Re: [gmx-users] Calculating diffusion coefficient in three dimension
Dear Justin, I have referred to an article (Vuorela T, Catte A, Niemela PS, Hall A, Hyvonen MT, et al. (2010) Role of Lipids in Spheroidal High Density Lipoproteins. PLoS Comput Biol 6(10): e1000964. doi:10.1371/journal.pcbi.1000964), where the authors have clearly described the fitting of 2D diffusion coefficient to the surface lipids (diffusion along the lipid-water interface ) and 3D diffusion coefficient to the core lipids. On Wed, Nov 13, 2013 at 7:19 PM, Justin Lemkul wrote: > > > On 11/13/13 12:20 AM, Venkat Reddy wrote: > >> Dear Justin and Piggot, >> Thanks for the suggestions. Actually, I have constructed a CG lipid >> vesicle >> by placing lipids in random conformation in a simulation box. My lipid >> system is heterogeneous, i.e., it has different types of lipids >> (POPC,CHOLESTEROL,PPC...etc). Some of them occupy the outer layer of >> vesicle (POPC), and some stay in the intermediate region (CHOL). So, I >> want >> to calculate the diffusion rates of these lipids. Since POPC forms the >> surface (polar heads interacting with water and their tails points to the >> core), I suppose we have to calculate 2D diffusion for POPC. For the >> lipids >> in the core, they can diffuse in 3-dimension. So, it requires a 3D >> diffusion coefficient for these core lipids. How to calculate 2D and 3D >> diffusion coeff.? Hope I am clear. >> >> > 2D diffusion coefficients are what the -lateral option does. I really > don't understand why you want a 2D value for anything with spherical > symmetry. If there is an outer layer of a vesicle, that's as much a sphere > as anything inside it. > > -Justin > > > >> On Wed, Nov 13, 2013 at 12:58 AM, Thomas Piggot > >wrote: >> >> Hi Venkat, >>> >>> Can you make it a bit clearer what you actually want? >>> >>> If it is the diffusion of the lipids along the curved surface of the >>> vesicle, rather than simply the overall 3D diffusion, this is not trivial >>> to calculate as I don't believe g_msd will do this for you. This property >>> has been studied before though, so I suggest you search the literature >>> for >>> papers simulating vesicles to see how the lipid diffusion was calculated. >>> >>> Cheers >>> >>> Tom >>> >>> >>> On 11/12/2013 06:35 PM, Justin Lemkul wrote: >>> >>> >>>> >>>> On 11/12/13 1:33 PM, Venkat Reddy wrote: >>>> >>>> Thanks Justin. So, I have to calculate diffusion coefficient three >>>>> times >>>>> (x,y,z) and finally add-up together to get in 3D??? >>>>> >>>>> >>>>> If you just want the overall diffusion constant, that's what g_msd >>>> does >>>> without any additional options. >>>> >>>> -Justin >>>> >>>> >>>> On Tue, Nov 12, 2013 at 11:25 PM, Justin Lemkul >>>>> wrote: >>>>> >>>>> >>>>> >>>>>> On 11/12/13 12:30 PM, Venkat Reddy wrote: >>>>>> >>>>>> Dear Sir, Thanks for the quick reply. >>>>>> >>>>>>> So, I have to declare -type no flag. Isn't it?? >>>>>>> >>>>>>> >>>>>>> The options for the -type flag are x, y, or z. You said you wanted >>>>>> the >>>>>> diffusion coefficient in each spatial dimension. That is precisely >>>>>> what >>>>>> this option will do. >>>>>> >>>>>> >>>>>>and I have recently gone through Justin's membrane protein >>>>>> tutorial, >>>>>> where >>>>>> >>>>>> >>>>>>> >>>>>>> You mean my tutorial :) >>>>>> >>>>>> >>>>>>he has calculated diffusion coefficient for lipids in a membrane by >>>>>> >>>>>> creating an index group for a particular atom. So, here also shall I >>>>>>> do >>>>>>> the >>>>>>> same thing? Moreover, mine is a coarse-grained system. >>>>>>> >>>>>>> >>>>>>> Yes, a representative atom is usually what is passed to g_msd. >>>>>>> >>>>>> >>>>>> >>>>>> -Justin >>>>>> >>>&g
Re: [gmx-users] Calculating diffusion coefficient in three dimension
Dear Justin and Piggot, Thanks for the suggestions. Actually, I have constructed a CG lipid vesicle by placing lipids in random conformation in a simulation box. My lipid system is heterogeneous, i.e., it has different types of lipids (POPC,CHOLESTEROL,PPC...etc). Some of them occupy the outer layer of vesicle (POPC), and some stay in the intermediate region (CHOL). So, I want to calculate the diffusion rates of these lipids. Since POPC forms the surface (polar heads interacting with water and their tails points to the core), I suppose we have to calculate 2D diffusion for POPC. For the lipids in the core, they can diffuse in 3-dimension. So, it requires a 3D diffusion coefficient for these core lipids. How to calculate 2D and 3D diffusion coeff.? Hope I am clear. On Wed, Nov 13, 2013 at 12:58 AM, Thomas Piggot wrote: > Hi Venkat, > > Can you make it a bit clearer what you actually want? > > If it is the diffusion of the lipids along the curved surface of the > vesicle, rather than simply the overall 3D diffusion, this is not trivial > to calculate as I don't believe g_msd will do this for you. This property > has been studied before though, so I suggest you search the literature for > papers simulating vesicles to see how the lipid diffusion was calculated. > > Cheers > > Tom > > > On 11/12/2013 06:35 PM, Justin Lemkul wrote: > >> >> >> On 11/12/13 1:33 PM, Venkat Reddy wrote: >> >>> Thanks Justin. So, I have to calculate diffusion coefficient three times >>> (x,y,z) and finally add-up together to get in 3D??? >>> >>> >> If you just want the overall diffusion constant, that's what g_msd does >> without any additional options. >> >> -Justin >> >> >>> On Tue, Nov 12, 2013 at 11:25 PM, Justin Lemkul wrote: >>> >>> >>>> >>>> On 11/12/13 12:30 PM, Venkat Reddy wrote: >>>> >>>> Dear Sir, Thanks for the quick reply. >>>>> So, I have to declare -type no flag. Isn't it?? >>>>> >>>>> >>>> The options for the -type flag are x, y, or z. You said you wanted the >>>> diffusion coefficient in each spatial dimension. That is precisely what >>>> this option will do. >>>> >>>> >>>> and I have recently gone through Justin's membrane protein tutorial, >>>> where >>>> >>>>> >>>>> >>>> You mean my tutorial :) >>>> >>>> >>>> he has calculated diffusion coefficient for lipids in a membrane by >>>> >>>>> creating an index group for a particular atom. So, here also shall I do >>>>> the >>>>> same thing? Moreover, mine is a coarse-grained system. >>>>> >>>>> >>>>> Yes, a representative atom is usually what is passed to g_msd. >>>> >>>> >>>> -Justin >>>> >>>> >>>> >>>>> On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul >>>>> wrote: >>>>> >>>>> >>>>> >>>>>> On 11/12/13 11:25 AM, Venkat Reddy wrote: >>>>>> >>>>>> Then, how to mention the direction for spherical particles Sir? >>>>>> >>>>>>> >>>>>>> >>>>>>> Read g_msd -h again, paying specific attention to the -type flag. >>>>>>> >>>>>> >>>>>> >>>>>> -Justin >>>>>> >>>>>> >>>>>> On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul >>>>>> wrote: >>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 11/12/13 8:55 AM, Venkat Reddy wrote: >>>>>>>> >>>>>>>>Thank you sir for the prompt reply. >>>>>>>> >>>>>>>> *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg >>>>>>>>> -tu >>>>>>>>> ns* >>>>>>>>> >>>>>>>>> Here I am giving -lateral z (like for membrane simulations). Is it >>>>>>>>> fine >>>>>>>>> for >>>>>>>>> spherical systems also? >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>No. The sy
Re: [gmx-users] Calculating diffusion coefficient in three dimension
Thanks Justin. So, I have to calculate diffusion coefficient three times (x,y,z) and finally add-up together to get in 3D??? On Tue, Nov 12, 2013 at 11:25 PM, Justin Lemkul wrote: > > > On 11/12/13 12:30 PM, Venkat Reddy wrote: > >> Dear Sir, Thanks for the quick reply. >> So, I have to declare -type no flag. Isn't it?? >> > > The options for the -type flag are x, y, or z. You said you wanted the > diffusion coefficient in each spatial dimension. That is precisely what > this option will do. > > > and I have recently gone through Justin's membrane protein tutorial, where >> > > You mean my tutorial :) > > > he has calculated diffusion coefficient for lipids in a membrane by >> creating an index group for a particular atom. So, here also shall I do >> the >> same thing? Moreover, mine is a coarse-grained system. >> >> > Yes, a representative atom is usually what is passed to g_msd. > > > -Justin > > >> >> On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul wrote: >> >> >>> >>> On 11/12/13 11:25 AM, Venkat Reddy wrote: >>> >>> Then, how to mention the direction for spherical particles Sir? >>>> >>>> >>>> Read g_msd -h again, paying specific attention to the -type flag. >>> >>> >>> -Justin >>> >>> >>> On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul wrote: >>>> >>>> >>>> >>>>> On 11/12/13 8:55 AM, Venkat Reddy wrote: >>>>> >>>>> Thank you sir for the prompt reply. >>>>> >>>>>> *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu >>>>>> ns* >>>>>> >>>>>> Here I am giving -lateral z (like for membrane simulations). Is it >>>>>> fine >>>>>> for >>>>>> spherical systems also? >>>>>> >>>>>> >>>>>> >>>>>> No. The system is a sphere, so what use is it to calculate motion >>>>>> >>>>> perpendicular to z when you have lipids moving in all three spatial >>>>> dimensions? A vesicle is very different from a membrane, in which the >>>>> lipids move in a plane, thus making "-lateral z" useful. >>>>> >>>>> -Justin >>>>> >>>>> >>>>>On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban < >>>>> vvcha...@gmail.com >>>>> >>>>> wrote: >>>>>> >>>>>>> >>>>>>> >>>>>>MSD is 3D by default. >>>>>> >>>>>> >>>>>>> >>>>>>> Dr. Vitaly V. Chaban >>>>>>> >>>>>>> >>>>>>> On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy >>>>>>> wrote: >>>>>>> >>>>>>> Dear all, >>>>>>> >>>>>>>> I am simulating a spherical lipid vesicle. I want to calculate the >>>>>>>> diffusion coefficient for each lipid component in 3D. How to >>>>>>>> calculate >>>>>>>> it >>>>>>>> using g_msd (or any other tool like g_velacc)? >>>>>>>> >>>>>>>> Thank you for your concern >>>>>>>> >>>>>>>> -- >>>>>>>> With Best Wishes >>>>>>>> Venkat Reddy Chirasani >>>>>>>> -- >>>>>>>> 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-users-requ...@gromacs.org. >>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>> gmx-users mailing listgmx-users@
Re: [gmx-users] Calculating diffusion coefficient in three dimension
Dear Sir, Thanks for the quick reply. So, I have to declare -type no flag. Isn't it?? and I have recently gone through Justin's membrane protein tutorial, where he has calculated diffusion coefficient for lipids in a membrane by creating an index group for a particular atom. So, here also shall I do the same thing? Moreover, mine is a coarse-grained system. On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul wrote: > > > On 11/12/13 11:25 AM, Venkat Reddy wrote: > >> Then, how to mention the direction for spherical particles Sir? >> >> > Read g_msd -h again, paying specific attention to the -type flag. > > > -Justin > > >> On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul wrote: >> >> >>> >>> On 11/12/13 8:55 AM, Venkat Reddy wrote: >>> >>> Thank you sir for the prompt reply. >>>> *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns* >>>> >>>> Here I am giving -lateral z (like for membrane simulations). Is it fine >>>> for >>>> spherical systems also? >>>> >>>> >>>> >>>> No. The system is a sphere, so what use is it to calculate motion >>> perpendicular to z when you have lipids moving in all three spatial >>> dimensions? A vesicle is very different from a membrane, in which the >>> lipids move in a plane, thus making "-lateral z" useful. >>> >>> -Justin >>> >>> >>> On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban >> >>>> wrote: >>>>> >>>> >>>> MSD is 3D by default. >>>> >>>>> >>>>> >>>>> Dr. Vitaly V. Chaban >>>>> >>>>> >>>>> On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy >>>>> wrote: >>>>> >>>>> Dear all, >>>>>> I am simulating a spherical lipid vesicle. I want to calculate the >>>>>> diffusion coefficient for each lipid component in 3D. How to calculate >>>>>> it >>>>>> using g_msd (or any other tool like g_velacc)? >>>>>> >>>>>> Thank you for your concern >>>>>> >>>>>> -- >>>>>> With Best Wishes >>>>>> Venkat Reddy Chirasani >>>>>> -- >>>>>> 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-users-requ...@gromacs.org. >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>> >>>>>> -- >>>>> 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-users-requ...@gromacs.org. >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> >>> == >>> >>> -- >>> 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-users-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_
Re: [gmx-users] Calculating diffusion coefficient in three dimension
Then, how to mention the direction for spherical particles Sir? On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul wrote: > > > On 11/12/13 8:55 AM, Venkat Reddy wrote: > >> Thank you sir for the prompt reply. >> *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns* >> >> Here I am giving -lateral z (like for membrane simulations). Is it fine >> for >> spherical systems also? >> >> >> > No. The system is a sphere, so what use is it to calculate motion > perpendicular to z when you have lipids moving in all three spatial > dimensions? A vesicle is very different from a membrane, in which the > lipids move in a plane, thus making "-lateral z" useful. > > -Justin > > > On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban > >wrote: >> >> MSD is 3D by default. >>> >>> >>> Dr. Vitaly V. Chaban >>> >>> >>> On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy >>> wrote: >>> >>>> Dear all, >>>> I am simulating a spherical lipid vesicle. I want to calculate the >>>> diffusion coefficient for each lipid component in 3D. How to calculate >>>> it >>>> using g_msd (or any other tool like g_velacc)? >>>> >>>> Thank you for your concern >>>> >>>> -- >>>> With Best Wishes >>>> Venkat Reddy Chirasani >>>> -- >>>> 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-users-requ...@gromacs.org. >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>> -- >>> 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-users-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >> >> >> > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Calculating diffusion coefficient in three dimension
