Re: [gmx-users] how to make index of a micelle

make_ndx. l . ri (residue nmbr of the sds given after parsing l) . Done On Mon, 18 Nov 2019, 10:13 pm Giuseppe R Del Sorbo, wrote: > Dear all, > > In my simulation I have a lysine + micelle of SDS. > > In the analysis, I want to find the spherical radial distribution >

Re: [gmx-users] How to Calculate tetrahedral order parameter

:24 pm David van der Spoel, wrote: > Den 2019-09-03 kl. 13:26, skrev Soham Sarkar: > > Dear all, > > I know this question was asked by many users before but > searching > > them all I did not get how to perform it in GROMACS. Please help me with > > this. Is t

[gmx-users] How to Calculate tetrahedral order parameter

Dear all, I know this question was asked by many users before but searching them all I did not get how to perform it in GROMACS. Please help me with this. Is there any in built command line exist for Tetrahedral order parameter calculation? If gmx hydorder is the existing tool for

Re: [gmx-users] Selection of water molecules

For doing that you first tag only those water molecules which are within 0.5nm of the protein surface throughout the trajectory. To do it you need to write a small python script using common_member option. And make an index file only with those water molecules and calculate the rdf. On Wed, 28

Re: [gmx-users] Selection of Water Molecules for Individual Frames

While using gmx select use -b and -e option for particular frame(s) you need On Wed, 28 Aug 2019, 10:26 am anupama sharma, wrote: > Dear users, > Currently, I have explored gmx select to identify the water molecules > present within 5 angstrom distance window from protein alpha carbon atom. >

[gmx-users] calculation of msd of water molecule

Hello, I want calculate the msd of water molecule which is within 0.4nm of the protein molecule for a 200ns trajectory. Could anyone please help me and provide the workflow. gmx msd is giving the msd of water molecules of the whole box. Thanks- Soham -- Gromacs Users mailing list * Please

[gmx-users] Analysis the dynamics of water molecules

Hello, I have a 200ns trajectory of protein-water-urea mixture, saved at 2ps interval. I want to calculate the angle distribution of water molecule (http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists *

[gmx-users] Analysis of water molecules

Hello, I have a 200ns trajectory of protein-water-urea mixture, saved at 2ps interval. I want to calculate the angle distribution of water molecule (http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists *

[gmx-users] Use of index file generated by gmx select

Hello, I have a 500ns trajectory of protein-water-urea mixture, saved at 2ps interval. I am using gmx select to generate a index.ndx of 25 index for water molecules within 0.5nm of the protein. I want to know how to use this index.ndx file for my calculation - For example: a) If I want to

[gmx-users] Use of index file generated by gmx select

Hello, I have a 500ns trajectory of protein-water-urea mixture, saved at 2ps interval. I am using gmx select to generate a index.ndx of 25 index for water molecules within 0.5nm of the protein. I want to know how to use this index.ndx file for my calculation - For example: a) If I want to

[gmx-users] Use of index file generated by gmx select

Hello, I have a 500ns trajectory of protein-water-urea mixture, saved at 2ps interval. I am using gmx select to generate a index.ndx of 25 index for water molecules within 0.5nm of the protein. I want to know how to use this index.ndx file for my calculation - For example: a) If I want to

Re: [gmx-users] How to calculate tetrahedral order parameter in GROMACS

Thanks. I am checking. On Wed, 8 May 2019, 2:30 pm David van der Spoel, wrote: > Den 2019-05-07 kl. 14:34, skrev Soham Sarkar: > > Hello, > >I have two systems. One containing only water and the other one > > contains protein and water. Using g_select I made w

[gmx-users] How to calculate tetrahedral order parameter in GROMACS

Hello, I have two systems. One containing only water and the other one contains protein and water. Using g_select I made water in 1st solvation shell but the use of g_hydorder I cannot understand. I read the disscussion so far disscussed. For these two systems which index I need to choose,

Re: [gmx-users] Gromacs Benchmarks for NVIDIA GeForce RTX 2080

Could you please tell me.. how big is your systrm.. How many atoms are there? Soham On Thu, 18 Apr 2019, 10:51 pm Jason Hogrefe, wrote: > Dear Gromacs Users, > > Exxact corporation has conducted benchmarks for Gromacs using NVIDIA RTX > 2080 GPUs. We ran them a few months back, but thought the

