[gmx-users] DSSP output

Hi ALL, Is there any way to get the percentage of each secondary structural content of a protein using do_dssp if I supply a single PDB to it? And how to plot the data of the -sc output from do_dssp? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Projection of crystal structure on PCA plot

. Regards, Anirban -- 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! * Please don't post (un)subscribe requests to the list. Use the www interface

Re: [gmx-users] Projection of crystal structure on PCA plot

won't be the exact crystal structure) as well. Right? Thanks a lot again. Regards, Anirban On Thu, Jun 6, 2013 at 3:56 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Anirban, The eigenvectors obtained from the simulation are a way of rewriting the coordinates of your structures

Re: [gmx-users] Projection of crystal structure on PCA plot

Thanks a lot Tsjerk :) -Anirban On Thu, Jun 6, 2013 at 4:42 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Anirban, Indeed. :) Tsjerk On Thu, Jun 6, 2013 at 1:11 PM, Anirban reach.anirban.gh...@gmail.com wrote: Dear Tsjerk, Thank you very much for the explanation. So

[gmx-users] trjcat: joining randomized PDB files

always joins them in proper frame order (inspite of completely random PDB file names). How can I join the randomly to get a randomized trajectory? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] trjcat: joining randomized PDB files

reads the randomized PDB files serially, so can't it just concatenate the files in that order? Or am I missing something? Thanks again. Regards, Anirban On Thu, May 9, 2013 at 7:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/9/13 9:35 AM, Anirban wrote: Dear ALL, I want to randomize

[gmx-users] Block average RMSD using g_analyze

thing, is this method same as the block average RMSD method outlined by Alan Grossfield in JCTC 2011:7;2464-2472, in order to test convergence of a trajectory? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

Re: [gmx-users] Lipid membrane partially broken and create huge voids after NVT

After NVT, usually the lipid bilayer move away from each other creating some voids, which occurs due to absence of pressure coupling. But its not a problem. You can go ahead and carry out NPT and see that bilayer has settled to normal position. -Anirban On Tue, Apr 9, 2013 at 3:04 PM, sdshine

Re: Fw: [gmx-users] water molecule can not be settled

or not, in the GROMACS forum, then it should not bother Mr. Luis Felipe Pineda de Castro, since to the best of my knowledge it is not affecting him. I would request the moderators of this forum to take adequate measures about such postings as Mr. Castro's. Regards, Anirban On Fri, Apr 5, 2013 at 10:55 PM, Luis Felipe

Re: [gmx-users] MD with Xenon

-Anirban -- 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! * Please don't post (un)subscribe requests to the list. Use the www interface or send

Re: [gmx-users] intermolecular H bond selection

with g_hbond. -Anirban Thanks very much! On Fri, May 18, 2012 at 7:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/18/12 7:22 PM, mu xiaojia wrote: Hi gmx-users, I have a question might be explained before but I cannot understand from the previous , how to calculation

Re: [gmx-users] Regarding error.

: http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database -Anirban Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] parameterization of new metal ion

file and tried but i got error atomtype not found.. You need to modify the .rtp file as well. Follow this: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Anirban can anyone please explain me elaborately how to set parameters .. please help me with your answer

[gmx-users] Software inconsistency error with GROMACS4.5.5

--- Why is this error coming? Is it a bug? Any suggestion is welcome. Thanks and regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] ATB SWISSPARAM Topologies

Thanks a lot Justin! On Tue, May 15, 2012 at 4:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/15/12 5:54 AM, Anirban wrote: Hi ALL, How accurate are the topologies of non-standard molecules generated by ATB or SWISSPARAM for GROMACS? Are they acceptable for publications? Are we

Re: [gmx-users] about the frame selection

with this protein. 2 . to change the box size how to proceed ?? Should I delete the line manually and adjust the box size You can change the box dimensions with editconf using the -box (desired dimensions) option. -Anirban All suggestion are welcome ... Than you in advance

Re: [gmx-users] about the frame selection

On Tue, May 15, 2012 at 11:48 AM, rama david ramadavidgr...@gmail.comwrote: Thank you ANIRBAN for your reply .. I think its better to remove the periodicity when you are going to start a fresh simulation with this protein. Could you told me how to remove the periodicity ??? You can use

