Re: [gmx-users] snapshot

2013-07-15 Thread Dr. Vitaly Chaban
look for either "-dt" or "-skip". Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 2:03 AM, Rama wrote: > Hi, > > How to get a snapshots in equal intervals of time (250ps) from production > MD > trajectory. I'm using -sep , -t0, -timestep but output came only one .gro > file. > > > > -- > View

[gmx-users] How to calculate enthalpy

2013-07-15 Thread pooja_gupta
Hi I want calculate the enthalpy of water molecule corresponding to protein folded and unfolded state. How much a single water molecule (enthalpy and free energy) contribute in folding ? Can we calculate enthapy from g_energy? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gro

Re: [gmx-users] How to calculate enthalpy

2013-07-15 Thread Dr. Vitaly Chaban
Sure, you can. Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 8:38 AM, wrote: > Hi > > I want calculate the enthalpy of water molecule corresponding to protein > folded and unfolded state. > How much a single water molecule (enthalpy and free energy) contribute in > folding ? > Can we calculat

Re: [gmx-users] How to calculate enthalpy

2013-07-15 Thread Albert
On 07/15/2013 10:20 AM, Dr. Vitaly Chaban wrote: Sure, you can. Dr. Vitaly V. Chaban I've got a question for it. Why the calculated entropy is negative? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

Re: [gmx-users] How to calculate enthalpy

2013-07-15 Thread pooja_gupta
Thanks Vitaly but how?? let's say the difference between unfolded to folded protein is 100 water molecules. What is the correct procedure to calculate (theoretically) the entrapy correspond to single water molecule for stabilizing/destabilizing the protein. help me > Sure, you can. > > > > Dr.

Re: [gmx-users] How to calculate enthalpy

2013-07-15 Thread Dr. Vitaly Chaban
H = U +pV, all these terms are available through g_energy. Your resulting values will be per mole, so I would perform no additional normalization. Personally, I would simulate all cases (folded, unfolded, etc) with the same number of waters -- to avoid any possible artifacts. Dr. Vitaly V. Cha

[gmx-users] enery conserving problem in NVE simulations with SMW4-NPD polarizable force field

2013-07-15 Thread Ding Yun
Hello, I'm trying to simulate liquid water (512 water molecules) with SMW4-NPD polarizable force field. The NVT simulation looks fine, but when I restart it with NVE runs, the total energy of the system keeps drifting down. The time step I'm using now is 0.5 fs and emtol=0.01 kJ/mol/nm. Gromac

[gmx-users] AMINOACIDS

2013-07-15 Thread fatemeh ramezani
 Dear Justin I don't know how can I detect the protonation state of amino acids in specific pH. Can you help me? Thank you Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromac

Re: [gmx-users] AMINOACIDS

2013-07-15 Thread Justin Lemkul
On 7/15/13 7:56 AM, fatemeh ramezani wrote: Dear Justin I don't know how can I detect the protonation state of amino acids in specific pH. Can you help me? There are various methods for pKa calculations, and based on those results you can choose the appropriate states with pdb2gmx comm

[gmx-users] Using the checkpoint file to restore corrupt trajectory.

2013-07-15 Thread Rajat Desikan
Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the a

Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.

2013-07-15 Thread Justin Lemkul
On 7/15/13 8:38 AM, Rajat Desikan wrote: Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part b

Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.

2013-07-15 Thread rajat desikan
Hi Justin, The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation will finish in one step. On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul wrote: > > > On 7/15/13 8:38 AM, Rajat Desikan wrote: > >> Hi, >> I have a 20 ns long trajectory which has become corrupted beyond 18ns. I

Fw: [gmx-users] AMINOACIDS

2013-07-15 Thread fatemeh ramezani
 Dear Justin I usepropka site for pKa calculation but I want to know if pKa is smaller than my desired pH , I must consider this amino acid  deprotonate? and if pKa of  aminoacids is bigger thanmy desired pH, I must protonate this amino acid? Thank you Fatemeh Ramezani - Forwarded

Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.

