[gmx-users] work calculation

, -- Aswathy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send

Re: [gmx-users] Umbrella sampling question

point that you suggested "check the probability histograms and ensuring that they tend away from the center of restraint and toward local minima". ? Thanks in advance. On Mon, Sep 20, 2010 at 6:22 PM, wrote: > Aswathy: > > We can't tell if you did US correctly unless you

[gmx-users] Umbrella sampling question

sport Smds the PMF was continuous maxima and minima. Can any one tell whether my US procedures were right or not? Thanks, -- Aswathy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Su

[gmx-users] Electrostatic interaction Vs Z axis

, -- Aswathy -- 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

Re: [gmx-users] Problem in pullx file

5.46432 1099.88008.45551-5.46076 1099.90008.45817-5.46827 1099.92008.460755.46829 1099.94018.46317-5.46782 1099.96018.465455.46577 1099.98018.46565-5.47014 1100.8.466515.46001 Thanks, Aswathy On Thu, Aug 5, 2010 at 4:28 PM, Justin A. Lemkul

Re: [gmx-users] Problem in pullx file

On Wed, Aug 4, 2010 at 4:31 PM, Justin A. Lemkul wrote: > > > Aswathy wrote: > >> Dear Gromacs users, >> >> I am doing SMD of a ligand pathway, and then want ot do the PMF analysis. >> Initially I pulled the ligand from extra to intracellular side of the >

[gmx-users] Problem in pullx file

you please suggest me where thing get wrong? http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en Thank you, -- -Aswathy -- gmx-users

[gmx-users] Pullx file

and the ligand. But that does not take the place of pullx. Please give your suggestions. Thanks, -- Aswathy -- 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

Re: [gmx-users] umbrella sampling-Bimodal Histograms

= 0 0 0 > > Please check this link for my histograms > > > https://docs.google.com/fileview?id=0B1PyTWWGrqt6MDU3NWYwMGUtNjY5Zi00NDBmLWE0YzMtYTNjODVlOGFlNWVl&hl=en > > I would greatly appreciate our suggestions. > > Thank you, > -Aswathy > > On Mon, Jun 21, 2010 at 8:14 PM, wrote: > > Please clarify: &

Re: [gmx-users] umbrella sampling-Bimodal Histograms

ions. Thank you, -Aswathy On Mon, Jun 21, 2010 at 8:14 PM, wrote: > Please clarify: > > Are doing SMD or are you doing US? If you're doing SMD then you should not > be using WHAM and you should not really be able to generate any sampling > histograms. > > Are the histog

[gmx-users] umbrella sampling-Bimodal Histograms

result? Do I need to repeat the sampling again with another pull_k1 value(higher value)? Thanks, -- Aswathy -- Aswathy -- 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

[gmx-users] Query on WHAM analysis

. Can anyone please explain me these two terms? I have the pullx files from 21 umbrella samplings.(I guess this will go as the first term in the meta data file.). Pull_k1 used for Us was 1000. Please let me know if you need any other details. Thanks in advance, -Aswathy -- gmx-users maili

Re: [gmx-users] Enough hydration of the channel

Thanks a lot. On Fri, Jun 18, 2010 at 9:30 AM, Justin A. Lemkul wrote: > > > Aswathy wrote: > >> Thank you very much. >> >> In some papers I have seen the graph for hydration of the channel. How can >> we calculate that using Gromacs ? (or any other pro

Re: [gmx-users] Enough hydration of the channel

Thank you very much. In some papers I have seen the graph for hydration of the channel. How can we calculate that using Gromacs ? (or any other program?) Regards, -Aswathy On Thu, Jun 17, 2010 at 7:52 PM, wrote: > Determining how many waters is sufficient is a tough problem, try > succ

[gmx-users] Enough hydration of the channel

how many water molecules will be sufficient for the channel? Thanks for your support. -- Aswathy -- 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