Thank you sir for the prompt reply. *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns* Here I am giving -lateral z (like for membrane simulations). Is it fine for spherical systems also? On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban wrote: > MSD is 3D by default. > > > Dr. Vitaly V. Chaban > > > On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy wrote: > > Dear all, > > I am simulating a spherical lipid vesicle. I want to calculate the > > diffusion coefficient for each lipid component in 3D. How to calculate it > > using g_msd (or any other tool like g_velacc)? > > > > Thank you for your concern > > > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > -- > > 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-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Calculating diffusion coefficient in three dimension
Dear all, I am simulating a spherical lipid vesicle. I want to calculate the diffusion coefficient for each lipid component in 3D. How to calculate it using g_msd (or any other tool like g_velacc)? Thank you for your concern -- With Best Wishes Venkat Reddy Chirasani -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] parallel simulation
Hi, Is it a local work station or cluster with multiple CPUs? Which gromacs version did you install? On Mon, Oct 7, 2013 at 1:55 PM, pratibha kapoor wrote: > I would like to run one simulation in parallel so that it utilises all the > available nodes and cores. For that, > I have compiled gromacs with mpi enabled and also installed openmpi on my > machine. > I am using the following command: > mpirun -np 4 mdrun_mpi -v -s *.tpr > > When i use top command, I get: > > PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND > > 22449 root 20 0 107m 59m 3152 R25 2.9 0:05.42 > mdrun_mpi > 22450 root 20 0 107m 59m 3152 R25 2.9 0:05.41 > mdrun_mpi > 22451 root 20 0 107m 59m 3152 R25 2.9 0:05.41 > mdrun_mpi > 22452 root 20 0 107m 59m 3152 R25 2.9 0:05.40 > mdrun_mpi > > Similarly when i use mpirun -np 2 mdrun_mpi -v -s *.tpr, I get > > PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND > 22461 root 20 0 108m 59m 3248 R 50 3.0 5:58.64 > mdrun_mpi > 22462 root 20 0 108m 59m 3248 R 50 3.0 5:58.56 > mdrun_mpi > > If I look at %CPU column, it is actually 100/(no. of processes) > Why is all the cpu not 100% utilised? > Also if I compare my performance, it is significantly hampered. > Please suggest me the way so that I can run one simulation on all available > nodes, cores and threads. > 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! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding g_membed
Dear all, I have a basic doubt regrading g_membed. Is it compulsory to solvate the membrane system before the protein's insertion or can we solvate after the protein's insertion? -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat after trjconv
Thank you sir. On Fri, Sep 27, 2013 at 11:47 AM, Tsjerk Wassenaar wrote: > Yes. > > Cheers, > > Tsjerk > > > On Fri, Sep 27, 2013 at 7:51 AM, Venkat Reddy wrote: > > > Thanks for the quick reply sir. > > So, does it mean I can apply "trjcat" on the processed xtc files??? > > > > > > On Thu, Sep 26, 2013 at 10:25 PM, Tsjerk Wassenaar > >wrote: > > > > > Hi Venkat, > > > > > > These options are 'frame intrinsic' or 'history independent', unlike > -pbc > > > nojump. > > > > > > Cheers, > > > > > > Tsjerk > > > > > > On Sep 26, 2013 6:46 PM, "Venkat Reddy" wrote: > > > > > > Dear Tsjerk sir, > > > I used trjconv -pbc mol -ur compact options. > > > > > > On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar > > > wrote: > Hi Venkat, > > It... > > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > > > > http://lists.gromacs.org/mailman/listinfo/g... > > > -- > > > 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-users-requ...@gromacs.org. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > -- > > 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-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat after trjconv
Thanks for the quick reply sir. So, does it mean I can apply "trjcat" on the processed xtc files??? On Thu, Sep 26, 2013 at 10:25 PM, Tsjerk Wassenaar wrote: > Hi Venkat, > > These options are 'frame intrinsic' or 'history independent', unlike -pbc > nojump. > > Cheers, > > Tsjerk > > On Sep 26, 2013 6:46 PM, "Venkat Reddy" wrote: > > Dear Tsjerk sir, > I used trjconv -pbc mol -ur compact options. > > On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar > wrote: > Hi Venkat, > > It... > > > -- > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/g... > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat after trjconv
Dear Tsjerk sir, I used trjconv -pbc mol -ur compact options. On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar wrote: > Hi Venkat, > > It depends on what you mean with "removing pbc". > > Cheers, > > Tsjerk > > On Sep 26, 2013 5:21 PM, "Venkat Reddy" wrote: > > Dear Sir, > Thanks for the quick reply. > I accidentally lost one of my raw .xtc files. But I have the noPBC xtc > file. So, when ever I extend my simulation, first I am removing PBC then > concatenating it with existing noPBC xtc file. Is it fine?? > > > On Thu, Sep 26, 2013 at 7:13 PM, Dr. Vitaly Chaban >wrote: > > > I do not think that I ever tried myself, but is seems all the same. > Why > do you ask? > > > Dr. V... > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat after trjconv
Dear Sir, Thanks for the quick reply. I accidentally lost one of my raw .xtc files. But I have the noPBC xtc file. So, when ever I extend my simulation, first I am removing PBC then concatenating it with existing noPBC xtc file. Is it fine?? On Thu, Sep 26, 2013 at 7:13 PM, Dr. Vitaly Chaban wrote: > I do not think that I ever tried myself, but is seems all the same. > Why do you ask? > > > Dr. Vitaly V. Chaban > > > On Thu, Sep 26, 2013 at 3:40 PM, Venkat Reddy wrote: > > Dear all, > > I have a basic doubt. Is there any difference between the two processes > > where > > 1) I concatenate the trajectories and do trjconv to remove PBC, which is > a > > default process > > 2) Do trjconv on all the xtc files separately and then concatenate them. > > > > Thank you for your time > > > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > -- > > 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-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] trjcat after trjconv
Dear all, I have a basic doubt. Is there any difference between the two processes where 1) I concatenate the trajectories and do trjconv to remove PBC, which is a default process 2) Do trjconv on all the xtc files separately and then concatenate them. Thank you for your time -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding g_sgangle index file
Hello Sir, I have been using the new tool "gmx gangle". My actual intention is to calculate the orientation between any two same molecules (say cholesterol) throughout the trajectory and there are 40 cholesterol molecules. But I couldn't calculate it. I am getting "0" as output. My command is: gmx gangle -f traj_noPBC.xtc -s topol.tpr -n -g1 vector -g2 vector -group1 'resname CHOL and name R5 R0' -group2 'resname CHOL and name R5 R0' -oav -oall -oh On Mon, Sep 23, 2013 at 11:19 PM, Teemu Murtola wrote: > Hi, > > On Thu, Sep 19, 2013 at 7:19 PM, Venkat Reddy wrote: > > > @Teemu Murtola: Are there any modifications to the other gmx tools? (eg: > > rdf calculation with dynamic selection...etc). I am trying to explore the > > new version. > > > > Unfortunately, there are currently very few tools using the new mechanisms. > http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 lists > most of the changes: in practice, there's 'gmx distance' as a more flexible > alternative to computing distances, and g_select (now 'gmx select') has > gotten a few extra output options. There's also at least one new tool, 'gmx > freevolume'. > > Best regards, > Teemu > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding g_sgangle index file
Dear Sir, The tool "gmx gangle" is wonderful. The additional options are very flexible and easy to use. @Teemu Murtola: Are there any modifications to the other gmx tools? (eg: rdf calculation with dynamic selection...etc). I am trying to explore the new version. Thank you On Tue, Sep 17, 2013 at 11:31 PM, Teemu Murtola wrote: > Hello, > > Please keep correspondence on the list so that others may benefit from it, > and you don't need to wait for some particular person to respond. > > On Tue, Sep 17, 2013 at 1:24 PM, Venkat Reddy wrote: > > > > On Tue, Sep 17, 2013 at 12:38 AM, Teemu Murtola > > >> wrote: > >> > >>> version (from the git master branch), you can use a much more powerful > >>> 'gmx > >>> gangle' tool, which can calculate multiple angles in one go. > >>> > >> > > I have installed the "gromacs-master" version from GIT, but I couldn't > see > > any changes between the old g_sgangle and the current one. Is the new > tool > > underway in development? > > > > Try "gmx gangle -h" per my original suggestion. The g_sgangle tool hasn't > been touched. > > Best regards, > Teemu > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding g_sgangle index file
Thank you sir for the nice tip. I will try it out and let you know if I have any problem. On Tue, Sep 17, 2013 at 12:38 AM, Teemu Murtola wrote: > Hello, > > On Sun, Sep 15, 2013 at 5:05 PM, Venkat Reddy wrote: > > > I found g_sgangle is the suitable tool > > to calculate the angle between two cholesterol rings. But the problem > is, I > > want to do this analysis for my whole system, which has 40 cholesterol > > molecules. Whereas I can input either two or three atoms in the g_sgangle > > index file. A quick surf through the gmx-archive yielded a suggestion > like: > > > > "An index group should contain all (1,2) pairs such that the overall > group > > size is a multiple of two. The index group has to be in a particular > > order, like 1 2 1 2 etc.," > > > > > > > > I got the output index file in the same order.,i.e., R5 R0 R5 R0etc. > > But when I execute g_sgangle, it is saying something wrong with the index > > file. How to solve this error? > > How to organize the index file in a multiple of 2? > > > > It is only possible to calculate a single angle in one invocation of > g_sgangle. You could script your calculation to run g_sgangle once for each > of your molecules, but that gets somewhat tedious. With the development > version (from the git master branch), you can use a much more powerful 'gmx > gangle' tool, which can calculate multiple angles in one go. As an added > bonus, you don't need to invoke g_select separately, but can simply provide > the selection to the tool. > > Best regards, > Teemu > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding g_sgangle index file
Dear Gmx-users, My system has cholesterol molecules and I want to do the orientation analysis for the cholesterol rings. I found g_sgangle is the suitable tool to calculate the angle between two cholesterol rings. But the problem is, I want to do this analysis for my whole system, which has 40 cholesterol molecules. Whereas I can input either two or three atoms in the g_sgangle index file. A quick surf through the gmx-archive yielded a suggestion like: "An index group should contain all (1,2) pairs such that the overall group size is a multiple of two. The index group has to be in a particular order, like 1 2 1 2 etc.," Accordingly, I have selected the atoms using g_select -f *.pdb -s *.tpr -select 'resname CHOL and name R5 R0' (R5 and R0 are bead types in CG system) I got the output index file in the same order.,i.e., R5 R0 R5 R0etc. But when I execute g_sgangle, it is saying something wrong with the index file. How to solve this error? How to organize the index file in a multiple of 2? Thank you for your valuable time and concern -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding g_densmap output
But its not a xpm file. Its a dat file On Fri, Aug 30, 2013 at 12:05 PM, Chandan Choudhury wrote: > On Fri, Aug 30, 2013 at 11:18 AM, Venkat Reddy > wrote: > > > Dear Gromacs users, > > I am analyzing the density of my spherical lipid vesicle using g_densmap > > tool with the following options. > > > > g_densmap -f vesicle_noPBC.xtc -s vesicle-12us.tpr -n index.ndx -dt > 1000 > > -od -amax 6 -rmax 6 -mirror > > > > I am getting densmap.dat as output, which is a text file. How to analyze > > this text file? Also Please suggest me any tool which can convert this > text > > file to some visually appealing grid map or a 2D (or) 3D graph? > > > use xpm2ps. > > > > > Thanks for your valuable time > > > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > -- > > 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-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding g_densmap output