2013-07-15 Thread rajat desikan
I guess, the more important question is whether the checkpoint file stores the previous checkpoints as well. If it stores only the last checkpoint at 20 ns, then I guess there is no way to rerun from 18 ns. I do not store a .trr because of space constraints and hence I do not have the velocities.

Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.

2013-07-15 Thread Justin Lemkul
On 7/15/13 8:52 AM, rajat desikan wrote: Hi Justin, The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation will finish in one step. You need a checkpoint file that corresponds to a good frame before the corruption. If you don't have that, you can't fix the broken traject

Re: Fw: [gmx-users] AMINOACIDS

2013-07-15 Thread Justin Lemkul
On 7/15/13 8:54 AM, fatemeh ramezani wrote: Dear Justin I usepropka site for pKa calculation but I want to know if pKa is smaller than my desired pH , I must consider this amino acid deprotonate? and if pKa of aminoacids is bigger thanmy desired pH, I must protonate this amino acid?

Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.

2013-07-15 Thread Justin Lemkul
On 7/15/13 8:56 AM, rajat desikan wrote: I guess, the more important question is whether the checkpoint file stores the previous checkpoints as well. If it stores only the last checkpoint at 20 ns, then I guess there is no way to rerun from 18 ns. It does not. Checkpoints are recycled every

Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.

2013-07-15 Thread rajat desikan
Thank you! On Mon, Jul 15, 2013 at 6:29 PM, Justin Lemkul wrote: > > > On 7/15/13 8:56 AM, rajat desikan wrote: > >> I guess, the more important question is whether the checkpoint file stores >> the previous checkpoints as well. If it stores only the last checkpoint at >> 20 ns, then I guess th

Re: [gmx-users] snapshot

2013-07-15 Thread Rama Krishna Koppisetti
Hi, The following command I used for the snapshots but I'm getting one frame time 0 time 500. what are the changes I need to do in the command to get snapshots in equal intervals of time for ex: 250ps. My production MD trajectory was 15ns. g_trjconv -s md.tpr -f md.trr -o beta.gro -skip 1 -dt 0 -d

Re: [gmx-users] snapshot

2013-07-15 Thread Justin Lemkul
On 7/15/13 9:02 AM, Rama Krishna Koppisetti wrote: Hi, The following command I used for the snapshots but I'm getting one frame time 0 time 500. what are the changes I need to do in the command to get snapshots in equal intervals of time for ex: 250ps. My production MD trajectory was 15ns. g_t

Re: [gmx-users] snapshot

2013-07-15 Thread Rama Krishna Koppisetti
Thank you very much *Justin*. -- Rama On Mon, Jul 15, 2013 at 8:06 AM, Justin Lemkul wrote: > > > On 7/15/13 9:02 AM, Rama Krishna Koppisetti wrote: > >> Hi, >> >> The following command I used for the snapshots but I'm getting one frame >> time 0 time 500. what are the changes I need to do in

Re: Fw: [gmx-users] AMINOACIDS

2013-07-15 Thread Justin Lemkul
On 7/15/13 9:11 AM, fatemeh ramezani wrote: Dear Justin I know the Henderson-Hasselbalch equation, but what should I consider [A-]/[HA] for amino acids? That's what you're solving for. You know pH and pKa, and that tells you the ratio of deprotonated to protonated species, which tells you

[gmx-users] Re: snapshot

2013-07-15 Thread Thomas Schlesier
Hi, the following: trjconv -s md.tpr -f md.trr -o beta.gro -dt 250 -sep should work. -dt 250 ; write output every 250 ps -sep ; to write each frame (but the output frequency gets overwritten by '-dt 250') the additional use of '-dump x' might be the problem, since with '-dump x' GMX writes o

Re: [gmx-users] Re: snapshot

2013-07-15 Thread Rama Krishna Koppisetti
Thanks *Thomas* --Rama On Mon, Jul 15, 2013 at 9:00 AM, Thomas Schlesier wrote: > Hi, > the following: > > trjconv -s md.tpr -f md.trr -o beta.gro -dt 250 -sep > > should work. > -dt 250 ; write output every 250 ps > -sep ; to write each frame (but the output frequency gets overwritten by >

[gmx-users] RE: Is non-linear data output/storage possible?