[gmx-users] ATB SWISSPARAM Topologies

Hi ALL, How accurate are the topologies of non-standard molecules generated by ATB or SWISSPARAM for GROMACS? Are they acceptable for publications? Are we required to carry out manual checks like that required for PRODRG outputs? Any suggestion is welcome. Thanks and regards, Anirban -- gmx

[gmx-users] Coupling groups in protein-ligand-lipid simulation

suggestion is welcome. Thanks and regards, Anirban -- 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! Please don't post (un)subscribe requests

Re: [gmx-users] mdrun_mpi issue with CHARMM36 FF

On Mon, May 14, 2012 at 11:35 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 14/05/2012 3:52 PM, Anirban wrote: Hi ALL, I am trying to simulate a membrane protein system using CHARMM36 FF on GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of arounf 1,17,000

[gmx-users] mdrun_mpi issue with CHARMM36 FF

. Thanks and regards, Anirban -- 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! Please don't post (un)subscribe requests to the list. Use the www

Re: [gmx-users] Simulation of POPC in water using CHARMM27

-Anirban Thanks in advance, Shima -- *From:* Anirban reach.anirban.gh...@gmail.com *To:* Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, May 11, 2012 9:22 PM *Subject:* Re: [gmx-users] Simulation

[gmx-users] mdrun_mpi issue for CHARMM36 FF

. Thanks and regards, Anirban -- 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! Please don't post (un)subscribe requests to the list. Use the www

[gmx-users] MPIRUN issue for CHARMM36 FF

, Anirban -- 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! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx

Re: [gmx-users] Simulation of POPC in water using CHARMM27

and nonbonded .itp files to include the Berger lipid parameters and have you included the POPC topology? You can follow this tutorial to get an idea: https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial -Anirban Thanks, Shima -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Simulation of POPC in water using CHARMM27

On Fri, May 11, 2012 at 9:10 PM, Anirban reach.anirban.gh...@gmail.comwrote: On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear gmx users, I'm going to simulate the POPC in water. I downloaded required files in Tielman site and made the .top file

Re: [gmx-users] Simulation of POPC in water using CHARMM27

worked fine for me (with grompp). Include the popc.itp file in your .top file. -Anirban Thanks, Shima -- *From:* Anirban reach.anirban.gh...@gmail.com *To:* Shima Arasteh shima_arasteh2...@yahoo.com *Sent:* Friday, May 11, 2012 8:58 PM *Subject:* Re: [gmx

Re: [gmx-users] Re: Justin lipid-position restraine

As the tutorial suggest you can restrain the heavy atoms, but I usually restrain the entire protein during the InflateGro steps (EMs) and let the lipids minimize around it. -Anirban All suggestions are welcome thank you in advance Rama David . -- gmx-users mailing listgmx

Re: [gmx-users] itp file problem

On Mon, May 7, 2012 at 5:11 PM, Sarath Kumar Baskaran bskumar.t...@gmail.com wrote: First i had simulation of the protein alone in united atom gromacs force field by -ff gmx in pdb2gmx now i am unable to run the protein-ligand complex for the same protein with a ligand, it says the

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

On Mon, May 7, 2012 at 10:17 AM, Bala S think_bey...@aol.com wrote: Justin and Anirban, I have another query on membrane simulation following your tutorials. How do I insert only a part of protein into the lipid bilayer and carryout the simulation? editconf with -box option helps you

Re: [gmx-users] membrane simulation

you can change them without any issue in the .gro file. -Anirban Any suggestion would be appreciated, Silvia -- 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

Re: [gmx-users] jointly-couple lipids to theromstat - MARTINI force-field

different coupling groups are used to increase the accuracy of the calculations (more realistic). In your system you can make make three groups: Protein, Lipids(DPPC+DPPG) and Sol+Ions(Na+Qd) -Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

[gmx-users] CHARMM36 and Dispersion correction

, then should I use vdwtype as switch? Any suggestion is welcome. Regards, Anirban -- 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! Please don't post (un