Dear Gromacs users, I am analyzing the density of my spherical lipid vesicle using g_densmap tool with the following options. g_densmap -f vesicle_noPBC.xtc -s vesicle-12us.tpr -n index.ndx -dt 1000 -od -amax 6 -rmax 6 -mirror I am getting densmap.dat as output, which is a text file. How to analyze this text file? Also Please suggest me any tool which can convert this text file to some visually appealing grid map or a 2D (or) 3D graph? Thanks for your valuable time -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Coordination number
Sir Thank you for the reply. The higher graph is also broader and I thought should then give a higher coordination number. Does gromacs use the box density? does it not use 4*pi*r2*g(r) for calculating rdf (thats what I read in a paper where the authors have used gromacs for simulation and analyses)?where is the density coming then? Thank you On Wed, Aug 21, 2013 at 4:20 AM, Dallas Warren wrote: > Peak can be higher, but if it is narrower the total area can still be > less. Remember it is an area under the curve. Additionally, that overall > system / box density that you are using may be different too, so that will > make a difference. > > Catch ya, > > Dr. Dallas Warren > Drug Discovery Biology > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > +61 3 9903 9304 > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > -Original Message- > > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > > boun...@gromacs.org] On Behalf Of Venkat Reddy > > Sent: Monday, 19 August 2013 8:11 PM > > To: Discussion list for GROMACS users > > Subject: [gmx-users] Coordination number > > > > Dear Gromacs Users, > > > > I have a query about the g_rdf utility. I have two different systems of > > water with Ionic Liquid 1 and Ionic Liquid 2. When I plot the rdf using > > > > g_rdf -f x_gro.pdb -s x.pdb -n rdf.ndx -o rdf1.xvg/rdf2.xvg -cn > > rdf1_cn.xvg/rdf2_cn.xvg -rdf res_com > > > > where rdf1/rdf2 is for water distribution around Ionic liquid 1/2, > > > > the rdf1.xvg clearly shows a higher first peak g(r) than the rdf2.xvg. > > Both > > also have minima at the same distance. However, the coordination number > > at > > first minima from rdf1_cn.xvg is lesser than the same from rd2_cn.xvg. > > How > > is this possible? If the peak is larger, the integration of it should > > give > > a higher value right? > > > > Please help. > > > > > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > -- > > 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-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Coordination number
Dear Gromacs Users, I have a query about the g_rdf utility. I have two different systems of water with Ionic Liquid 1 and Ionic Liquid 2. When I plot the rdf using g_rdf -f x_gro.pdb -s x.pdb -n rdf.ndx -o rdf1.xvg/rdf2.xvg -cn rdf1_cn.xvg/rdf2_cn.xvg -rdf res_com where rdf1/rdf2 is for water distribution around Ionic liquid 1/2, the rdf1.xvg clearly shows a higher first peak g(r) than the rdf2.xvg. Both also have minima at the same distance. However, the coordination number at first minima from rdf1_cn.xvg is lesser than the same from rd2_cn.xvg. How is this possible? If the peak is larger, the integration of it should give a higher value right? Please help. -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] psf to tpr
Dear All, I would like to convert my NAMD psf file to GROMACS tpr file? First of all, is it possible? If so, is there any script available? Please help me in this regard. Thanks for your valuable time. -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding g_order
Thanks Justin for the quick reply. I am simulating a protein with bound lipids. I am in a dilemma to choose the direction of the normal to calculate order parameter. In your *Membrane-protein *simulation tutorial, you have chosen normal to the bilayer along the z-axis. But in my case, there is no bilayer, infact, only few bound lipids are there. In which direction I should choose the normal (*-d option*)? On Thu, Aug 1, 2013 at 10:54 PM, Justin Lemkul wrote: > > > On 8/1/13 12:07 PM, Venkat Reddy wrote: > >> Dear Gmx-users, >> In the GROMACS site, it has been mentioned that there is a bug (Instead of >> numbering carbons from 2-17, the numbering starts from 1-16) in g_order >> program up to, and including, v4.5.4. But when I am using v4.5.5, I am >> getting the same sort of numbering. Is it normal or I should renumber from >> 2-17? >> >> > If you're getting a number starting with 1, it's probably wrong. You > can't calculated Scd for the first carbon in a chain because there is no > n-1 carbon from which to determine the necessary vectors. Someone > (probably me) updated the wiki when version 4.5.4 was current, so probably > any 4.5.x version is really affected, and 4.6.x may be as well, since this > really is just a trivial bug that requires simple reinterpretation. > > -Justin > > -- > ==** > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu | > (410) > 706-7441 > > ==** > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding g_order
Dear Gmx-users, In the GROMACS site, it has been mentioned that there is a bug (Instead of numbering carbons from 2-17, the numbering starts from 1-16) in g_order program up to, and including, v4.5.4. But when I am using v4.5.5, I am getting the same sort of numbering. Is it normal or I should renumber from 2-17? Thank you -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding mdrun
Dear gmx-users, I am experiencing some strange things while performing mdrun. I am running a CG simulation and it is terminating with LINCS warnings after approx. 500ns of simulation. If I restart it with the check point file, then its running with out any errors. Is my simulation is reliable?? I am using Gromacs-4.5.5. Thank you -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] residues interaction with ligand
You can use g_select utility. For more details check the following link http://www.gromacs.org/Documentation/Gromacs_Utilities/g_select On Sun, May 19, 2013 at 1:20 PM, Arunima Shilpi wrote: > Respected Sir > > If we have to find the residues surrounding the ligand in protein ligand > complex... than which gromacs command should be used... > > Looking forward for your reply. > > -- > > Thanking You with Regards. > > Arunima Shilpi > > Ph. D Research Scholar(Cancer & Epigenetics) > Department of Life Science > National Institute of Technology > Rourkela > Odisha > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] CHARMM lipid parameters
Dear all, How can I generate a particular lipid itp file compatible with CHARMM27 (say Cholesteryl oleate). The link for CHARMM compatible cholesterol parameters in the lipidbook website is also dead. Thanks a lot -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Cholesteryl oleate parameters for CHARMM27 ff in Gromacs
Dear all, How can I generate a particular lipid itp file compatible with CHARMM27 (say Cholesteryl oleate). The link for CHARMM compatible cholesterol parameters in *lipidbook *website is also dead. Thanks a lot -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Usage of g_spatial
Sir Yes, trjconv works without tpr. Thanks for that. I want to see the distribution of anion around cation. Is it not possible to see an averaged spatial distribution of all anions around all cations? Do I need to make a selection of a single cation molecule? I did the selection of a single cation molecule which is approximately at the center of the box and did the following step 1: trjconv -s 1md.pdb -f 11md_gro.pdb -o 11md_gro_mod.pdb -center -ur compact -pbc none when it asked for group for centering and output, I selected the whole system for both. step 2: trjconv -s 1md.pdb -f 11md_gro_mod.pdb -o 11md_gro_mod1.pdb -fit rot+trans when it asked for group for least square once again I selected the whole system I selected the whole system as a previous discussion http://lists.gromacs.org/pipermail/gmx-users/2010-May/050879.html suggested the same because of an error that was happening in step 2. *Fatal error: Index[2385] 2410 is larger than the number of atoms in** the trajectory file (2409). * Since I was getting the same error if I made any form of selections in the first two steps, I output the whole system. step 3: g_spatial. and used ANI as group to generate SDF and a single cation residue as the group to output coords When I loaded the resultant cube in vmd I could see the whole distribution. Where am I going wrong? On Tue, May 7, 2013 at 6:23 PM, Christopher Neale < chris.ne...@mail.utoronto.ca> wrote: > Try this: > > trjconv -s my.pdb -f my.pdb -o mymod.pdb > g_spatial -s mymod.pdb -f mymod.pdb > > For the pre-processing, there must also be AMBER tools that will do this > for you if for some reason the above does not work for you (e.g. Option > -pbc mol requires a .tpr file for the -s option) > > Chris. > > -- original message -- > > I am analyzing trajectories of an ionic liquid system generated using AMBER > MD package. The force field parameters are typical of this IL system and > not from the existing libraries. Hence, it is difficult for me to generate > a tpr file. I understand that running the g_spatial command needs > pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I > need tpr file for that. So there is no way of doing g_spatial without a > tpr file is it? Then how do I generate tpr file for my system? > > Thanks for all the help > -- > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 On Tue, May 7, 2013 at 6:23 PM, Christopher Neale < chris.ne...@mail.utoronto.ca> wrote: > Try this: > > trjconv -s my.pdb -f my.pdb -o mymod.pdb > g_spatial -s mymod.pdb -f mymod.pdb > > For the pre-processing, there must also be AMBER tools that will do this > for you if for some reason the above does not work for you (e.g. Option > -pbc mol requires a .tpr file for the -s option) > > Chris. > > -- original message -- > > I am analyzing trajectories of an ionic liquid system generated using AMBER > MD package. The force field parameters are typical of this IL system and > not from the existing libraries. Hence, it is difficult for me to generate > a tpr file. I understand that running the g_spatial command needs > pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I > need tpr file for that. So there is no way of doing g_spatial without a > tpr file is it? Then how do I generate tpr file for my system? > > Thanks for all the help > -- > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Usage of g_spatial
Sorry for my ignorance, since the help manual uses tpr file for the first two steps before running g_spatial, could you please tell me how I should do them without tpr. Also when I just run g_spatial (without the first two steps) I get the distribution of all the anions around cations, so it is not informative. Thank you so much for all the help On Tue, May 7, 2013 at 2:48 PM, Dr. Vitaly Chaban wrote: > I think you can process the trajectories without generating TPR. > > Dr. Vitaly Chaban > > > On Tue, May 7, 2013 at 12:12 PM, Venkat Reddy wrote: > > > Dear gromacs users, > > > > I am analyzing trajectories of an ionic liquid system generated using > AMBER > > MD package. The force field parameters are typical of this IL system and > > not from the existing libraries. Hence, it is difficult for me to > generate > > a tpr file. I understand that running the g_spatial command needs > > pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I > > need tpr file for that. So there is no way of doing g_spatial without a > > tpr file is it? Then how do I generate tpr file for my system? > > > > Thanks for all the help > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > -- > > 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-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Usage of g_spatial
Dear gromacs users, I am analyzing trajectories of an ionic liquid system generated using AMBER MD package. The force field parameters are typical of this IL system and not from the existing libraries. Hence, it is difficult for me to generate a tpr file. I understand that running the g_spatial command needs pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I need tpr file for that. So there is no way of doing g_spatial without a tpr file is it? Then how do I generate tpr file for my system? Thanks for all the help -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Manual installation of new analysis tool
Dear Mark & Junghans,
I have got it. There is some problem in the Makefile. Thanks for your
suggestions and help
On Fri, Apr 26, 2013 at 11:12 AM, Venkat Reddy wrote:
> Dear Mark & Junghans,
> Thanks for your valuable suggestions.
> I have gone through the README file. It says compatibility with 4.5.x
> version. I am using 4.5.5. So, I think its not a problem.
> @Junghans: I have installed pkg-config in fact the $ pkg-config --libs
> libgmx returns
>the expected output; -lgmx -lm
>
> Here I am sending you the README file as attachment. Please go through it.
> If needed, I am happy to provide the code also.
>
> Thanks a lot
>
>
> On Fri, Apr 26, 2013 at 4:21 AM, Christoph Junghans wrote:
>
>> > Date: Thu, 25 Apr 2013 22:57:55 +0200
>> > From: Mark Abraham
>> > Subject: Re: [gmx-users] Manual installation of new analysis tool
>> > To: Discussion list for GROMACS users
>> > Message-ID:
>> > > 4wko947kc_y7s_gsyrxg8nms...@mail.gmail.com>
>> > Content-Type: text/plain; charset=ISO-8859-1
>> >
>> > On Wed, Apr 24, 2013 at 8:14 AM, Venkat Reddy
>> wrote:
>> >
>> >> Dear all,
>> >> I have got an analysis tool for analyzing membrane density from
>> Dr.Luca
>> >> monticelli. I have followed the installation instructions as given.