2013-07-15 Thread Neha
Justin Lemkul wrote > The .cpt file stores information related to output frequency. The > existing.cpt > file designates output every X steps, while the new .tpr file specifies > output > every Y steps, and X != Y, so mdrun complains. I'm assuming mdrun aborts > at > that point? Have you tried w

Re: [gmx-users] RE: Is non-linear data output/storage possible?

2013-07-15 Thread Justin Lemkul
On 7/15/13 11:48 AM, Neha wrote: Justin Lemkul wrote The .cpt file stores information related to output frequency. The existing.cpt file designates output every X steps, while the new .tpr file specifies output every Y steps, and X != Y, so mdrun complains. I'm assuming mdrun aborts at that

[gmx-users] How to make changes on Trajectory file?

2013-07-15 Thread Rama
Hi, I saved my coordinates every 500ps in production MD run, could I alter now .xtc file by saving different coordinates for ex: every 100ps. Is there any command to alter the files. Thanks in Advance --Rama -- View this message in context: http://gromacs.5086.x6.nabble.com/How-to-make-cha

Re: [gmx-users] How to make changes on Trajectory file?

2013-07-15 Thread Justin Lemkul
On 7/15/13 12:08 PM, Rama wrote: Hi, I saved my coordinates every 500ps in production MD run, could I alter now .xtc file by saving different coordinates for ex: every 100ps. Is there any command to alter the files. You can't create frames that aren't there. You can decrease the frame int

Re: [gmx-users] How to make changes on Trajectory file?

2013-07-15 Thread Rama Krishna Koppisetti
O kay... T hanks for prompt reply *Justin* * . --Rama ** * On Mon, Jul 15, 2013 at 11:11 AM, Justin Lemkul wrote: > > > On 7/15/13 12:08 PM, Rama wrote: > >> >> Hi, >> >> I saved my coordinates every 500ps in production MD run, could I alter now >> .xtc file by saving different coordinates f

Aw: Re: [gmx-users] How to calculate enthalpy

2013-07-15 Thread lloyd riggs
Whats the energy of each waters hydrogen bonding strength respective of each one...as they vary by a couple kcal/mol according to the new IUPAC standard deffinition of hydrogen bonds (2011)?  And the energy of the internal structural hydrogen bonds that were disrupted?  Assuming no acidic enviornme

[gmx-users] Re: enery conserving problem in NVE simulations with SMW4-NPD polarizable force field

2013-07-15 Thread S. Alireza Bagherzadeh
On Mon, Jul 15, 2013 at 3:00 AM, wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'he

[gmx-users] Reverse_MICELLE>Fatel error, moleculetype SOL is redefined

2013-07-15 Thread Hari Pandey
Hi Gromaxers, Thanks for previous answers. I have to simulate reverse micelle after solvation with isooctane.My system now is: ISOOCTANE(solvent)+AOT(surfactant)+coreWATER.     When I do grompp, it says moleculetype SOL is redefined and lo

[gmx-users] Chlorate ion force field

2013-07-15 Thread Sushma Yadav
Dear users, How do I get the force-field for ClO4- ion in the gromacs? Thanks in advance. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * P

Re: [gmx-users] Re: extreme projections

2013-07-15 Thread Rashmi
Hi, If you have VMD installed, load the "extreme.pdb". Then in graphics> Representations--->Trajectory---> put values in "Draw Multiple Frames", for e.g. 0:10 this will show the extremes of 0th frame to 10th frame (you can change this a/c to your representation). After this selecting Draw sty