat was to blame. I want to write out only the final frames from a set of trr trajectories. This was discussed here with apparently only a workaround: http://www.mail-archive.com/gmx-users@gromacs.org/msg19545.html however intuitively i

[gmx-users] Polyethylene Surface generation

Hi, A few days ago I had posted a request regarding help with Polyethylene surface generation. I had earlier taken help of an older thread to create a gmx file for PE

Re: [gmx-users] Fw: last frame in trr

Hey Floris, Here's a python script to write out the last frame from a .trr file: # #!/usr/bin/env python import sys # Read a 32 bit unsigned int def i(x): return sum([ord(x[j])<<(24-j*8) for j in range(4)]) # Open the file, find the end and go back f = open(sys.argv[1],'rb') f.seek(0,2) eof =

Re: [gmx-users] resolved pdm2gmx

- Original Message - From: ahmet yıldırım Date: Monday, October 4, 2010 18:41 Subject: [gmx-users] resolved pdm2gmx To: Discussion list for GROMACS users > Hi, > > I've written the Gromacs Mail list before, but I did not get the answer that > I wanted. I am new user Gromacs. > > 1.

[gmx-users] Re: pdb2gmx problem

On 2010-10-03 23.16, ahmet yıldırım wrote: Dear Prof. Spoel, I am a Ph.D. student, Department of Physics, Harran University, Turkey. I've written the Gromacs Mail list before, but I did not get the answer that I wanted. I am new user Gromacs. I need your helps. *1. I installed fftw-3.2.2 as fol

Re: [gmx-users] Split pmf

On 10/2/10 Oct 2,10:51 PM, Петр Попов wrote: Hello, dears gmx-users! I posted a message, but didn't get a response, it was my first one, so may be I did something wrong. Anyway, here it is: I've already run md and got pmf and it's correct. But I want to get not just a pmf of total force, bu

Re: [gmx-users] an example to test mdrun-gpu x mdrun

> If using Tcoupl and Pcoupl = no and then I can compare mdrun x mdrun-gpu, > being my gpu ~2 times slower than only one core. Well, I definitely don't > intended to use mdrun-gpu but I am surprised that it performed that bad (OK, > I am using a low-end GPU, but sander_openmm seems to work fine and

[gmx-users] last frame in trr

Hi, I want to write out only the final frames from a set of trr trajectories. This was discussed here: however intuitively it seems trjconv should do this with the -dump option documented like this: -dumptime -1 Dump frame nearest specified time (ps) if I give e.g. -dump 99

Re: [gmx-users] Reg: Putting molecules on one side of the box

hi Mark After deleting half the molecules of decane from the box and if i use genbox to add water then i will only get a mixture where as i want an interface to be formed.that will be more useful to me. Regards Vinoth On Mon, Oct 4, 2010 at 4:44 PM, Mark Abraham wrote: > Yes, giving you a set

[gmx-users] about COM pulling and g_dist

Dear Zhongjin: First, I see no reason why you would not expect your g_dist values to be negative. If you want the positive distances, then reverse the order of the groups as you pass then to g_dist. Also, what type of values do you get directly out of mdrun and into the pull_x.xvg file? S

Re: [gmx-users] numerical matrix from xpm file

Hi Anupam, I recently wrote a small python script to convert gromacs .xpm files to numbers. Maybe it'll be of some use to you: Cheers, Tsjerk ### #!/usr/bin/env python import sys def unquote(s): return s[1+s.find('"'):s.rfind('"')] def uncomment(s): return s[2+s.find('/*'):s.rfind('

Re: [gmx-users] charmm c36 lipids

> Date: Fri, 1 Oct 2010 16:27:29 +0100 > From: Thomas Piggot > Subject: Re: [gmx-users] charmm c36 lipids > To: Discussion list for GROMACS users > Message-ID: <4ca5fde1.8050...@soton.ac.uk> > Content-Type: text/plain; charset="ISO-8859-1"; format=flowed > For a POPC bilayer then both your and

Re: [gmx-users] Polyethylene Surface generation

- Original Message - From: Yash Gandhi Date: Monday, October 4, 2010 20:32 Subject: [gmx-users] Polyethylene Surface generation To: gmx-users@gromacs.org > Hi, > A few days ago I had posted a request regarding help with Polyethylene > surface generation. I had earlier taken help of an