[gmx-users] CHARMM36 format POPC

different atom-types (like P1 in place of P, etc.) and hence pdb2gmx throws up error when processed with CHARMM36 FF option. Is there any CHARMM36 FF format equilibrated POPC bilayer available online, or can someone provide, please? Thanks a lot in advance. Regards, Anirban -- gmx-users mailing

Re: [gmx-users] CHARMM36 format POPC

Thanks a lot Peter. Will try out with this. -Anirban On Wed, May 2, 2012 at 9:42 PM, Peter C. Lai p...@uab.edu wrote: http://uab.hyperfine.info/~pcl/files/popc36/ These were generated for the following work: (please reference): Lai, P.C. and Crasto, C.J. Beyond Modeling: All-Atom Olfactory

[gmx-users] POPC: ff53a6 and CHARMM36 formats

pdb2gmx gives error. Can these atom names (hydrogens can be ignored) of my equilibrated POPC bilayer be changed manually and then used with CHARMM36 FF? Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] POPC: ff53a6 and CHARMM36 formats

Thanks Angel and Justin. Will try out the options! Regards, -Anirban On Tue, May 1, 2012 at 5:46 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/1/12 8:05 AM, Ángel Piñeiro wrote: I guess there are better solutions but an alternative is to map your bilayer to MARTINI (http

Re: [gmx-users] Regarding error

://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database -Anirban Suryanarayna Seera, PhD student. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

Re: [gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun

this command: mpirun -machinefile mymachines -np 8 mdrun -s topol.tpr I suppose this mdrun executable is not mpi-enabled. Have you compiled mdrun with --enable-mpi option? -Anirban where mymachines is an (extensionless) file containing only the text c60 slots=8. (c60 is the name of the node that I am

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

On Fri, Apr 27, 2012 at 1:01 PM, Bala S think_bey...@aol.com wrote: Dear Justin Thanks for the explanation. I am following your tutorial of KALP membrane simulation. I am stuck in between two steps of InflateGRO. After the first step, the tutorial requests to perform EM. Should I be

Re: [gmx-users] Regarding errors

On Fri, Apr 27, 2012 at 3:17 PM, seera suryanarayana paluso...@gmail.comwrote: Respected Sir, While i am running gromacs software i am getting the following error.Kindly knowing me how to over come the error. Fatal error:

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

On Fri, Apr 27, 2012 at 3:27 PM, Bala S think_bey...@aol.com wrote: Thank you for that clarification. I found that there were SOL molecules in .top file. I could run the EM now. Coming to the Solvation step, I'm facing a problem. I have made the mentioned change (0.15 to 0.375 for C) in

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

for the dimensions in the last line of the FINAL (compressed and minimized) .gro file and then solvate Thanks, Anirban But I could see in the visualizer that SOL molecules were added on top and bottom but only 1/3 of the length of the bilayer. How to add SOL molecules to whole length or how

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

same). Anirban Bala S -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933854.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

On Fri, Apr 27, 2012 at 7:00 PM, Bala S think_bey...@aol.com wrote: Anirban, Thank you. You guys are doing miracles with the biomolecules and solving almost all of my problems. I have followed your suggestion and could see now some more SOL molecules by increasing the z value. But I am

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

On Fri, Apr 27, 2012 at 7:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 4/27/12 10:00 AM, Bala S wrote: Anirban, Exactly.. That's the gap (either side of the leaflets) I was mentioning about. I'll try EM and check itagain. EM won't fill in solvent gaps. If you're using my protocol

[gmx-users] GPCR MD Tutorial Using GROMACS

by Justin Lemkul. Regards, Anirban -- 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! Please don't post (un)subscribe requests to the list. Use

[gmx-users] GPCR MD Tutorial Using GROMACS

and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

[gmx-users] GPCR MD Tutorial Using GROMACS (URL)

and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

in the tutorial. But one can surely add CHARMM36 to GROAMCS by doing all the necessary topology conversions. Regards, Anirban On Thu, Apr 26, 2012 at 3:08 PM, Albert mailmd2...@gmail.com wrote: it seesm to be good. just one pieces of advices, why not use CHARMM36 for this tutorial ? since

Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

Hello Albert, Good to know that! I have carried out simulations using this FF in the range of 600 ns. Regards, Anirban On Thu, Apr 26, 2012 at 3:47 PM, Albert mailmd2...@gmail.com wrote: Hello Anirban: thanks for kind comments. How long did you mean fairly long simulation time ? does

Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

Hello Albert, On our cluster I usually get around 25-30 ns/day running on 120 cores (system size around 85K atoms) with PME. Regards, Anirban On Thu, Apr 26, 2012 at 5:28 PM, Albert mailmd2...@gmail.com wrote: Hi Anirban: how many ns/day for your simulations? Did you use PME? best

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

. And secondly again as Justin mentioned, the choice of lipid depends upon the system you wish to replicate. Regards, Anirban On Thu, Apr 26, 2012 at 11:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 4/26/12 9:35 AM, Bala S wrote: Dear Anirban, Thanks for the tutorial you have created

[gmx-users] Best Force Field for a Membrane Protein

losing its secondary structures? Your experience please. Thanks a lot in advance. Regards, Anirban -- 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

Re: [gmx-users] Best Force Field for a Membrane Protein

Hi ALL, Thanks a lot for the replies. By long simulation I mean 500 ns to 1000 ns. Has anybody tried with the ff43a1 with any membrane protein? Thanks, Anirban On Fri, Apr 20, 2012 at 3:26 AM, Peter C. Lai p...@uab.edu wrote: Define long simulations? CHARMM27/36 in the sub-100ns timescale

[gmx-users] Membrane Proteins pdb2gmx

) to be processed through pdb2gmx using gromos53a6_lipid force-field, right? And to process a membrane using pdb2gmx we need to change the aminoacids.rtp file with the relevent POPC/DSPC/DPPC etc. entries. Right? Or can we somehow make pdb2gmx use the POPC/DPPC/DSPC.itp file? Thanks a lot. Anirban -- gmx

Re: [gmx-users] Membrane Proteins pdb2gmx

Hello Peter, Thanks a lot for clarifying my doubt! I have got it right now. Thanks, Anirban On Thu, Dec 8, 2011 at 3:34 PM, Peter C. Lai p...@uab.edu wrote: On 2011-12-08 02:43:13AM -0600, Anirban Ghosh wrote: Hello Justin, In your membrane protein simulation tutorial after making

[gmx-users] CPHMD in GROMACS4.5

Hi ALL, Is it possible to run constant pH MD simulation (CPHMD) in Gromacs4.5? Any suggestion is welcome. Thanks, Anirban -- 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

[gmx-users] g_rdf query

correctly then x-axis values represent the radius of calculation around the protein. right? It says r. Whats its unit? And what does the y-axis values stand for? Can someone please explain me the g_rdf plot attached here. Thanks a lot in advance. Regards, Anirban attachment: try_rdf.jpg-- gmx-users

[gmx-users] GridMatMD and CGMD

in the input file for GridMatMD in order to properly recognize the CG lipids? Thanks a lot in advance. Regards, Anirban -- 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

Re: [gmx-users] GridMatMD and CGMD

of some PBC issue. What -pbc options should I use to generate a proper .gro file to be used as input for GridMatMD? Thanks a lot again. Regards, Anirban On Mon, May 30, 2011 at 4:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I have simulated a CGMD system consisting

[gmx-users] About -pbc option of trjconv

in advance. Thanks, Anirban -- 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! Please don't post (un)subscribe requests to the list. Use the www

Re: [gmx-users] g_sas query

Hello Tsjerk, Thanks for the reply. But if I consider the ions also in the calculation group, then it is not wrong. Right? Thanks, Anirban On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey Anirban, I would consider the ions part of the solvent

Re: [gmx-users] g_sas query

and Protein as the output group? Thanks again, Anirban On Sat, May 7, 2011 at 1:05 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 7/05/2011 4:36 PM, Anirban Ghosh wrote: Hello Tsjerk, Thanks for the reply. But if I consider the ions also in the calculation group, then it is not wrong

