RE: [gmx-users] Crashed run

2010-12-05 Thread Mark Abraham
On 12/06/10, "Shi Wenxiong (Dr)" wrote: > > > > > > > > > > > > > I think you can use the command "trjcat -f MD1.xtc MD2.xtc -o MD.xtc", you > will get one xtc data. > > > > Indeed, or  circumvent the problem with appropriate use of mdrun -append Mark > > > > > > > >

Subject: [gmx-users] : MOPAC gromacs mdreun error (vidhya sankar)

2010-12-05 Thread Gerrit Groenhof
Please check if your stand-alone mopac binary works properly. Also check if the mdrun binary is linked against the libmopac.a Gerrit Message: 2 Date: Mon, 6 Dec 2010 11:55:58 +0530 (IST) From: vidhya sankar Subject: [gmx-users] : MOPAC gromacs mdreun error (vidhya sankar) To: gmx-users@gromacs

RE: [gmx-users] Crashed run

2010-12-05 Thread Shi Wenxiong (Dr)
I think you can use the command "trjcat -f MD1.xtc MD2.xtc -o MD.xtc", you will get one xtc data. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of shiva birgani [sh.birg...@gmail.com] Sent: Monday, December 06, 2010 3:16 PM To: gmx-

[gmx-users] Crashed run

2010-12-05 Thread shiva birgani
Dear Justin I had a crashed run and continued it by tpbconv and mdrun. After that in order to analysis the results of new MD run I used of this command trjcat -s md2.tpr -settime But when I want to compute RMSD, DSSP, ... I do not know how I can put together the results of MD1 (crashed run) and MD2

[gmx-users] : MOPAC gromacs mdreun error (vidhya sankar)

2010-12-05 Thread vidhya sankar
Dear Gerrit  sir,    Thank you for your previous reply i tried as u said with  -nt 1 option in mdrun but still i have got hte following error when i run mdrun_d QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 2 QMlevel: PM3/STO-3G Program mdrun_d, VERSION 4.5.3 Source

Re: [gmx-users] dna, lipid simulation

2010-12-05 Thread Amit Choubey
Thank you all. At least now I have an idea of the starting point. On Sun, Dec 5, 2010 at 12:31 PM, Thomas Piggot wrote: > I would tend to agree with Justin rather than Itamar. The GROMOS DNA > parameters are not especially good (see > http://www.ncbi.nlm.nih.gov/pubmed/20614923) but it depends

Re: [gmx-users] g_hbond results inconsistent between v4.0.7 and v4.5.1

2010-12-05 Thread Erik Marklund
Hi, No. But I hope to get it done this week. Thanks for the reminder. Erik Robin C. Underwood skrev 2010-12-05 19.19: Hi All: Has there been further resolution on the difference between g_hbond in v 4.0 and 4.5 (I'm running 4.5.3)? For counting water-water (tip4p) h-bonds in a box of 506 wate

Re: [gmx-users] dna, lipid simulation

2010-12-05 Thread Thomas Piggot
I would tend to agree with Justin rather than Itamar. The GROMOS DNA parameters are not especially good (see http://www.ncbi.nlm.nih.gov/pubmed/20614923) but it depends on what you are wanting to look at. Another option (rather than CHARMM, which for what it is worth is the force field I would

Re: [gmx-users] Re: polymer simulations in gromacs

2010-12-05 Thread ms
On 05/12/10 19:41, Justin A. Lemkul wrote: Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private help service. I do not do polymer simulations, nor do I have any real clue as to how to help you, aside from suggesting the following, which may or may not be rele

[gmx-users] Re: polymer simulations in gromacs

2010-12-05 Thread Justin A. Lemkul
Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private help service. I do not do polymer simulations, nor do I have any real clue as to how to help you, aside from suggesting the following, which may or may not be relevant: http://www.gromacs.org/Documenta

Re: [gmx-users] g_hbond results inconsistent between v4.0.7 and v4.5.1

2010-12-05 Thread Robin C. Underwood
Hi All: Has there been further resolution on the difference between g_hbond in v 4.0 and 4.5 (I'm running 4.5.3)? For counting water-water (tip4p) h-bonds in a box of 506 waters I get the following nhbdist output, which appears to neglect pbc since there are such a large number of unbound donor-H

[gmx-users] Re: Re: Discrepancy between -chargegrp and -nochargegrp in simulations with CHARMM ff, Why ?