RE: [gmx-users] last frame in trr

Hi, The frame time has to be within 0.5*frame spacing of the wanted frame. If you have checkpoint files, you can use those. Berk > Date: Mon, 4 Oct 2010 02:24:57 -0700 > From: floris_buel...@yahoo.com > To: gmx-users@gromacs.org > Subject: [gmx-users] last frame in trr > > Hi, > > I want to

Re: [gmx-users] numerical matrix from xpm file

right. I also came to see one of them but with no result. and since it was done some time back so I thought if some one has come up with some method to get that. right now I wanted the matrix information obtained from command g_mdmat. can you suggest some way to get that. thanks anupam > N

[gmx-users] about COM pulling and g_dist

Hi all, I have done a simulation about pulling a K+ throug a (9,9)CNT. The results may be strange. The length of the CNT is 1.477nm,the box is 5*5*5nm.I use the Umbrella Sampling to calculate PMF ,following the tutorial by Justin A. Lemkul. I have pulled (along Z direction) a K+ (pulling

Re: [gmx-users] Reg: Putting molecules on one side of the box

- Original Message - From: vinothkumar mohanakrishnan Date: Monday, October 4, 2010 22:35 Subject: Re: [gmx-users] Reg: Putting molecules on one side of the box To: Discussion list for GROMACS users > > hi Mark > > After deleting half the molecules of decane from the box and if i use

Re: [gmx-users] Reg: Putting molecules on one side of the box

can you tell this with the help of the command that will be more useful Regards Vinoth On Fri, Sep 24, 2010 at 12:58 PM, Mark Abraham wrote: > Use genconf to replicate some suitable smaller box of decane to the full > size, delete the second half of the decane molecules, then use genbox to >

Re: [gmx-users] Reg: Putting molecules on one side of the box

Hi Vinoth !! Try genbox with increasing the vander Waal's radii. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Oct 4, 2010 at 5:03 PM, vinothkumar mohanakrishnan < kmvin...@gmail.com> wrote: > > hi Mark > > After deleting half the molecules of decane from the box and if i use > g

[gmx-users] protein embedded into membrane.

Hi, When I tried to pack different proteins around the lipids (this protein I put it in the position which was nearly going to jump out of the lipids, so it's not exactly inserted into it, just very shallow into it), I used the vmd to see the system.gro, which without being inflated first, I no

Re: [gmx-users] protein embedded into membrane.

#ZHAO LINA# wrote: Hi, When I tried to pack different proteins around the lipids (this protein I put it in the position which was nearly going to jump out of the lipids, so it's not exactly inserted into it, just very shallow into it), I used the vmd to see the system.gro, which without bei

RE: [gmx-users] protein embedded into membrane.

Thanks for your answering. I will check those further later. The unclear question was that, to the final .gro. How can I tell it that one (protein embedded in membrane) is okay or nice, so I can continue. based on area per lipids, or after EM ... are there some criteria? Thanks and best regards

[gmx-users] Can I customize Gromacs (e.g., on-fly-analysis) with multi-threading enabled?

Dear All: I am trying to do trajectory analysis on-the-fly and encountered some difficulty. What did I do: I inserted a small piece of code into "md.c" to READ the position of atoms and do some simple analysis. In the GMX3.2, my code works fine. The problem: In GMX4.5.1, my code works only if I

Re: [gmx-users] numerical matrix from xpm file

Hi Tsjerk It's very useful in my problem also. thanks again. regards anupam > Hi Anupam, > > I recently wrote a small python script to convert gromacs .xpm files > to numbers. Maybe it'll be of some use to you: > > Cheers, > > Tsjerk > > ### > > #!/usr/bin/env python > > import sys > > def unqu

Re: [gmx-users] protein embedded into membrane.

#ZHAO LINA# wrote: Thanks for your answering. I will check those further later. The unclear question was that, to the final .gro. How can I tell it that one (protein embedded in membrane) is okay or nice, so I can continue. based on area per lipids, or after EM ... are there some criteria?

[gmx-users] charmm tip5p in Gmx 4.5.2

--- Begin Message --- Dear Gmxers, Does anyone have an idea about what time the Gmx 4.5.2 will be released?And in 4.5.2, would the modified tip5p.itp in charmm27 force field be the same as that in current git version? Thanks, Yao --- End Message --- -- gmx-users mailing list

Re: [gmx-users] Can I customize Gromacs (e.g., on-fly-analysis) with multi-threading enabled?