[gmx-users] g_sas query

as the calculation group. Right? Thanks a lot in advance. Regards, Anirban -- 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! Please don't post (un)subscribe

[gmx-users] trjcat error of different spacing

output trajectory for further analysis like g_sas, then a portion between around 10 ns and 300 ns is simply joined by a straight line. How to remove this inconsistency from the two trajectories? Any suggestion is welcome. Thanks, Anirban -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] trjcat error of different spacing

--- So gmxcheck does not show any warning/error. Then why I am getting the warning from trjcat. And how to remove it? Thanks, Anirban On Thu, May 5, 2011 at 7:19 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban

Re: [gmx-users] trjcat error of different spacing

Hello Justin, I am using Gromacs 4.0.7 Actually, I am joining around 20 trajectories of around 300 ns each. Its a CGMD run. But I reported here only those two trajectories between which trjcat has shown the warning while joining. So what should i do? Thanks, Anirban On Thu, May 5, 2011 at 7:58

[gmx-users] CG to FG transformation error

only multiple copies of a protein. How to solve this issue? Any suggestion is welcome. Thanks, -Anirban -- 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

[gmx-users] Error: No such moleculetype Protein

: No such moleculetype Protein - I have checked all the include statements and .itp files, but cannot fix the issue. Is seems to be very trivial but still exists. Any suggestion is welcome. Thanks, Anirban

Re: [gmx-users] Error: No such moleculetype Protein

to this command or how to mention this refering of 'Protein' group here. Thanks, Anirban On Thu, Feb 10, 2011 at 5:28 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Anirban, Probably you have a reference to a group 'Protein' in your .mdp file. Cheers, Tsjerk On Thu, Feb 10, 2011

Re: [gmx-users] Error: No such moleculetype Protein

410288 Number of cg atoms 57296 Reading frames from gro file 'Protein in DSPC Bilayer', 57296 atoms. Reading frame 0 time0.000 1297343010 Segmentation fault Why is this happening? Thanks, Anirban On Thu, Feb 10, 2011 at 5:45 PM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote

[gmx-users] DSPC all atom .itp file

Hi ALL, Can anyone please send me an all-atom DSPC .itp file at * reach.anirban.gh...@gmail.com *or* anirba...@gmail.com* * * Thanks a lot. -Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] CG to FG transformation error

0.125 0.5 #include ffG43a2nb.itp #include ffG43a2bon.itp Is this correct? where I am going wrong? I think the problem is with pro_cg.top file only. Any suggestion is welcome. Thanks, -Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] DSPC all atom .itp file

Hi ALL, Can anyone please send me an all-atom DSPC .itp file at * reach.anirban.gh...@gmail.com *or* anirba...@gmail.com* * * Thanks a lot. -Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

Re: [gmx-users] g_lie query

to do this? And why am I getting only a single value of DGbind for all the frames captured in the .edr file? Thanks a lot. Anirban On Mon, Dec 27, 2010 at 11:51 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks Justin for the reply. I have through the threads about

Re: [gmx-users] g_lie query

Thanks a lot Justin for the reply. Yes I am going through all the relevant literature on LIE. Actually the lie.xvg file contains the same value of -25.4 for all the frames. So I am getting a straight line plot. Why is this happening? Am I missing out something? Thanks a lot again. Anirban

Re: [gmx-users] g_lie query

Thanks a lot Justin !!! --Anirban On Tue, Dec 28, 2010 at 11:03 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks a lot Justin for the reply. Yes I am going through all the relevant literature on LIE. Actually the lie.xvg file contains the same value of -25.4

Re: [gmx-users] g_lie query

Thanks a lot Justin for the reply !!! While calculating the Elj and Eqq values should we consider the short-ranged LJ (LJ-SR) or LJ-14, the two components that are present in the .edr file? And for Coulomb also? Which one should we consider? Thanks again. Anirban On Tue, Dec 28, 2010 at 11:03