Re: [gmx-users] make index for protein multiple ligand md simulation

It should be Protein_index_number | ligand_index_number | cofactor_index_number (In a single line) and you are done!!! On Sun, 14 Apr 2019, 4:14 am m mar, wrote: > dear users > I want to run md simulation for protein with cofactor and ligand > simultaneously, but I dont know how I should

Re: [gmx-users] Citrate parameters

Which force field you are using and how you made the itp of the citrate molecule? On Fri, 12 Apr 2019, 8:23 pm Pandya, Akash, wrote: > Hi all, > > My simulation contains citrate molecules. When I try to solvate the > system, I get this error. Can anybody help with this? > > WARNING 1 [file

Re: [gmx-users] Doubt in nmol tool

No need to use -nmol On Mon, 8 Apr 2019, 4:21 pm nidhi, wrote: > That means there is no need of using -nmol option. > > Thank You very much :) > > > On Mon, Apr 8, 2019 at 3:57 PM Soham Sarkar wrote: > > > In that case select all c-alpha and make a group in index

Re: [gmx-users] Doubt in nmol tool

is I have selected Rg for "C-alpha" atoms plus "-nmol 3" . > > Thank You, > Sundari > > On Mon, Apr 8, 2019 at 2:50 PM Soham Sarkar wrote: > > > What do you want? > > Do you want to calculate the radius of gyration of the three chain at a > > t

Re: [gmx-users] Doubt in nmol tool

What do you want? Do you want to calculate the radius of gyration of the three chain at a time? If so then make a index of these protein chains together and calculate rg by selecting it. If not then calculate the chain's rg individually. -Soham On Mon, 8 Apr 2019, 2:36 pm Sundari, wrote: > Dear

Re: [gmx-users] For parametrisation

Generate an itp file for your molecule according to your force field. In the respective force field folder in aminoacids.rtp file define your molecule's atom name and bond connectivity and you are done. On Sun, 7 Apr 2019, 1:24 am subrat ranjan tripathy, < subratlipatripathy...@gmail.com> wrote:

Re: [gmx-users] (no subject) (Soham Sarkar)

be solved > > PS : next time add a title in you message. > > Good luck > > - > -- > > Message: 1 > Date: Fri, 5 Apr 2019 14:26:00 +0530 > From: Soham Sarkar > To: gmx-us...@gromacs.org >

[gmx-users] (no subject)

Dear all, I am using GROMACS-2018. I want to simulate a system which contain Tertiary Butyl alcohol (TBA) in it. I am facing problems while executing the GROMPP command. I have defined this residue in aminoacids.rtp. The error is like "NOTE 1 [file ions.mdp]: With Verlet lists the optimal

[gmx-users] problems with itp files

Dear all, I am using GROMACS-2018. I want simulate a system which contain Tertiary Butyl alcohol (TBA) in it. I am facing problems while executing the GROMPP command. I have defined the this residue in aminoacids.rtp. The error is like "NOTE 1 [file ions.mdp]: With Verlet lists the optimal

Re: [gmx-users] dssp error

sometimes it happened if there is any residue that is unknown to DSSP, then it might show this kind of error. I faced it once. On Fri, Mar 22, 2019 at 1:10 AM Mario Andres Rodriguez Pineda < mand...@iq.usp.br> wrote: > I downloaded this from dssp ftp page: dssp-2.0.4-linux-amd64, this is an >

Re: [gmx-users] generation of rtp and itp files

nerate itp file, which you can > find from documentation. > All the server generated datas need not be accurate for every molecule. > Anyway you have to do some ground work. > > Thank you > > On Fri, Mar 15, 2019 at 1:43 PM Soham Sarkar wrote: > > > Dear all, >

[gmx-users] generation of rtp and itp files

Dear all, I have a small molecule pdb file. I need the itp and rtp entry for the molecule in OPLS ff. TPPMKTOP is not working properly. Can any one please suggest me with a server that can automatically produce the itp entry and rtp entry for aminoacids.rtp. Thanks in advance- Soham --

[gmx-users] Steps for Markov State Modelling

Dear all, I have a protein trajectory in xtc format. I want to do the MSM analysis on this trajectory to see how the process is going on and the meta-stable states. I have followed the Video series by Frank Noe and team on MSM, but it is not clear to me how to start it. I have some