2010-12-05 Thread sa
Dear all, I come back to you with my problem between -chargegrp and -nochargegrp with new results which are contradict my previous findings. Indeed, in my previous message i have suggested that the discrepancies between -chargegrp and -nochargegrp in my simulations of a 25 AA peptide in TIP3P wate

Re: [gmx-users] Change in structure after solvation_Gromacs

2010-12-05 Thread ms
On 05/12/10 13:20, Justin A. Lemkul wrote: ms wrote: On 05/12/10 10:39, swagata chakraborty wrote: I was trying to run MD simulation of my protein in DMSO. I used the force field ffG53a6 and did the energy minimization after solvating the protein in DMSO box. But after solvating in DMSO, the

Re: [gmx-users] LINCS WARNING

2010-12-05 Thread Justin A. Lemkul
Raymond.nuist wrote: Dear users Here is my problem: I just changed my GMX version from 4.0 to 4.5. But the task was in a Segmentation fault, whileI can "mdrun" it well in 4.0 environment . Providing an .mdp file and a description of your system would be useful.

Re: [gmx-users] Change in structure after solvation_Gromacs

2010-12-05 Thread Justin A. Lemkul
ms wrote: On 05/12/10 10:39, swagata chakraborty wrote: I was trying to run MD simulation of my protein in DMSO. I used the force field ffG53a6 and did the energy minimization after solvating the protein in DMSO box. But after solvating in DMSO, the structure is changing. My protein is a hom

Re: [gmx-users] dna, lipid simulation

2010-12-05 Thread Justin A. Lemkul
Amit Choubey wrote: Hi all, This is a question unrelated to gromacs but would pose it anyway to get some hints from the experts. I wish to set up DNA and DPPC lipid membrane simulation. Could someone please refer to a relevant forcefield/tutorial for simulation of lipids with DNA? I wou

Re: [gmx-users] dna, lipid simulation

2010-12-05 Thread Itamar Kass (Med)
Hi Amit, The GROMOS force field had both DNA and lipids parameters, hence you can use it in your simulations. Moreover, there are new lipids parameters by David Poger and Alan Mark which I should give better results compared to the old set. Good luck. On 5 December 2010 18:09, Amit Choubey wro

Re: [gmx-users] Restraining water

2010-12-05 Thread Oliver Grant
I would use grep and cut to take the atom numbers of the residues I want to restrain and direct them into an index file with [res_sol] at the top. Then use genrestr to generate restraints for these atoms using the -n option. Then conditionally include this restraint file (.itp file) in my topology

[gmx-users] LINCS WARNING

2010-12-05 Thread Raymond.nuist
Dear users Here is my problem: I just changed my GMX version from 4.0 to 4.5. But the task was in a Segmentation fault, whileI can "mdrun" it well in 4.0 environment . Here is the error: Step 1902, time 1.902 (ps) LINCS WARNING relative constraint deviation

Re: [gmx-users] Change in structure after solvation_Gromacs

2010-12-05 Thread ms
On 05/12/10 10:39, swagata chakraborty wrote: I was trying to run MD simulation of my protein in DMSO. I used the force field ffG53a6 and did the energy minimization after solvating the protein in DMSO box. But after solvating in DMSO, the structure is changing. My protein is a homodimer and the

[gmx-users] Change in structure after solvation_Gromacs

2010-12-05 Thread swagata chakraborty
Hi, I was trying to run MD simulation of my protein in DMSO. I used the force field ffG53a6 and did the energy minimization after solvating the protein in DMSO box. But after solvating in DMSO, the structure is changing. My protein is a homodimer and the loop at the dimer interface is converting i

[gmx-users] Re: MOPAC gromacs mdreun error (vidhya sankar)

2010-12-05 Thread Gerrit Groenhof
> > 2. MOPAC gromacs mdreun error (vidhya sankar) It seems that you are trying to run with multiple threads. Use mdrun -nt 1 to use only a single thread. Gerrit > Dear gmx users > > i have successfuly installed Mopac gromacs/interface. but when i run > the QM/MM in mdr