Re: [gmx-users] g_lie query

Thanks Justin. Yes I did use PME during the simulations. But still when I process the .edr file with g_energy, it gives both the options...LJ-1-4 and LJ(SR). So if I am not wrong, I should be using the LJ(SR) value as the Elj in the LIE calculation. Right? Thanks again. Anirban On Tue, Dec 28

[gmx-users] Energy due to Hydrogen bonds

, Anirban -- 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! Please don't post (un)subscribe requests to the list. Use the www interface or send

Re: [gmx-users] g_lie query

? Thanks a lot. Anirban On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How

Re: [gmx-users] Which .tpr file to use for g_rms?

picture of what has happened to my protein at the end of the simulation. Should I use the first .tpr file or the last .tpr file? Thanks a lot again. Anirban On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, Its a very basic question

Re: [gmx-users] Which .tpr file to use for g_rms?

this which .tpr file should I supply to trjconv, the first one or the last one? Thanks again. Anirban On 12/4/10, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference

Re: [gmx-users] Which .tpr file to use for g_rms?

should I use? Thanks, Anirban On Sat, Dec 4, 2010 at 12:29 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/12/2010 4:33 PM, Anirban Ghosh wrote: Thanks a lot for the reply. Actually I am running a protein in lipid bilayer. Now I want to calculate the thickness of the bilayer at the end

[gmx-users] Free Energy Calculation: dVpot/dlambda is always zero

that in my log file the values for dVpot/dlambda is always coming to be zero. What I am doing wrong? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] Free Energy Calculation: dVpot/dlambda is always zero

that in my log file the values for dVpot/dlambda is always coming to be zero. What I am doing wrong? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

Re: [gmx-users] Free Energy Calculation: dVpot/dlambda is always zero

. Regards, Anirban On Sat, Nov 27, 2010 at 9:15 AM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I am trying to run free energy calculation and for that in the md.mdp file I am keeping the following option: ; Free energy control stuff free_energy = yes

[gmx-users] WHAM

suggestion in this regard is welcome. Regards, Anirban -- 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! Please don't post (un)subscribe

Re: [gmx-users] WHAM

code or there is some other way? Any suggestion is welcome. Thanks again. Regards, Anirban On Thu, Sep 16, 2010 at 5:28 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I have carried out REMD simulation on a protein (20 replicas). Now I want to carry 2D PMF

[gmx-users] Bioinformatics Symposium at C-DAC, Pune

The Bioinformatics Group at C-DAC, Pune is going to organize a Symposium on Accelerating Biology from December 14-16 2010 at VITS, Pune. You can register for the same at: http://pune.cdac.in/html/events/bioinfo/accelerating_biology/index.aspx Regards, -- Anirban Ghosh C-DAC, Pune, India

[gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells

- How can I resolve this error? Any suggestion is welcome. Regards, Anirban attachment: sim.jpeg-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un

Re: [gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells

Thanks a lot XAvier for clarifying my doubt. You mean to say -rdd option with mdrun, right? And why does this curvature of the membrane occurs? Thanks a lot once again. Regards, Anirban On Mon, Aug 16, 2010 at 3:53 PM, XAvier Periole x.peri...@rug.nl wrote: Although a bit worrying

[gmx-users] Centre of mass removal in CGMD

relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DSPC W - Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users

Re: [gmx-users] Centre of mass removal in CGMD

Thanks a lot XAvier. And if one wants to study the self assembly of a GPCR using CGMD (like you did for rhodopsin), should he/she use the same parameters for COM motion removal? Regards, Anirban On Fri, Aug 13, 2010 at 3:18 PM, XAvier Periole x.peri...@rug.nl wrote: On Aug 13, 2010, at 10

[gmx-users] g_lie query

? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] g_lie query

? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] g_lie query

? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Removing water from a trajectory

is showing the default options and I am not able to select the protein and the ligand simultaneously to generate the output. How can I do this? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] Helix Tilt Calculation

Thanks XAvier and George for the reply. Yes the N and C terminus are on the opposite sides of the bilayer. So I can take the values of the even TMs as (180 - respective value), correct? Regards, Anirban On Fri, Jun 4, 2010 at 8:00 PM, George Khelashvili gek2...@med.cornell.eduwrote: Hi

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