>> >>
>> >> 1) First thing is to load GROMACS
>> >>$ *source /usr/local/gromacs/bin/GMXRC*
>> >> 2) Enter the source directory of the program then make
>> >>$ cd g_mydensity
>> >>$ make
>> >> According to the instructions, it should create an executable
>> >> "*g_mydensity*"
>> >> but I am getting the following errors
>> >>
>> >> *cc `pkg-config --libs libgmx` g_mydensity.o matrix.o distances.o
>> >>
>> >
>> > Looks like his Makefile is relying on valid pkg-config registration.
>> I've
>> > no idea for what GROMACS versions under what conditions pkg-config
>> actually
>> > works, but I suggest you follow his instructions really precisely,
>> and/or
>> > contact him to resolve any doubtful points.
>> I added the pkg-config support with version 4.0.7 if I remember correctly.
>> Without knowing further details, two things come to my mind:
>> 0.) [Trivial] Make sure that pkg-config is actually installed.
>> 1.) Try if
>> $ pkg-config --libs libgmx
>> returns some useful output like "-lgmx -lm". If not, you might need to
>> set PKG_CONFIG_PATH to ${GMXLDLIB}/pkgconfig, but normally GMXRC does
>> that for you automatically.
>> 2.) Some functions in libgmx have been renamed/changed in the
>> development from 4.0 to 4.5 to 4.6, so you might actually need to
>> change the code, or use the same version as Dr.Luca Monticelli.
>>
>> Cheers,
>>
>> Christoph
>>
>>
>> >
>> > Mark
>> >
>> >
>> >> dist_mode.o grid_mode.o -o g_mydensity*
>> >> *g_mydensity.o: In function `gmx_log2':*
>> >> *g_mydensity.c:(.text+0xa8): undefined reference to `log'*
>> >> *g_mydensity.o: In function `gmx_invsqrt':*
>> >> *g_mydensity.c:(.text+0xf2): undefined reference to
>> `gmx_invsqrt_exptab'*
>> >> *g_mydensity.c:(.text+0x101): undefined reference to
>> >> `gmx_invsqrt_fracttab'*
>> >> *g_mydensity.o: In function `matrix_convert':*
>> >> *g_mydensity.c:(.text+0x381): undefined reference to `cos'*
>> >> *g_mydensity.c:(.text+0x3ad): undefined reference to `sin'*
>> >> *g_mydensity.c:(.text+0x3da): undefined reference to `cos'*
>> >> *g_mydensity.c:(.text+0x403): undefined reference to `cos'*
>> >> *g_mydensity.c:(.text+0x416): undefined reference to `cos'*
>> >> *g_mydensity.c:(.text+0x429): undefined reference to `cos'*
>> >> *g_mydensity.c:(.text+0x447): undefined reference to `sin'*
>> >> *g_mydensity.c:(.text+0x4ad): undefined reference to `sqrt'*
>> >> *g_mydensity.o: In function `get_electrons':*
>> >> *g_mydensity.c:(.text+0x527): undefined reference to `ffopen'*
>> >> *g_mydensity.c:(.text+0x564): undefined reference to `gmx_fatal'*
>> >> *g_mydensity.c:(.text+0x5b6): undefined reference to `gmx_fatal'*
>> >> *g_mydensity.c:(.text+0x600): undefined reference to `gmx_fatal'*
>> >> *g_mydensity.c:(.text+0x62e): undefined reference to `save_calloc'*
>>
Re: [gmx-users] Re: Manual installation of new analysis tool
Dear Mark & Junghans,
Thanks for your valuable suggestions.
I have gone through the README file. It says compatibility with 4.5.x
version. I am using 4.5.5. So, I think its not a problem.
@Junghans: I have installed pkg-config in fact the $ pkg-config --libs
libgmx returns
the expected output; -lgmx -lm
Here I am sending you the README file as attachment. Please go through it.
If needed, I am happy to provide the code also.
Thanks a lot
On Fri, Apr 26, 2013 at 4:21 AM, Christoph Junghans wrote:
> > Date: Thu, 25 Apr 2013 22:57:55 +0200
> > From: Mark Abraham
> > Subject: Re: [gmx-users] Manual installation of new analysis tool
> > To: Discussion list for GROMACS users
> > Message-ID:
> > 4wko947kc_y7s_gsyrxg8nms...@mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > On Wed, Apr 24, 2013 at 8:14 AM, Venkat Reddy
> wrote:
> >
> >> Dear all,
> >> I have got an analysis tool for analyzing membrane density from Dr.Luca
> >> monticelli. I have followed the installation instructions as given.
> >>
> >> 1) First thing is to load GROMACS
> >>$ *source /usr/local/gromacs/bin/GMXRC*
> >> 2) Enter the source directory of the program then make
> >>$ cd g_mydensity
> >>$ make
> >> According to the instructions, it should create an executable
> >> "*g_mydensity*"
> >> but I am getting the following errors
> >>
> >> *cc `pkg-config --libs libgmx` g_mydensity.o matrix.o distances.o
> >>
> >
> > Looks like his Makefile is relying on valid pkg-config registration. I've
> > no idea for what GROMACS versions under what conditions pkg-config
> actually
> > works, but I suggest you follow his instructions really precisely, and/or
> > contact him to resolve any doubtful points.
> I added the pkg-config support with version 4.0.7 if I remember correctly.
> Without knowing further details, two things come to my mind:
> 0.) [Trivial] Make sure that pkg-config is actually installed.
> 1.) Try if
> $ pkg-config --libs libgmx
> returns some useful output like "-lgmx -lm". If not, you might need to
> set PKG_CONFIG_PATH to ${GMXLDLIB}/pkgconfig, but normally GMXRC does
> that for you automatically.
> 2.) Some functions in libgmx have been renamed/changed in the
> development from 4.0 to 4.5 to 4.6, so you might actually need to
> change the code, or use the same version as Dr.Luca Monticelli.
>
> Cheers,
>
> Christoph
>
>
> >
> > Mark
> >
> >
> >> dist_mode.o grid_mode.o -o g_mydensity*
> >> *g_mydensity.o: In function `gmx_log2':*
> >> *g_mydensity.c:(.text+0xa8): undefined reference to `log'*
> >> *g_mydensity.o: In function `gmx_invsqrt':*
> >> *g_mydensity.c:(.text+0xf2): undefined reference to
> `gmx_invsqrt_exptab'*
> >> *g_mydensity.c:(.text+0x101): undefined reference to
> >> `gmx_invsqrt_fracttab'*
> >> *g_mydensity.o: In function `matrix_convert':*
> >> *g_mydensity.c:(.text+0x381): undefined reference to `cos'*
> >> *g_mydensity.c:(.text+0x3ad): undefined reference to `sin'*
> >> *g_mydensity.c:(.text+0x3da): undefined reference to `cos'*
> >> *g_mydensity.c:(.text+0x403): undefined reference to `cos'*
> >> *g_mydensity.c:(.text+0x416): undefined reference to `cos'*
> >> *g_mydensity.c:(.text+0x429): undefined reference to `cos'*
> >> *g_mydensity.c:(.text+0x447): undefined reference to `sin'*
> >> *g_mydensity.c:(.text+0x4ad): undefined reference to `sqrt'*
> >> *g_mydensity.o: In function `get_electrons':*
> >> *g_mydensity.c:(.text+0x527): undefined reference to `ffopen'*
> >> *g_mydensity.c:(.text+0x564): undefined reference to `gmx_fatal'*
> >> *g_mydensity.c:(.text+0x5b6): undefined reference to `gmx_fatal'*
> >> *g_mydensity.c:(.text+0x600): undefined reference to `gmx_fatal'*
> >> *g_mydensity.c:(.text+0x62e): undefined reference to `save_calloc'*
> >> *g_mydensity.c:(.text+0x68d): undefined reference to `gmx_fatal'*
> >> *g_mydensity.c:(.text+0x6eb): undefined reference to `gmx_fatal'*
> >> *g_mydensity.c:(.text+0x74f): undefined reference to `ffclose'*
> >> *g_mydensity.o: In function `center_coords':*
> >> *g_mydensity.c:(.text+0x88f): undefined reference to `calc_box_center'*
> >> *g_mydensity.o: In function `calc_electron_density':*
> >> *g_mydensity.c:(.text+0x945): undefined reference to `gmx_fatal'*
> >> *g_mydensi
[gmx-users] Manual installation of new analysis tool
ave_free'* *dist_mode.c:(.text+0x948): undefined reference to `save_free'* *grid_mode.o: In function `build_grids':* *grid_mode.c:(.text+0x81): undefined reference to `save_calloc'* *grid_mode.c:(.text+0x177): undefined reference to `gmx_fatal'* *grid_mode.c:(.text+0x1a2): undefined reference to `save_calloc'* *grid_mode.c:(.text+0x201): undefined reference to `ffopen'* *grid_mode.o: In function `clean_grids':* *grid_mode.c:(.text+0x2b8): undefined reference to `save_free'* *grid_mode.c:(.text+0x2c6): undefined reference to `ffclose'* *grid_mode.c:(.text+0x2e9): undefined reference to `save_free'* *grid_mode.o: In function `grid_store':* *grid_mode.c:(.text+0x41a): undefined reference to `put_atom_in_box'* *collect2: ld returned 1 exit status* *make: *** [g_mydensity] Error 1* Please help me in this regard. Thanks for your valuable time and concern. -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding top2psf script
Dear all, I want to reverse transform my CG lipid system to AA. I have been using g_fg2cg but I am getting some errors (like "Atoms in the .top are not numbered consecutively from 1"). So, I intend to use the script top2psf.plwritten by Dr.Lemkul, so that I can avail the help of VMD in cg2aa conversion. Can we use it for pure lipid systems (say POPC+CHOL+triglyceride+CE)? When I tried to execute it, I am getting the following error "Cannot open angles for reading: No such file or directory" Thanks for your concern -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Plotting data from g_spatial
Dear users I have a question regarding the cube file output we get from g_spatial analysis. My system comprises of hundreds of ionic liquids (composed of cation and anion). If I would like to see the spatial distribution of anions around cation, how do I get an average distribution. E.g, the way I am using it now, spatial distribution of all the anions in simulation box is shown, which is very inconclusive. I cannot specify a particular set of cations and anions, as they separate over time. Please help -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: RDF output has no data
Thank you sir for the valuable input. I will look into the matter and get to you. On Thu, Apr 11, 2013 at 2:40 AM, Mark Abraham wrote: > You have a box with negligible dimensions, so as forecast above, your > conversion process from AMBER was not as effective as it might have been. > As you can see with g_rdf -h, it defaults to using periodic boundary > conditions. You need to do something different. > > Mark > > > On Wed, Apr 10, 2013 at 2:38 PM, Venkat Reddy wrote: > >> Sir >> >> I truncated my file so it has only 10 molecules of water and 5 frames. >> gmxcheck gives the following information >> Checking file test.trr >> trn version: GMX_trn_file (single precision) >> Reading frame 0 time0.000 >> # Atoms 30 >> Last frame 5 time0.500 >> >> >> Item#frames Timestep (ps) >> Step 60.1 >> Time 60.1 >> Lambda 60.1 >> Coords 60.1 >> Velocities 0 >> Forces 0 >> Box 60.1 >> >> And the output file for gmxdump is attached. They look fine in my limited >> knowledge of gromacs that I have gained in the past couple of days. >> >> Please advice >> >> >> On Tue, Apr 9, 2013 at 6:39 PM, Mark Abraham wrote: >> >>> On Tue, Apr 9, 2013 at 8:33 AM, Dr. Vitaly Chaban >>> wrote: >>> > So there is a problem with your trajectory file. Try to understand what >>> > kind of problem it is. >>> >>> e.g. by using gmxcheck and/or gmxdump (on a small version of your >>> data!) to see what information is present. >>> >>> Mark >>> >>> > >>> > I can recollect that I experienced something like that why translating >>> CPMD >>> > trajectory to GROMACS. Maybe, it does not write time for each frame at >>> the >>> > right place -- just a guess. >>> > >>> > Dr. Vitaly Chaban >>> > >>> > >>> > >>> > >>> > On Tue, Apr 9, 2013 at 7:44 AM, Venkat Reddy >>> wrote: >>> > >>> >> Sir >>> >> >>> >> I tried g_msd, after asking for group selection the program appears >>> not to >>> >> read the frames as it remains stuck at reading frame 0, time 0.00. >>> >> >>> >> What to do? >>> >> >>> >> Thanks >>> >> >>> >> >>> >> >>> >> >>> >> On Mon, Apr 8, 2013 at 11:16 PM, Dr. Vitaly Chaban < >>> vvcha...@gmail.com>wrote: >>> >> >>> >>> Do you experience this problem with g_rdf only, or with all gromacs >>> >>> analysis utilities? >>> >>> >>> >>> >>> >>> On Mon, Apr 8, 2013 at 7:33 PM, Venkat Reddy >>> wrote: >>> >>> >>> >>>> Sir >>> >>>> >>> >>>> I loaded the trajectory. There doesn't seem to be anything wrong >>> with >>> >>>> it. Have no clue whats going wrong >>> >>>> >>> >>>> Thanks >>> >>>> >>> >>>> >>> >>>> On Mon, Apr 8, 2013 at 5:28 PM, Dr. Vitaly Chaban < >>> vvcha...@gmail.com>wrote: >>> >>>> >>> >>>>> I believe the problem is in the way which you used to convert AMBER >>> >>>>> trajectory to the GROMACS trajectory >>> >>>>> >>> >>>>> I would suggest to try gmxdump and see what your trajectory looks >>> like. >>> >>>>> Oe >>> >>>>> maybe even better - try to visualize it in VMD to see if the >>> format is >>> >>>>> correct. >>> >>>>> >>> >>>>> Dr. Vitaly Chaban >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> Sir >>> >>>>> > >>> >>>>> > I was using an old version. Now I used 4.5.5, it still gives me >>> the >>> >>>>> same >>> >>>>> > blank output file. >>> >>>>> > >>> >>>>> > Kindly suggest how to go about solving this >>> >>>>> > >>> >>>>> >
Re: [gmx-users] Re: RDF output has no data