- Original Message - From: 吴鹏 Date: Tuesday, October 5, 2010 3:24 Subject: [gmx-users] Can I customize Gromacs (e.g., on-fly-analysis) with multi-threading enabled? To: Discussion list for GROMACS users > Dear All: > > I am trying to do trajectory analysis on-the-fly and encountered

[gmx-users] unconstrained_start vs. continuation in Gromacs 4.5.x manual

Dear Gromacs Community, as I understand the MDP option "continuation" is the new name for the option "unconstrained_start". I think the 4.5 series manual should be updated to mention that fact, since it still only mentions "unconstrained_start" (at least the html version of gromacs 4.5.1 : /usr/l

[gmx-users] about COM pulling and g_dist

> Dear Chris, > 牋營 use g_wham to calculate PMF.g_wham -if > pullf-files.dat -it tpr-files.dat -b 500 -unit kT -temp 300 > -o -hist >    g_dist -f pull.xtc -s pull.tpr -n > index.ndx -o dist.xvg,first I select the reference > group,then pull group > Zhongjin He > > >       <>-- gmx-users

[gmx-users] about COM pulling and g_dist

> > Dear Chris, > > 鐗嬬嚐 use g_wham to calculate PMF.g_wham -if > > pullf-files.dat -it tpr-files.dat -b 500 -unit kT > -temp 300 > > -o -hist > > 聽聽聽g_dist -f pull.xtc -s pull.tpr -n > > index.ndx -o dist.xvg,first I select the reference > > group,then pull group > > Zhongjin He     <>--

[gmx-users] about COM pulling and g_dist

--- 10年10月5日，周二, zhongjin 写道： > 发件人: zhongjin > 主题: about COM pulling and g_dist > 收件人: gmx-users@gromacs.org > 日期: 2010年10月5日,周二,上午9:51 > Dear Chris, >   I use g_wham to calculate PMF.g_wham -if > pullf-files.dat -it tpr-files.dat -b 500 -unit kT -temp 300 > -o -hist >    g_dist -f pull.xtc -s

Re: [gmx-users] unconstrained_start vs. continuation in Gromacs 4.5.x manual

Agreed. Both are equivalent and legal, but I've updated mdp_opt.html, from which the manual is generated. Mark - Original Message - From: Oliver Stueker Date: Tuesday, October 5, 2010 10:58 Subject: [gmx-users] unconstrained_start vs. continuation in Gromacs 4.5.x manual To: Discussion

[gmx-users] 转发: about COM pulling and g_dist

--- 10年10月5日，周二, zhongjin 写道： > 发件人: zhongjin > 主题: about COM pulling and g_dist > 收件人: gmx-users@gromacs.org > 日期: 2010年10月5日,周二,上午9:53 > Dear Chris, > Snap7.jpg shows distance in one umbrella sampling window. > Zhongjin He >     > > >       <>-- gmx-users mailing listgmx-user

[gmx-users] Reg: Prodrg topology

Hi all I want to generate a topology file for say decane from prodrg for oplsaa force field. is it possible?. i get a topology file from prodrg for gromos96.1 force field and i am able to process it further. when i use the topology file generated for gromos96.1(from prodrg) for oplsaa i get the er

Re: [gmx-users] Reg: Prodrg topology

Pre-supposing the suitability of only one tool is pretty limiting - and that's before you consider the weaknesses of PRODRG even for its target forcefields. For decane, writing the topology by hand is feasible. There's at most 3 atom types and only 32 atoms, after all. Otherwise, consider http:

Re: [gmx-users] Reg: Prodrg topology

Thank you mark for your suggestion. can i use x2top to generate topology for oplsaa force field by using (all atom) .gro file from PRODRG?.Is it worth using it. Regards Vinoth On Tue, Oct 5, 2010 at 11:30 AM, Mark Abraham wrote: > Pre-supposing the suitability of only one tool is pretty limiting

Re: [gmx-users] resolved pdm2gmx

Dear Dr. Abraham, I have been trying to install gromacs-4.5.1 for a week but I could not it. I review the installation instructions step by step, but I failed again. *1.* I installed fftw-3.2.2 as following a...@ab-desktop:~/Masaüstü/ cd fftw-3.2.2 a...@ab-desktop:~/Masaüstü/fftw-3.2.2 a...@ab-d