[gmx-users] Steps for executing Markov state Modelling (MSM) analysis

Dear all, I have a protein trajectory in xtc format. I want to do the MSM analysis on this trajectory to see how the process is going on and the meta-stable states. I have followed the Video series by Frank Noe and team on MSM, but it is not clear to me how to start it. I have some

[gmx-users] (no subject)

Hello Everyone, I want to calculate some properties of the solvent molecules within 6angstrom from the protein backbone, for that I need a index group which only contain that number of solvent molecules in the index.ndx file so that I can specifically select that index to calculate different

[gmx-users] (no subject)

Hello Everyone, I want to calculate some properties of the solvent molecules within 6angstrom from the protein backbone, for that I need a index group which only contain that number of solvent molecules in the index.ndx file so that I can specifically select that index to calculate different

[gmx-users] Fwd:

Dear all, This is the error I get while executing the grompp command " Program grompp, VERSION 4.5.6 Source code file: topio.c, line: 582 Fatal error: Syntax error - File tris.itp, line 19 Last line read: ' #error CORRECT VERSION OF FORCE FIELD [TPPREV_jun16] WAS NOT " I gave the command

[gmx-users] (no subject)

Dear all, This is the error I get while executing the grompp command " Program grompp, VERSION 4.5.6 Source code file: topio.c, line: 582 Fatal error: Syntax error - File tris.itp, line 19 Last line read: ' #error CORRECT VERSION OF FORCE FIELD [TPPREV_jun16] WAS NOT " I gave the command

Re: [gmx-users] secondary structure analysis

You can use do_dssp utility to generate the secondary structure On Mon, 24 Sep 2018, 5:34 pm SHAHEE ISLAM, wrote: > hi, > i am doing martini based coarsed coarse grained simulation in > gromacs.after getting the coarse grained structure ,i can convert cg > pdb it to the gro file.using vmd,

Re: [gmx-users] Aggregation Analysis

gmx make_ndx is the tool to use for making grouos of your choice On Fri, 21 Sep 2018, 8:51 pm Aishwarya Dhar, wrote: > Hi, > > What do you mean by atom selection and how do I do that ? > > By using gmx clustersize we can get the index file containing the atom > numbers of the largest cluster.

Re: [gmx-users] residue not found

, Aug 8, 2018 at 7:44 PM Justin Lemkul wrote: > > > > > > > On 8/8/18 10:09 AM, Soham Sarkar wrote: > > > Put your residue name in the residuetypes.dat file and designate it as > > > nucleic acid. Keep the same file in your ff folder, which in turn > should

Re: [gmx-users] residue not found

Put your residue name in the residuetypes.dat file and designate it as nucleic acid. Keep the same file in your ff folder, which in turn should be in the working directory. On Wed, 8 Aug 2018, 6:54 pm abhisek Mondal, wrote: > Hi, > I'm facing a very odd issue in gromacs. I'm trying to execute

Re: [gmx-users] (no subject)

re you trying to observe something about the transition, or merely the > > different end points? > > > > Mark > > > >> On Tue, Jul 10, 2018 at 4:12 PM Soham Sarkar > wrote: > >> > >> Dear all, > >> I am planning to do a simulation where a

Re: [gmx-users] (no subject)

Thanks a lot.. On Sat, 21 Jul 2018, 9:57 pm Mark Abraham, wrote: > Hi, > > If you want to see whether a helix forms in a given solution, start from a > random coil in that solution. Don't start from a helix in another solution. > > Marm > > On Sat, Jul 21, 2018, 1

Re: [gmx-users] (no subject)

> > On Sat, Jul 21, 2018, 05:11 Soham Sarkar wrote: > > > I want to see the helix transition.. whether it is coming back or not in > > the presence of the protecting osmolyte where urea is already there in > the > > system > > > > On Sat, 21 Jul 2018, 2:2

Re: [gmx-users] (no subject)

uggler keeping > five balls in the air, froze time and added two knives to the items in the > air, it's not going to be consistent with any pattern in which a set of > five balls and two knives can be juggled. > > Mark > > > On Fri, Jul 20, 2018, 16:12 Soham Sarkar wro

Re: [gmx-users] (no subject)

to the effect of a chemicals in the system. Thanks in advance. - Soham On Tue, 10 Jul 2018, 4:51 pm Soham Sarkar, wrote: > Dear all, > I am planning to do a simulation where after 50ns of simulation I want to > add some other chemicals in the system and continue it for another 50ns, so > tha