Sir I truncated my file so it has only 10 molecules of water and 5 frames. gmxcheck gives the following information Checking file test.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 30 Last frame 5 time0.500 Item#frames Timestep (ps) Step 60.1 Time 60.1 Lambda 60.1 Coords 60.1 Velocities 0 Forces 0 Box 60.1 And the output file for gmxdump is attached. They look fine in my limited knowledge of gromacs that I have gained in the past couple of days. Please advice On Tue, Apr 9, 2013 at 6:39 PM, Mark Abraham wrote: > On Tue, Apr 9, 2013 at 8:33 AM, Dr. Vitaly Chaban > wrote: > > So there is a problem with your trajectory file. Try to understand what > > kind of problem it is. > > e.g. by using gmxcheck and/or gmxdump (on a small version of your > data!) to see what information is present. > > Mark > > > > > I can recollect that I experienced something like that why translating > CPMD > > trajectory to GROMACS. Maybe, it does not write time for each frame at > the > > right place -- just a guess. > > > > Dr. Vitaly Chaban > > > > > > > > > > On Tue, Apr 9, 2013 at 7:44 AM, Venkat Reddy > wrote: > > > >> Sir > >> > >> I tried g_msd, after asking for group selection the program appears not > to > >> read the frames as it remains stuck at reading frame 0, time 0.00. > >> > >> What to do? > >> > >> Thanks > >> > >> > >> > >> > >> On Mon, Apr 8, 2013 at 11:16 PM, Dr. Vitaly Chaban >wrote: > >> > >>> Do you experience this problem with g_rdf only, or with all gromacs > >>> analysis utilities? > >>> > >>> > >>> On Mon, Apr 8, 2013 at 7:33 PM, Venkat Reddy > wrote: > >>> > >>>> Sir > >>>> > >>>> I loaded the trajectory. There doesn't seem to be anything wrong with > >>>> it. Have no clue whats going wrong > >>>> > >>>> Thanks > >>>> > >>>> > >>>> On Mon, Apr 8, 2013 at 5:28 PM, Dr. Vitaly Chaban >wrote: > >>>> > >>>>> I believe the problem is in the way which you used to convert AMBER > >>>>> trajectory to the GROMACS trajectory > >>>>> > >>>>> I would suggest to try gmxdump and see what your trajectory looks > like. > >>>>> Oe > >>>>> maybe even better - try to visualize it in VMD to see if the format > is > >>>>> correct. > >>>>> > >>>>> Dr. Vitaly Chaban > >>>>> > >>>>> > >>>>> > >>>>> Sir > >>>>> > > >>>>> > I was using an old version. Now I used 4.5.5, it still gives me the > >>>>> same > >>>>> > blank output file. > >>>>> > > >>>>> > Kindly suggest how to go about solving this > >>>>> > > >>>>> > Thanks > >>>>> > > >>>>> > > >>>>> > On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham < > >>>>> mark.j.abra...@gmail.com > >>>>> > >wrote: > >>>>> > > >>>>> > > On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy < > venkat...@gmail.com> > >>>>> > wrote: > >>>>> > > > >>>>> > > > There was no fatal error preceding the output. After selecting > the > >>>>> > groups > >>>>> > > > following are the output on the screen > >>>>> > > > Reading frame 1 time0.100 > >>>>> > > > Warning: can not make broken molecules whole without a run > input > >>>>> file, > >>>>> > > > don't worry, mdrun doesn't write broken molecules > >>>>> > > > > >>>>> > > > >>>>> > > This message is from a prehistoric version of g_rdf. Please get a > >>>>> new > >>>>> > one. > >>>>> > > > >>>>> > > Mark > >>>>> > > > >>>>> > > > >>>>> > > > > >>>>> > > &g
Re: [gmx-users] Re: RDF output has no data
Sir I tried g_msd, after asking for group selection the program appears not to read the frames as it remains stuck at reading frame 0, time 0.00. What to do? Thanks On Mon, Apr 8, 2013 at 11:16 PM, Dr. Vitaly Chaban wrote: > Do you experience this problem with g_rdf only, or with all gromacs > analysis utilities? > > > On Mon, Apr 8, 2013 at 7:33 PM, Venkat Reddy wrote: > >> Sir >> >> I loaded the trajectory. There doesn't seem to be anything wrong with it. >> Have no clue whats going wrong >> >> Thanks >> >> >> On Mon, Apr 8, 2013 at 5:28 PM, Dr. Vitaly Chaban wrote: >> >>> I believe the problem is in the way which you used to convert AMBER >>> trajectory to the GROMACS trajectory >>> >>> I would suggest to try gmxdump and see what your trajectory looks like. >>> Oe >>> maybe even better - try to visualize it in VMD to see if the format is >>> correct. >>> >>> Dr. Vitaly Chaban >>> >>> >>> >>> Sir >>> > >>> > I was using an old version. Now I used 4.5.5, it still gives me the >>> same >>> > blank output file. >>> > >>> > Kindly suggest how to go about solving this >>> > >>> > Thanks >>> > >>> > >>> > On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham >> > >wrote: >>> > >>> > > On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy >>> > wrote: >>> > > >>> > > > There was no fatal error preceding the output. After selecting the >>> > groups >>> > > > following are the output on the screen >>> > > > Reading frame 1 time0.100 >>> > > > Warning: can not make broken molecules whole without a run input >>> file, >>> > > > don't worry, mdrun doesn't write broken molecules >>> > > > >>> > > >>> > > This message is from a prehistoric version of g_rdf. Please get a new >>> > one. >>> > > >>> > > Mark >>> > > >>> > > >>> > > > >>> > > > Reading frame2000 time 200.000 >>> > > > >>> > > > >>> > > > gcq#69: "The Wheels On the Bus Go Round and Round" (J. Richman) >>> > > > >>> > > > And the rdf.xvg file looks like this >>> > > > >>> > > > #This file was created Sat Apr 6 10:54:13 2013 >>> > > > # by the following command: >>> > > > # g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg >>> > > > # >>> > > > # g_rdf is part of G R O M A C S: >>> > > > # >>> > > > # GROningen MAchine for Chemical Simulation >>> > > > # >>> > > > @title "Radial Distribution" >>> > > > @xaxis label "r" >>> > > > @yaxis label "" >>> > > > @TYPE xy >>> > > > @ subtitle "O21-H2_&_CAT" >>> > > > 0.001 1 >>> > > > ~ >>> > > > >>> > > > Whats going wrong? Please help. >>> > >>> -- >>> 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-users-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> >> -- >> With Best Wishes >> Venkat Reddy Chirasani >> PhD student >> Laboratory of Computational Biophysics >> Department of Biotechnology >> IIT Madras >> Chennai >> INDIA-600036 >> > > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: RDF output has no data
Sir I loaded the trajectory. There doesn't seem to be anything wrong with it. Have no clue whats going wrong Thanks On Mon, Apr 8, 2013 at 5:28 PM, Dr. Vitaly Chaban wrote: > I believe the problem is in the way which you used to convert AMBER > trajectory to the GROMACS trajectory > > I would suggest to try gmxdump and see what your trajectory looks like. Oe > maybe even better - try to visualize it in VMD to see if the format is > correct. > > Dr. Vitaly Chaban > > > > Sir > > > > I was using an old version. Now I used 4.5.5, it still gives me the same > > blank output file. > > > > Kindly suggest how to go about solving this > > > > Thanks > > > > > > On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham > >wrote: > > > > > On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy > > wrote: > > > > > > > There was no fatal error preceding the output. After selecting the > > groups > > > > following are the output on the screen > > > > Reading frame 1 time0.100 > > > > Warning: can not make broken molecules whole without a run input > file, > > > > don't worry, mdrun doesn't write broken molecules > > > > > > > > > > This message is from a prehistoric version of g_rdf. Please get a new > > one. > > > > > > Mark > > > > > > > > > > > > > > Reading frame2000 time 200.000 > > > > > > > > > > > > gcq#69: "The Wheels On the Bus Go Round and Round" (J. Richman) > > > > > > > > And the rdf.xvg file looks like this > > > > > > > > #This file was created Sat Apr 6 10:54:13 2013 > > > > # by the following command: > > > > # g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg > > > > # > > > > # g_rdf is part of G R O M A C S: > > > > # > > > > # GROningen MAchine for Chemical Simulation > > > > # > > > > @title "Radial Distribution" > > > > @xaxis label "r" > > > > @yaxis label "" > > > > @TYPE xy > > > > @ subtitle "O21-H2_&_CAT" > > > > 0.001 1 > > > > ~ > > > > > > > > Whats going wrong? Please help. > > > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RDF output has no data
Sir I was using an old version. Now I used 4.5.5, it still gives me the same blank output file. Kindly suggest how to go about solving this Thanks On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham wrote: > On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy wrote: > > > There was no fatal error preceding the output. After selecting the groups > > following are the output on the screen > > Reading frame 1 time0.100 > > Warning: can not make broken molecules whole without a run input file, > > don't worry, mdrun doesn't write broken molecules > > > > This message is from a prehistoric version of g_rdf. Please get a new one. > > Mark > > > > > > Reading frame2000 time 200.000 > > > > > > gcq#69: "The Wheels On the Bus Go Round and Round" (J. Richman) > > > > And the rdf.xvg file looks like this > > > > #This file was created Sat Apr 6 10:54:13 2013 > > # by the following command: > > # g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg > > # > > # g_rdf is part of G R O M A C S: > > # > > # GROningen MAchine for Chemical Simulation > > # > > @title "Radial Distribution" > > @xaxis label "r" > > @yaxis label "" > > @TYPE xy > > @ subtitle "O21-H2_&_CAT" > > 0.001 1 > > ~ > > > > Whats going wrong? Please help. > > > > > > On Sat, Apr 6, 2013 at 12:41 AM, Justin Lemkul wrote: > > > > > On Fri, Apr 5, 2013 at 2:30 PM, Venkat Reddy > > wrote: > > > > > > > Dear users > > > > > > > > I have used AMBER MD package to run simulation for a solvent box. I > am > > > now > > > > using the gromacs utility to calculate rdf as follows: > > > > > > > > g_rdf -f file.trr -s file.pdb -n rdf.ndx -o rdf.xvg > > > > > > > > However, I get no data in the output rdf.xvg. Since Im using > specially > > > > generated force field parameters, I do not know how to go about > > > generating > > > > a tpr file (in case that is the problem). The rdf.ndx file is correct > > for > > > > my atom selection. Please suggest how to go about solving this. > > > > > > > > > > > Blank output usually indicates the command failed, which should have > been > > > preceded by a rather obvious fatal error. If a .tpr file is required, > > g_rdf > > > will tell you (again, a fatal error). > > > > > > -Justin > > > > > > -- > > > > > > > > > > > > Justin A. Lemkul, Ph.D. > > > Research Scientist > > > Department of Biochemistry > > > Virginia Tech > > > Blacksburg, VA > > > jalemkul[at]vt.edu | (540) > > > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > > > > -- > > > 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-users-requ...@gromacs.org. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > -- > > 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-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RDF output has no data
There was no fatal error preceding the output. After selecting the groups following are the output on the screen Reading frame 1 time0.100 Warning: can not make broken molecules whole without a run input file, don't worry, mdrun doesn't write broken molecules Reading frame2000 time 200.000 gcq#69: "The Wheels On the Bus Go Round and Round" (J. Richman) And the rdf.xvg file looks like this #This file was created Sat Apr 6 10:54:13 2013 # by the following command: # g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg # # g_rdf is part of G R O M A C S: # # GROningen MAchine for Chemical Simulation # @title "Radial Distribution" @xaxis label "r" @yaxis label "" @TYPE xy @ subtitle "O21-H2_&_CAT" 0.001 1 ~ Whats going wrong? Please help. On Sat, Apr 6, 2013 at 12:41 AM, Justin Lemkul wrote: > On Fri, Apr 5, 2013 at 2:30 PM, Venkat Reddy wrote: > > > Dear users > > > > I have used AMBER MD package to run simulation for a solvent box. I am > now > > using the gromacs utility to calculate rdf as follows: > > > > g_rdf -f file.trr -s file.pdb -n rdf.ndx -o rdf.xvg > > > > However, I get no data in the output rdf.xvg. Since Im using specially > > generated force field parameters, I do not know how to go about > generating > > a tpr file (in case that is the problem). The rdf.ndx file is correct for > > my atom selection. Please suggest how to go about solving this. > > > > > Blank output usually indicates the command failed, which should have been > preceded by a rather obvious fatal error. If a .tpr file is required, g_rdf > will tell you (again, a fatal error). > > -Justin > > -- > > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RDF output has no data
Dear users I have used AMBER MD package to run simulation for a solvent box. I am now using the gromacs utility to calculate rdf as follows: g_rdf -f file.trr -s file.pdb -n rdf.ndx -o rdf.xvg However, I get no data in the output rdf.xvg. Since Im using specially generated force field parameters, I do not know how to go about generating a tpr file (in case that is the problem). The rdf.ndx file is correct for my atom selection. Please suggest how to go about solving this. Thank you -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Radial density calculation
Thank you sir for the nice suggestion On Wed, Apr 3, 2013 at 9:58 AM, Dallas Warren wrote: > Just calculate the radial distribution function from particle-to-particle. > > You can then integrate that probability to get a mass density at a given > radius, using the average overall system density. > > Catch ya, > > Dr. Dallas Warren > Drug Discovery Biology > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > +61 3 9903 9304 > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Radial density calculation
Dear gmx-users, I would like to calculate radial density plot (not rdf plot) for my heterogeneous droplet system. I need distance on the X-axis and density (g/ml) on the Y-axis for each constituent of my droplet. I would much appreciate if some one could help me in this regard. Thank you for your valuable time With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromos43A1-S3 lipid parameters
Thanks Justin and Kukol for the info. Kukol, Can you please upload the cholesterol parameters also in the site you provided, if you have??. On Fri, Mar 1, 2013 at 2:02 PM, Kukol, Andreas wrote: > Hello Venkat, > > You can use Gromos96 53a6 lipid parameters for DPPC, DMPC, POPC and POPG > with the Gromos96 53a6 force field. > > They can be downloaded from here: > https://sites.google.com/site/bioherts/home/lipid-topologies > > Reference: > Kukol, A., 2009. Lipid models for united-atom molecular dynamics > simulations of proteins. J. Chem. Theor. Comput., 5(3), 615-626. > > Andreas > > > -Original Message- > > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > > boun...@gromacs.org] On Behalf Of Justin Lemkul > > Sent: 28 February 2013 13:51 > > To: Discussion list for GROMACS users > > Subject: Re: [gmx-users] Gromos43A1-S3 lipid parameters > > > > > > > > On 2/28/13 2:16 AM, Venkat Reddy wrote: > > > Dear all, > > > Can I use Gromos43A1-S3 lipid parameters provided in the GROMACS site > > > along with the GROMOS53a6 forcefield in the same manner as Justin has > > > explained in his KALP15 tutorial? > > > > > > > It's probably more sensible to use 43A1, since that's the basis for the > 43A1-S3 > > lipids. > > > > -Justin > > > > -- > > > > > > Justin A. Lemkul, Ph.D. > > Research Scientist > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > -- > > 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-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Lipid topologies generated by ATB
Dear all, Are the topologies generated for lipids by ATB accurate enough? (I have mentioned the molecule type as "*Lipid*" prior to submission to ATB) Thanks for your valuable time With best wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] doubt regarding make_ndx
Dear all, I try to make my residues of interest as an index group using the command make_ndx -f conf.gro -o index.ndx. I have entered my residues as > r 15 23 27 30 82 84 125 127 129 140 143 184 187 188 191 194 195 198 201 205 206 208 211 228 236 261 263 273 277 282 283 428 429 432 433 438 441 457 459 463 then I renamed the index file using > name 26 tunnel >q When I checked back my index file, I found some water molecule atoms also inserted in the tunnel group. What could be the problem? Am I doing in the proper way? Thanks a lot for your valuable time. -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gen-vel=no
The check point file you submit will have the velocity information. On Tue, Dec 11, 2012 at 10:55 AM, Bahar Mehrpuyan wrote: > hi gmx user > > I've done a production simulation with gen_vel= no, but in grompp I forgot > that use .trr file of equlibration simulation for initial velocities, > my question is how gromacs treats with initial velocities in this case? > > 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! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error during minimization
Probably..there is a problem in spacing at the bottom of your gro file. The line mentioning the vectors should be like this eg:, 5012OBC49 47 1.088 1.094 2.775 0.0 0.0 0.0 On Tue, Nov 27, 2012 at 3:01 PM, Shine A wrote: > Sir, > >I am studying the dynamics of membrane proteins using KALP-15 in DPPC. > But during minimization (after shrinking), getting error like this. > Fatal error: > Invalid line in system_shrink26.gro for atom 8703: > 6.4140 6.44350 6.59650.why this error?plz give me a solution to > overcome it. > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0
Thank yo Justin for your help...I have generated the same topology using *ATB. *Now, I got the masses correctly (as pointed out by you). So, I'm afraid that is there any bug in PRODRG server? On Mon, Nov 26, 2012 at 8:09 PM, Justin Lemkul wrote: > > > On 11/26/12 9:35 AM, Venkat Reddy wrote: > >> Dear Justin, >> >> One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate >> topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I >> mix 53A6 and 43A1? >> >> >> > PRODRG doesn't even do a very good job of being compatible with 43A1, so > if you re-derive the charges correctly, the result is compatible with 53A6. > PRODRG basically just uses 43A1 atom types, the names of which are largely > the same in 53A6, even if the parameters are slightly different, and thus I > view PRODRG as a method to create generic Gromos96 topologies, given that > the user has to do a fair amount of work to create a usable topology anyway. > > -Justin > > On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul wrote: >> >> >>> >>> On 11/26/12 9:12 AM, Venkat Reddy wrote: >>> >>> Dear Justin, >>>> I haven't touched the *Mass column.* I have edited the charges only >>>> using >>>> "gedit" in linux. >>>> >>>> >>>> Regardless, the masses I pointed out are wrong. You should still do >>> the >>> test to #include the original topology and see if it works, then if it >>> does, figure out the source of the error in your file. >>> >>> -Justin >>> >>> >>> On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul wrote: >>>> >>>> >>>> >>>>> On 11/26/12 12:58 AM, Venkat Reddy wrote: >>>>> >>>>> Dear all, >>>>> >>>>>> I am simulating a Protein-Drug complex. I am following Justin's >>>>>> tutorial. >>>>>> I >>>>>> have used *PRODRG *for generating topology. *Gaussian *has given me >>>>>> the >>>>>> ESP >>>>>> charges. I have edited the charges in the itp file using the >>>>>> *Gaussian*'s >>>>>> ESP charges*. *Then I am getting this strange error. >>>>>> >>>>>> *ERROR 1 [file protein.top, line 75]:* >>>>>> * atom C4 (Res ORP-1) has mass 0* >>>>>> * >>>>>> * >>>>>> * >>>>>> * >>>>>> * >>>>>> * >>>>>> *ERROR 2 [file protein.top, line 75]:* >>>>>> * atom C14 (Res ORP-1) has mass 0* >>>>>> >>>>>> >>>>>> Probably there are some hidden line ending problems. Did you edit >>>>>> the >>>>>> >>>>> file with a plain text editor? >>>>> >>>>> Also note... >>>>> >>>>> 24 CH2 1 ORP C5 40.354 13.0190 >>>>> >>>>> *25 CH1 1 ORP C4 4 -0.024 14.0270* >>>>>> >>>>>> >>>>>> These masses don't make sense. CH2 should have a mass of 14.027 and >>>>> CH1 >>>>> should have a mass of 13.019. I've never seen PRODRG get something >>>>> like >>>>> this wrong; were you sure to carefully change the file? It seems >>>>> something >>>>> has gone very wrong here. >>>>> >>>>> Compare the original topology (from PRODRG) with the one you edited. >>>>> If >>>>> grompp succeeds using the PRODRG topology (stop using it after that >>>>> point), >>>>> then the error arose due to something you did when editing the file. >>>>> >>>>> -Justin >>>>> >>>>> -- >>>>> ==**== >>>>> >>>>> >>>>> >>>>> Justin A. Lemkul, Ph.D. >>>>> Research Scientist >>>>> Department of Biochemistry >>>>> Virginia Tech >>>>> Blacksburg, VA >>>>> jalemkul[at]vt.edu | (540) 231-9080 >>>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin**< >>>>> http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin> >>&
Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0
Dear Justin, One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I mix 53A6 and 43A1? On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul wrote: > > > On 11/26/12 9:12 AM, Venkat Reddy wrote: > >> Dear Justin, >> I haven't touched the *Mass column.* I have edited the charges only using >> "gedit" in linux. >> >> > Regardless, the masses I pointed out are wrong. You should still do the > test to #include the original topology and see if it works, then if it > does, figure out the source of the error in your file. > > -Justin > > >> On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul wrote: >> >> >>> >>> On 11/26/12 12:58 AM, Venkat Reddy wrote: >>> >>> Dear all, >>>> I am simulating a Protein-Drug complex. I am following Justin's >>>> tutorial. >>>> I >>>> have used *PRODRG *for generating topology. *Gaussian *has given me the >>>> ESP >>>> charges. I have edited the charges in the itp file using the >>>> *Gaussian*'s >>>> ESP charges*. *Then I am getting this strange error. >>>> >>>>*ERROR 1 [file protein.top, line 75]:* >>>> * atom C4 (Res ORP-1) has mass 0* >>>> * >>>> * >>>> * >>>> * >>>> * >>>> * >>>> *ERROR 2 [file protein.top, line 75]:* >>>> * atom C14 (Res ORP-1) has mass 0* >>>> >>>> >>>> Probably there are some hidden line ending problems. Did you edit the >>> file with a plain text editor? >>> >>> Also note... >>> >>>24 CH2 1 ORP C5 40.354 13.0190 >>> >>>> *25 CH1 1 ORP C4 4 -0.024 14.0270* >>>> >>>> >>> These masses don't make sense. CH2 should have a mass of 14.027 and CH1 >>> should have a mass of 13.019. I've never seen PRODRG get something like >>> this wrong; were you sure to carefully change the file? It seems >>> something >>> has gone very wrong here. >>> >>> Compare the original topology (from PRODRG) with the one you edited. If >>> grompp succeeds using the PRODRG topology (stop using it after that >>> point), >>> then the error arose due to something you did when editing the file. >>> >>> -Justin >>> >>> -- >>> ==== >>> >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> > >>> >>> ==== >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search>> Mailing_Lists/Search<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-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> >> >> >> > -- > ==**== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0
Thanks Justin...I will certainly do. On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul wrote: > > > On 11/26/12 9:12 AM, Venkat Reddy wrote: > >> Dear Justin, >> I haven't touched the *Mass column.* I have edited the charges only using >> "gedit" in linux. >> >> > Regardless, the masses I pointed out are wrong. You should still do the > test to #include the original topology and see if it works, then if it > does, figure out the source of the error in your file. > > -Justin > > >> On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul wrote: >> >> >>> >>> On 11/26/12 12:58 AM, Venkat Reddy wrote: >>> >>> Dear all, >>>> I am simulating a Protein-Drug complex. I am following Justin's >>>> tutorial. >>>> I >>>> have used *PRODRG *for generating topology. *Gaussian *has given me the >>>> ESP >>>> charges. I have edited the charges in the itp file using the >>>> *Gaussian*'s >>>> ESP charges*. *Then I am getting this strange error. >>>> >>>>*ERROR 1 [file protein.top, line 75]:* >>>> * atom C4 (Res ORP-1) has mass 0* >>>> * >>>> * >>>> * >>>> * >>>> * >>>> * >>>> *ERROR 2 [file protein.top, line 75]:* >>>> * atom C14 (Res ORP-1) has mass 0* >>>> >>>> >>>> Probably there are some hidden line ending problems. Did you edit the >>> file with a plain text editor? >>> >>> Also note... >>> >>>24 CH2 1 ORP C5 40.354 13.0190 >>> >>>> *25 CH1 1 ORP C4 4 -0.024 14.0270* >>>> >>>> >>> These masses don't make sense. CH2 should have a mass of 14.027 and CH1 >>> should have a mass of 13.019. I've never seen PRODRG get something like >>> this wrong; were you sure to carefully change the file? It seems >>> something >>> has gone very wrong here. >>> >>> Compare the original topology (from PRODRG) with the one you edited. If >>> grompp succeeds using the PRODRG topology (stop using it after that >>> point), >>> then the error arose due to something you did when editing the file. >>> >>> -Justin >>> >>> -- >>> ==== >>> >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> > >>> >>> ==== >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search>> Mailing_Lists/Search<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-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> >> >> >> > -- > ==**== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0
Dear Justin, I haven't touched the *Mass column.* I have edited the charges only using "gedit" in linux. On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul wrote: > > > On 11/26/12 12:58 AM, Venkat Reddy wrote: > >> Dear all, >> I am simulating a Protein-Drug complex. I am following Justin's tutorial. >> I >> have used *PRODRG *for generating topology. *Gaussian *has given me the >> ESP >> charges. I have edited the charges in the itp file using the *Gaussian*'s >> ESP charges*. *Then I am getting this strange error. >> >> *ERROR 1 [file protein.top, line 75]:* >> * atom C4 (Res ORP-1) has mass 0* >> * >> * >> * >> * >> * >> * >> *ERROR 2 [file protein.top, line 75]:* >> * atom C14 (Res ORP-1) has mass 0* >> >> > Probably there are some hidden line ending problems. Did you edit the > file with a plain text editor? > > Also note... > > 24 CH2 1 ORP C5 40.354 13.0190 >> *25 CH1 1 ORP C4 4 -0.024 14.0270* >> > > These masses don't make sense. CH2 should have a mass of 14.027 and CH1 > should have a mass of 13.019. I've never seen PRODRG get something like > this wrong; were you sure to carefully change the file? It seems something > has gone very wrong here. > > Compare the original topology (from PRODRG) with the one you edited. If > grompp succeeds using the PRODRG topology (stop using it after that point), > then the error arose due to something you did when editing the file. > > -Justin > > -- > ==**== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0