Re: [gmx-users] (no subject)

is exclusively dedicated to the effect of a chemicals in the system. Thanks in advance. - Soham On Tue, 10 Jul 2018, 7:42 pm Soham Sarkar, wrote: > Dear all, > I am planning to do a simulation where after 50ns of simulation I want to > add some other chemicals in the system and

[gmx-users] (no subject)

Dear all, I am planning to do a simulation where after 50ns of simulation I want to add some other chemicals in the system and continue it for another 50ns, so that I can have the effect of that chemicals exclusively before and after adding it to the system.Is it at all possible? If yes please

[gmx-users] (no subject)

Dear all, I am planning to do a simulation where after 50ns of simulation I want to add some other chemicals in the system and continue it for another 50ns, so that I can have the effect of that chemicals exclusively before and after adding it to the system.Is it at all possible? If yes please

Re: [gmx-users] Force field parameter

I have already mailed them... waiting for their reply.. On Sat, 7 Jul 2018, 11:22 pm Mark Abraham, wrote: > Hi, > > Your other good approach is to contact the authors to ask them to share > their methodology fully, ie force field files. > > Mark > > On Sat, Jul 7,

Re: [gmx-users] 500ns simulation

Increase the number of steps On Wed, 4 Jul 2018, 12:07 pm Quyen V. Vu, wrote: > Take simulation time= timestep (dt) * number of steps (nstep) > > On Wed, Jul 4, 2018, 12:48 Soham Sarkar wrote: > > > Change in the number of time steps > > > > On Wed, 4 Jul 2018

Re: [gmx-users] 500ns simulation

Change in the number of time steps On Wed, 4 Jul 2018, 10:54 am Raag Saluja, wrote: > Hi! > > What changes do I make to the mdp files provided by you in the lysozyme > tutorial, to make it a 500ns simulation? > > Thanks in advance! > > Regards, > Raag > -- > Gromacs Users mailing list > > *

Re: [gmx-users] secondary structure query

Do you have any allien group in your structure? If you have, then remove that by indexing.. As per my understanding DSSP is very much residue specific. Probably cannot read anything but the biomolecules. On Tue, 12 Jun 2018, 7:01 pm SHAHEE ISLAM, wrote: > hi, > i am following this tutorial >

Re: [gmx-users] gmx conver-tpr error

tpbconv -s md.tpr -o md_new.tpr -extend 5 On Wed, 30 May 2018, 3:22 pm Amali Guruge, wrote: > Dear Gromacs users, > > I did a simulation for a 50 ns and I want to extend it by anther 50 ns. > Therefore, I used the command, > gmx convert-tpr -s run01.tpr -extend 5 -o run02.tpr > But I

Re: [gmx-users] calculation of distance between the center of geometry of two proteins

m> wrote: > > after deleting -select > > this error is coming > > Invalid command line argument: > > cog of group "Chain_A" plus cog of group "Chain_B" > > > > > > On 5/28/18, Soham Sarkar <soham9...@gmail.com> wrote: > >&g

Re: [gmx-users] calculation of distance between the center of geometry of two proteins

Invalid command line argument: > cog of group "Chain_A" plus cog of group "Chain_B" > > > On 5/28/18, Soham Sarkar <soham9...@gmail.com> wrote: > > Delete from -select.. previous are ok > > > > On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, <i

Re: [gmx-users] calculation of distance between the center of geometry of two proteins

Delete from -select.. previous are ok On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, wrote: > hi, > to calculate the distance between the center of geometry of two > proteins, i am using this command > g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg >

Re: [gmx-users] Colchicine topology

cs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- SOHAM SARKAR Junior Research Fellow Department of Chemistry INDIAN INSTITUTE OF T

Re: [gmx-users] topology file

Concatenate the drug and the CNT into a songle file by using cat ( see multiple protein in a box) renumber the combined gro... then take pdb from the gro file and use it as the initial structure.. put in any topology building server On Mon, 28 May 2018, 1:00 am mostafa paknia,

Re: [gmx-users] Problem in installing GROMACS 2018

Follow installation by Sridhar Manchu On Sun, 27 May 2018, 4:23 am Ali Ahmed, wrote: > Hello GROMACS users, > > I'm trying to install GROMACS 2018 on my laptop. I followed the > instructions on GROMACS website and everything looks fine. > But when I check the version. it