Dear all, I am simulating a Protein-Drug complex. I am following Justin's tutorial. I have used *PRODRG *for generating topology. *Gaussian *has given me the ESP charges. I have edited the charges in the itp file using the *Gaussian*'s ESP charges*. *Then I am getting this strange error. *ERROR 1 [file protein.top, line 75]:* * atom C4 (Res ORP-1) has mass 0* * * * * * * *ERROR 2 [file protein.top, line 75]:* * atom C14 (Res ORP-1) has mass 0* But itp file has corresponding masses for both *C14 *and *C4.* * * My itp file is * * [ moleculetype ] ; Name nrexcl ORP 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 F 1 ORP F4 1 -0.203 18.9984 2 CCl4 1 ORP C23 10.727 12.0110 3 F 1 ORP F5 1 -0.213 18.9984 4 F 1 ORP F6 2 -0.230 18.9984 5 C 1 ORP C21 2 -0.123 12.0110 6 CR1 1 ORP C22 2 -0.096 12.0110 7HC 1 ORP H9Q 20.100 1.0080 8 CR1 1 ORP C20 2 -0.049 12.0110 9HC 1 ORP H20 20.061 1.0080 10 C 1 ORP C19 2 -0.112 12.0110 11 CCl4 1 ORP C24 20.746 12.0110 12 F 1 ORP F8 2 -0.220 18.9984 13 F 1 ORP F9 3 -0.221 18.9984 14 F 1 ORP F7 3 -0.226 18.9984 15 CR1 1 ORP C18 3 -0.153 12.0110 16HC 1 ORP H18 30.079 1.0080 17 C 1 ORP C17 30.161 12.0110 18 CH2 1 ORP C16 30.086 14.0270 19 N 1 ORP N2 3 -0.612 14.0067 20 C 1 ORP C25 30.846 12.0110 21 O 1 ORP O3 4 -0.449 15.9994 22OA 1 ORP O4 4 -0.299 15.9994 23 CH3 1 ORP C26 40.142 15.0350 24 CH2 1 ORP C5 40.354 13.0190 *25 CH1 1 ORP C4 4 -0.024 14.0270* 26 CH2 1 ORP C3 40.268 13.0190 27 CH2 1 ORP C2 40.066 14.0270 28 CH3 1 ORP C1 5 -0.073 15.0350 29 C 1 ORP C6 5 -0.194 12.0110 30 CR1 1 ORP C7 60.075 12.0110 31HC 1 ORP H7 60.005 1.0080 32 C 1 ORP C8 6 -0.168 12.0110 33 CCl4 1 ORP C15 60.711 12.0110 34 F 1 ORP F2 6 -0.214 18.9984 35 F 1 ORP F3 6 -0.208 18.9984 36 F 1 ORP F1 6 -0.215 18.9984 37 CR1 1 ORP C9 7 -0.030 12.0110 38HC 1 ORP H9 70.066 1.0080 39 CR1 1 ORP C10 7 -0.146 12.0110 40HC 1 ORP H10 70.094 1.0080 41 C 1 ORP C11 70.340 12.0110 42NR 1 ORP N1 7 -0.647 14.0067 43 C 1 ORP C12 70.843 12.0110 44 O 1 ORP O1 7 -0.409 15.9994 45OA 1 ORP O2 8 -0.466 15.9994 46 CH2 1 ORP C13 80.292 14.0270 *47 CH3 1 ORP C14 9 -0.064 15.0350* Thanks for your valuable time -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem in running md simulation
I think the system is not well energy minimized. Do it for 1000kj/mol. Also check for bad contacts in your starting structure using Ramachandran plot. One more important thing is that, you have to generate an index file with Protein_GTP as one group and water_Ions as another. Then change your tc-groups as tc-grps = Protein_GTP Water_Ions tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee < ananyachatter...@iiserkol.ac.in> wrote: > Hi all, > > I was running a md simulation of protein complexed with GTP in water, > neutralised with Mg2+ and Cl- ions.I have also em the system to 2000kj/mol > and also equilibrated the water molecules in 300K temperature and 1 bar > pressure. And then run the md simulation using md parameters as follow: > > title = Protein-ligand complex > ; Run parameters > integrator = md; leap-frog integrator > nsteps = 50 ; 2 * 500 = 1000 ps (1 ns) > dt = 0.002 ; 2 fs > ; Output control > nstxout = 500 ; save coordinates every 1ps > nstvout = 500 ; save coordinates every 1ps > nstenergy = 500 ; save energies every 1 ps > nstlog = 500 ; update log file every 1 ps > nstxtcout = 500 ; write .xtc trajectory every 1 ps > energygrps = Protein GTP SOL MG2+ > ; Bond parameters > constraints = none; No constrains > ; Neighborsearching > ns_type = grid ; search neighboring grid cells > nstlist = 5 ; 10 fs > rlist = 0.9 ; short-range neighborlist cutoff (in nm) > rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) > rvdw= 1.4 ; short-range van der Waals cutoff (in nm) > ; Temperature coupling > tcoupl = v-rescale ; modified Berendsen thermostat > tc-grps = Protein GTP SOL MG2+ CL-; two coupling groups - more > accurate > tau_t = 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps > ref_t = 300 300 300 300 300; reference temperature, one > for each group, in K > ; Pressure coupling > pcoupl = Parrinello-Rahman ; pressure coupling is on for > NPT > pcoupltype = isotropic ; uniform scaling of box > vectors > tau_p = 2.0 ; time constant, in ps > ref_p = 1.0 ; reference pressure, in bar > compressibility = 4.5e-5; isothermal compressibility > of water, bar^-1 > refcoord_scaling= com > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > > > Now I am getting the following error. > > > Warning: 1-4 interaction between 3231 and 3234 at distance 10.730 which is > larger than the 1-4 table size 2.400 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size > > t = 226.610 ps: Water molecule starting at atom 236548 can not be settled. > Check for bad contacts and/or reduce the timestep. > Wrote pdb files with previous and current coordinates > > --**- > Program mdrun, VERSION 4.0.7 > Source code file: ../../../../src/mdlib/nsgrid.**c, line: 348 > > Fatal error: > Number of grid cells is zero. Probably the system and box collapsed. > > kindly help me I am not getting where I am getting wrong. > > > > -- > Ananya Chatterjee, > Senior Research Fellow (SRF), > Department of biological Science, > IISER-Kolkata. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to launch mdrun_mpi using g_tune_pme on a cluster
Dear Gromacs users, How to launch mdrun_mpi using g_tune_pme on a cluster, because * * *g_tune_pme -launch *launches mdrun but not mdrun_mpi. Thanks for your valuable time -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Continuous mdrun vs step-by-step mdrun
Hi Francesco, Thanks for ur reply and wishes. I couldn't remember exactly where I read this but what is your opinion on this discrete vs continuous runs ? On Mon, Nov 12, 2012 at 2:10 PM, francesco oteri wrote: > Hi, > happy diwali to you, too. > Can you please post a link where what you said is stated? > it seems quite strange to me! > > > > 2012/11/12 Venkat Reddy > > > Dear gromacs users, > > > > I have a very basic doubt regarding mdrun. Is there any difference > between > > "doing final MD for 100 ns at a stretch" and "doing the same with a 10 > ns > > step size (*i.e., 10ns20ns30ns100ns*) " on a cluster of > 256 > > processors. I have read some where that continuous MD of longer > simulations > > will cause spurious drifts in velocity and energy, errors in velocity > > correlation....etc. Please advise me in this regard. > > > > Thank you and Happy DIWALI > > > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > -- > > 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-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Cordiali saluti, Dr.Oteri Francesco > -- > 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-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to restart a stopped simulation
State_prev.cpt is the previous check point file to state.cpt. Usually the check point file generates for every 15 mins. You can use the state_prev.cpt because your state.cpt has no data (0 bytes) On Mon, Nov 12, 2012 at 11:54 AM, ananyachatterjee < ananyachatter...@iiserkol.ac.in> wrote: > Hi all, > > I have restarted my simulation stopped due to power failure by using the > command: > > mdrun -s md.tpr -cpi state.cpt -append > > And now I am getting the following error: > > Program mdrun, VERSION 4.0.7 > Source code file: ../../../../src/gmxlib/**checkpoint.c, line: 547 > > Fatal error: > The checkpoint file is empty/corrupted, or maybe you are out of quota? > > can any one help in this regards. > > I have two .cpt files one state.cpt (0 bytes) and another state_prev.cpt > file(5.4 MB). Should I have to use state_prev.cpt file to restart the > simulation? > > > On Mon, 12 Nov 2012 11:37:02 +0530, Kavyashree M wrote: > >> Hi Ananya, >> >> You can refer this. >> >> http://www.gromacs.org/**Documentation/How-tos/Doing_** >> Restarts?highlight=restarting<http://www.gromacs.org/Documentation/How-tos/Doing_Restarts?highlight=restarting> >> >> bye >> kavya >> On Mon, Nov 12, 2012 at 11:27 AM, ananyachatterjee < >> ananyachatter...@iiserkol.ac.**in > >> wrote: >> >> >>> Hi all, >>> >>> my simulation has stopped due to power failure, can anyone tell me how to >>> restart it from the same point. >>> -- >>> Ananya Chatterjee, >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> * Please search the archive at http://www.gromacs.org/** >>> >>> Support/Mailing_Lists/Search>> Mailing_Lists/Search<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-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> > -- > Ananya Chatterjee, > Senior Research Fellow (SRF), > Department of biological Science, > IISER-Kolkata. > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Continuous mdrun vs step-by-step mdrun
Dear gromacs users, I have a very basic doubt regarding mdrun. Is there any difference between "doing final MD for 100 ns at a stretch" and "doing the same with a 10 ns step size (*i.e., 10ns20ns30ns100ns*) " on a cluster of 256 processors. I have read some where that continuous MD of longer simulations will cause spurious drifts in velocity and energy, errors in velocity correlationetc. Please advise me in this regard. Thank you and Happy DIWALI -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding g_tune_pme optimization
Dear all Gromacs users, I have *two *questions: 1) I have been doing my simulation on a computer having 24 processors. I issued *g_tune_pme -s *.tpr -launch *command to directly launch my *mdrun *with the optimized settings. At the end of optimization, g_tune_pme has given -npme as *'0'*. My doubt is, how could it be possible to get best performance without dedicated PME nodes? 2) What could be the optimum value for *-rcom *to get the best performance on a super cluster (*i.e., 256 nodes*)? Thanks in advance With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Confusion in passing check point file
Thanks Justin for the information. By the way, Could you please give me a hint on the release of new GPU-version (4.6)? On Thu, Oct 11, 2012 at 4:20 PM, Justin Lemkul wrote: > > > On 10/10/12 11:53 PM, Venkat Reddy wrote: > >> Dear all, >> I am doing a protein-ligand simulation and following Justin's tutorials. I >> have confusion in passing check point file to the next step in position >> restrain simulation (during NPT). I am slowly releasing the restraints >> during NPT simulation, *viz., 1000100.101**noPR*. So, >> during >> >> NPT-PR, is it required to pass the check-point file generated in the >> previous step to the next step (100010010...1**noPR)? or is >> it >> fine if I use directly the check point file generated during NPT-no PR >> step >> to final MD step? >> >> > You seem to be asking two questions, so it's not really a matter of "or." > One should always pass the final checkpoint of the previous stage of > simulation to the current stage. So during your reduction of restraints, > you should pass the checkpoint from the previous restraint strength. At > the outset of MD, you should pass the checkpoint from whatever the step > immediately prior to it was, which, from the description, is NPT in the > absence of restraints. > > -Justin > > -- > ==**== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] CG representation for Organic molecules
Dear All, I would like to run CG Dynamics for my system, which includes two organic molecules (GTP,GDP) and Mg2+ ion. I would like to add K+ and CL- as counter balancing ions. I have referred the MARTINI tutorial web page, but there is nothing about HETATM inclusion. Please help me in this regard. Thanking you With Best Wishes Venkat Reddy Chirasani IIT Madras -- 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-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Problem in the inclusion of Potassium ion topology
Dear Gromacs users, I have a problem in simulating microtubule hetero-dimer. I was trying to include K+ and CL- ions to counter balance as well as to maintain the desired concn (intra cellular concentration of KCl is approx 140mM) using the command genion -s ions.tpr -o solv_ions.gro -p topol.top -pname K -nname CL -conc 0.14 -neutral But I got an error like "*Molecule type K is not found*" (gromos43a1ff). Even after the inclusion of K+ ion topology in gromos43a1ff/ions.itp, I got the same error. Next time I have changed the forcefield to *Amber99sb-ildn*. But this time it has given some different error like *atom type NR is not found *(I suppose this is due to the ligand topology generated by PRODRG). Please help me in this regard. Thanking you With Best Wishes Venkat Reddy Chirasani IITM -- 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-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] make_ndx option
Hi Anirban ! First u hav to notedown the C-alpha atoms nos seperately from ur atom file. Then execute the command "make_ndx -f input.gro -o index.ndx".After this command, it gives a prompt. At that prompt you have to make a new group for the core region, for this you need to have the list of residues in the core region. So prepare a list of residues that form the core region ready. Suppose your list has residues 10,11,12...,101,102 etc., At the prompt give r10|r11|r12|.so on and press enter. You can rename the newly formed group by giving command, name On Thu, Jul 9, 2009 at 3:38 PM, Anirban Ghosh wrote: > Hi ALL, > > I want to create an index file using make_ndx which will contain only > C-alpha atoms of some residues (like from residue no 2-10, res 25-30, res > 36-40). How should I give this option in make_ndx. Any suggestion is > welcome. > > Regards, > > > > *Anirban Ghosh* > *Grade Based Engineer > Bioinformatics Team > Centre for Development of Advanced Computing (C-DAC) > Pune, India > * > > -- > Yahoo! recommends that you upgrade to the new and safer Internet Explorer > 8<http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/> > . > > ___ > 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)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- With Best Wishes Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ 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)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Regarding RMSF !