Re: [gmx-users] AMP_simulation

Try with 1ps time step On Thu, 24 May 2018, 6:33 pm , wrote: > Hello, > > I have tried doing the Molecular dynamics simulation of AMP using the > Gromos54a7 forcefield. > > ITP parameters for the AMP molecule has been generated using the ATB > builder. Minimization of the

Re: [gmx-users] regarding rmsd calculation of protein

No mention On Thu, 24 May 2018, 11:51 am SHAHEE ISLAM, <islamsha...@gmail.com> wrote: > thank you so much for your continuous help. > > On 5/24/18, Soham Sarkar <soham9...@gmail.com> wrote: > >>Selecting two chains at a time is of no work because each chain beha

Re: [gmx-users] regarding rmsd calculation of protein

h residue names ENAME CHAIN_A > Group is empty > > > On 5/24/18, Soham Sarkar <soham9...@gmail.com> wrote: > > You should give like ri 1-120 > > > > On Thu, 24 May 2018, 11:14 am SHAHEE ISLAM, <islamsha...@gmail.com> > wrote: > > > >> y

Re: [gmx-users] regarding rmsd calculation of protein

t; > ri 120 > > > 15 r_120 : 2 atoms > should i give this in the way. > > On 5/24/18, Soham Sarkar <soham9...@gmail.com> wrote: > > Put L(small) > > It will give the residue number > > > > On Thu, 24 May 2018, 11:00 am SHAHEE ISLAM, <islamsha...@

Re: [gmx-users] regarding rmsd calculation of protein

> these all options are shown on the screen. > but when i am giving > > | > > > Syntax error: "|" > can you please tell me what should i give. > > > > > On 5/24/18, Soham Sarkar <soham9...@gmail.com> wrote: > > It is any .gro file of

Re: [gmx-users] regarding rmsd calculation of protein

calculate rmsd. > > On 5/23/18, SHAHEE ISLAM <islamsha...@gmail.com> wrote: > > thank you so much for your quick reply. > > > > On 5/23/18, Soham Sarkar <soham9...@gmail.com> wrote: > >> Do proper indexing of each chain > >>> make_ndx -f em.

Re: [gmx-users] regarding rmsd calculation of protein

h the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > s

[gmx-users] Quantification of overcharging

. Please help me with the detail procedure, how I can show that there is overcharging at the higher concentration regime but not at the lower concentration. Thanks in advance. -- SOHAM SARKAR Junior Research Fellow Department of Chemistry INDIAN INSTITUTE OF TECHNOLOGY BOMBAY -- Gromacs Users mailing

[gmx-users] Quantification of overcharging

. Please help me with the detail procedure, how I can show that there is overcharging at the higher concentration regime but not at the lower concentration. Thanks in advance. - Soham -- SOHAM SARKAR Junior Research Fellow Department of Chemistry INDIAN INSTITUTE OF TECHNOLOGY BOMBAY -- Gromacs Users

Re: [gmx-users] Does a logical pressure (1 Bar) can be reached in REMD?

Thanks for clarification.. On Sat, 19 May 2018, 11:11 pm Justin Lemkul, <jalem...@vt.edu> wrote: > > > On 5/19/18 1:37 PM, Soham Sarkar wrote: > > Thanks for your reply Justin... > > But these pressure I provided here are by doing the gmx energy -f > ene

Re: [gmx-users] Does a logical pressure (1 Bar) can be reached in REMD?

is the actual pressure of my system? Or is there any pressure convergence protocol in REMD? Thanks in advance -Soham On Sat, 19 May 2018, 9:11 pm Justin Lemkul, <jalem...@vt.edu> wrote: > > > On 5/19/18 8:45 AM, Soham Sarkar wrote: > > Thanks for reply.. but what is the actual pressu

Re: [gmx-users] Does a logical pressure (1 Bar) can be reached in REMD?

://www.gromacs.org/Documentation/Terminology/Pressure > > Mark > > On Sat, May 19, 2018, 13:04 Soham Sarkar <soham9...@gmail.com> wrote: > > > Dear All, > > I have a small system including a 4 residue peptide. I have chosen 8 > > temperature windows for doing

[gmx-users] Does a logical pressure (1 Bar) can be reached in REMD?

1273.92 448.873 1628.61 469.438 2005.04 490.272 2392.50 -- SOHAM SARKAR Junior Research Fellow Department of Chemistry INDIAN INSTITUTE OF TECHNOLOGY BOMBAY -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support