Hai Everyone ! I hav a small doubt regarding RMSF . How can we calculate rmsf for helices and sheets only in a protein (excluding loops )??? Thanks for ur valuable time. -- With Best Wishes Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to calculate the dihedral angle variations ???
Hai Sir ! Actually i want to see the dihedral angle (Cβ-S-S-Cβ) variation over time.I used the commands "g_angle -f trajout.xtc -s gp123_b4full.tpr -n angle.ndx -od angdist.xvg -ov angaver.xvg -of dihfrac.xvg -ot dihtrans.xvg -oc dihcorr.xvg -type dihedral -all" "g_chi -s gp123_full.gro -f gp123_full.trr -o order.xvg -jc Jcoupling.xvg -g chi.log -rama -all" Please suggest me the right options Thanks for ur concern 2009/4/1 Tsjerk Wassenaar > Hi Venkat, > > What exactly do you mean with variations. Do you want to follow the > angle over time, or do you want distributions with mean and variance > estimates? g_angle and g_chi seem to be the appropriate tools. You > mention you tried all suitable options, but fail to explain what you > tried and what exactly it is you want. We need that sort of > information to be able to help you out. > > Cheers, > > Tsjerk > > 2009/4/1 Venkat Reddy : > > First of all Thanks for ur reply ! > > I tried both g_angle and g_chi with all suitable options, but i didn't > get > > the required result.Can u plz help me in this regard ??? > > > > 2009/4/1 Antonia V. > >> > >> Did you try g_angle?? > >> > >> Antonia > >> > >> Date: Wed, 1 Apr 2009 11:35:29 +0530 > >> From: venkat...@gmail.com > >> To: gmx-users@gromacs.org > >> Subject: [gmx-users] How to calculate the dihedral angle variations ??? > >> > >> Hi Everyone ! > >> How can i see the variations in the "Cβ-S-S-Cβ" (Disulfide bridge) > >> dihedral angle during a simulation ? > >> Thanks in advance > >> > >> > >> > >> Cheers from > >> Venkat Reddy Chirasani > >> M.Tech Bioinformatics > >> UNIVERSITY OF HYDERABAD > >> > >> > >> check out the rest of the Windows LiveT. More than mail-Windows LiveT > goes > >> way beyond your inbox. More than messages > >> ___ > >> gmx-users mailing listgmx-users@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before > posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > -- > > Venkat Reddy Chirasani > > M.Tech Bioinformatics > > UNIVERSITY OF HYDERABAD > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to calculate the dihedral angle variations ???
First of all Thanks for ur reply ! I tried both g_angle and g_chi with all suitable options, but i didn't get the required result.Can u plz help me in this regard ??? 2009/4/1 Antonia V. > > Did you try g_angle?? > > Antonia > -- > Date: Wed, 1 Apr 2009 11:35:29 +0530 > From: venkat...@gmail.com > To: gmx-users@gromacs.org > Subject: [gmx-users] How to calculate the dihedral angle variations ??? > > > Hi Everyone ! > How can i see the variations in the "Cβ-S-S-Cβ" (Disulfide bridge) > dihedral angle during a simulation ? > Thanks in advance > > > > > Cheers from > Venkat Reddy Chirasani > M.Tech Bioinformatics > UNIVERSITY OF HYDERABAD > > -- > check out the rest of the Windows LiveT. More than mail-Windows LiveT goes > way beyond your inbox. More than > messages<http://www.microsoft.com/windows/windowslive/> > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to calculate the dihedral angle variations ???
Hi Everyone ! How can i see the variations in the "Cβ-S-S-Cβ" (Disulfide bridge) dihedral angle during a simulation ? Thanks in advance Cheers from Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: Re: [gmx-users] How to break a disulfide bond ???
Thanks Sharada madam n justin sir for ur kind attention.I followed ur command "pdb2gmx -ss".its asking like Link CYS-37 SG-306 and CYS-59 SG-453 (y/n) ?n Link CYS-44 SG-358 and CYS-50 SG-390 (y/n) ?y Link CYS-72 SG-560 and CYS-101 SG-764 (y/n) ?y Link CYS-82 SG-628 and CYS-93 SG-707 (y/n) ?y Link CYS-150 SG-1137 and CYS-156 SG-1173 (y/n) ?y Link CYS-203 SG-1546 and CYS-258 SG-1984 (y/n) ?y Link CYS-210 SG-1603 and CYS-231 SG-1767 (y/n) ?y actually i want to break the s-s bond between CYS37 n CYS59 . so i've given the options like as shown above. When i again visualized the pdb in pymol,its showing the disulfides as it is (no break between CYS37 n CYS59). Can u suggest me wat to do Thanks for giving reply. On Fri, Mar 6, 2009 at 7:24 PM, sharada wrote: > Do you intend to protonate a pair of cysteins and not make a SS bond? > Then pdb2gmx -ss should do the job. > > Sharada > > > *-- Original Message --* > From: sharada > To: Discussion list for GROMACS users > Date: Fri, 6 Mar 2009 12:28:54 +0530 (IST) > Subject: Re: Re: [gmx-users] How to break a disulfide bond ??? > > If you donot make it, it is as good as breaking it... > > Sharada > > *-- Original Message --* > From: Venkat Reddy > To: Discussion list for GROMACS users > Date: Fri, 6 Mar 2009 11:31:57 +0530 > Subject: Re: [gmx-users] How to break a disulfide bond ??? > > Hai ! > > with "pdb2gmx -ss", i can select the ss bonds. But after that, how to break > a particular ss bond (not all). > Thank you > > > On Fri, Mar 6, 2009 at 11:01 AM, sharada wrote: > >> >> pdb2gmx -h >> >> sharada >> >> >> >> *-- Original Message --* >> From: Venkat Reddy >> To: Discussion list for GROMACS users >> Date: Fri, 6 Mar 2009 10:50:24 +0530 >> Subject: [gmx-users] How to break a disulfide bond ??? >> >> Hai Every one ! Is it possible to break a disulfide bridge using gromacs >> ?If so,Can anybody suggest me, how to do it??? >> >> Thanks for ur valuable time >> >> With best wishes >> Venkat Reddy Chirasani >> M.Tech Bioinformatics >> UNIVERSITY OF HYDERABAD >> ___ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> ___ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Venkat Reddy Chirasani > M.Tech Bioinformatics > UNIVERSITY OF HYDERABAD > ___ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD Laboratory of Computational Biology Centre for DNA Fingerprinting and Diagnostics ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to break a disulfide bond ???
Hai ! with "pdb2gmx -ss", i can select the ss bonds. But after that, how to break a particular ss bond (not all). Thank you On Fri, Mar 6, 2009 at 11:01 AM, sharada wrote: > > pdb2gmx -h > > sharada > > > *-- Original Message --* > From: Venkat Reddy > To: Discussion list for GROMACS users > Date: Fri, 6 Mar 2009 10:50:24 +0530 > Subject: [gmx-users] How to break a disulfide bond ??? > > Hai Every one ! Is it possible to break a disulfide bridge using gromacs > ?If so,Can anybody suggest me, how to do it??? > > Thanks for ur valuable time > > With best wishes > Venkat Reddy Chirasani > M.Tech Bioinformatics > UNIVERSITY OF HYDERABAD > ___ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to break a disulfide bond ???
Hai Every one ! Is it possible to break a disulfide bridge using gromacs ?If so,Can anybody suggest me, how to do it??? Thanks for ur valuable time With best wishes Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Dear Sir !
how to save the coordinates of atoms at regular intervals that were generated during "mdrun" ?? Is it automatic or we need to modify .mdp file ???? Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs 4 with mpi interface
U just have to modify the .top file, Just add the line "Na+ 2" at the bottom of the file where u can find "SOL "and also u have to substract 2 from the SOL number. Thats it. Regarding MPI, if u r using MULTIPLE MACHINESthen MPI is useful otherwise , if u r using single machine with multiple processors,run the command "mdrun -np -s topol -v -N " That's it.Regarding the installation of MPI, first u should install the all library files that are mentioned in the Gromacs web site, "lam-7.0.6-5.x86_64.rpm,libaio-0.3.103-3.x86_64.rpm,libaio-devel-0.3.103-3.x86_64.rpm and fftw ". On Thu, Dec 18, 2008 at 1:03 AM, Chitrita Dutta Roy wrote: > Can anyone give me a detailed notes on how to install gromacs 4 with mpi > feature..I am using Intel Q9300 and fedora 10.It's very urgent as i am new > to using gromacs plz give me as detailed note as possible.. > > And after adding some ions using genion when i try to run grompp again > before final mdrun i get some error telling mismatches in .top and .gro file > in some atoms although i have changed the top files as normally we should > adding the ions and changing the total number of solvents accordingly..Why > is it happening Can anybody help..plzz?? > > Thanks. > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Hai Sir !
Dear Sir ! I am Currently running the Simulation of gp120. I got an error in middle of it. It states that "Constraint error in algorithm Lincs at step 19462839 " t=38925.684 ps : Water molecule starting at atom 17889 can't be settled. Please consider my problem. Thanking you sir Urs sincerely Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Regarding an Error !
Hai Sir ! This is Venkat Reddy, from the University Of Hyderabd,pursuing M.Tech Bioinformatics. Iam Currently using GROMACS in my project work. I got an error. It states that Range Checking error : Explanation: During Neibor searching, we assign each particle to a grid based on its coordinates. If ur system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +- Infinity or NaN. Obviously, we can't put theses on a grid, so thius is usually where we detect those errors. Make sure ur system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -1429249165.It should have been with in [0 377693999 ]. Please help me in this regard. Thank you Urs Sincerely Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