[gmx-users] Fwd: reproducibility of PMF plot with two different starting structures?

position are slightly different). I performed the sampling of these two pathways, the plots obtained are of similar overall shapes, but peaks (max , min) have some variations? Could you please give your comment on this attempt? Is that expectable? Thank you, -- Aswathy -- Aswathy

Re: [gmx-users] PMF of ligand transport

On Mon, May 17, 2010 at 12:14 PM, Aswathy wrote: > Hi, > > I tried to calculate PMF for the ligand transport using > pull_geometry=position. > > Let me explain you what I did so far, > > I picked a small collection of backbone atoms nearly from the centre of the > ch

Re: [gmx-users] PMF of ligand transport

problem is that the ligand undergoes a displacement to wrong direction during sampling. My idea was pull_k1 = 1000 is the force to keep ligand in one place where it get sampled? Is there anything wrong that I am doing? any suggestions will be appreciated. -Aswathy On Tue, May 11, 2010 at 11:15 AM

Re: [gmx-users] PMF of ligand transport

Chris, I understand, Sorry for that . Actually I mixed up the concept of SteeredMd with umbrella sampling. So I was confused whenever you people gave suggestions. Now I thing I got the idea , Thanks for you people. I will try myself and see. Thanks once again. -Aswathy On Tue, May 11, 2010 at

Re: [gmx-users] PMF of ligand transport

suppose so, if its true how?) When it should be negative and positive? Could you please explain this. Thanks for your valuable time Thanks & Regards, Aswathy On Mon, May 10, 2010 at 9:55 PM, Chris Neale wrote: > Pick a small collection of backbone atoms near the center of your channel &g

Re: [gmx-users] Re: PMF of ligand transport

your maximum effort to make me understand this thing) And if we use a dummy particle, will the movement of that particle will also matter ? How can we fix that? Thank you. Aswathy On Mon, May 10, 2010 at 8:45 PM, Thomas Schlesier wrote: > Would it be possible to use a dummy particle near the en

Re: [gmx-users] PMF of ligand transport

th large > fluctuatuion in the loop, will it affect the result)? > > Aswathy wrote: > >> I am pulling through the channel with respect to a single residue on one >> "side"(extracellular) of the structure. I have used pull_geometry = distance >> & pull_dim

Re: [gmx-users] PMF of ligand transport

0 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = r_57 pull_group1 = r_C1 pull_k1 = 1000 pull_init1 = 0 On Mon, May 10, 2010 at 4:50 PM, Justin A. Lemkul wrote: > > > Aswathy wrote: > >> Thanks for

Re: [gmx-users] PMF of ligand transport

Thanks for your reply. In this case reference (r57) is not the part of the channel. But it is a residue in the loop above the channel entry. Thats why I used pull_geometry=distance. Therefore I am pulling the ligand away from this reference. Thanks -Aswathy On Mon, May 10, 2010 at 3:05 PM

Re: [gmx-users] PMF of ligand transport

Can any one help me please? I looking forward to hear from any of you. Thank you. On Thu, May 6, 2010 at 1:19 PM, Aswathy wrote: > Ok i will explain you in detail. > > Initially i pulled the ligand through the protein channel , using the > given paramete

Re: [gmx-users] PMF of ligand transport

increasing potential with some small curves here and there. The PMF is not at all converged. Did I made any mistake any where , I am confused. If you want I can attach the PMF profile Thank you. -Aswathy On Thu, May 6, 2010 at 12:56 PM, Jochen Hub wrote: > Aswathy wrote: > >> &

[gmx-users] PMF of ligand transport

. -Aswathy -- 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

Re: [gmx-users] Water atoms cannot be settled

condition) attaching the mdp file. Thanks & Regards, Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: Wednesday, July 8, 2009 5:27:42 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi

[gmx-users] Water atoms cannot be settled

se tell me your comments, Thanks Aswathy Dept. Biotechnology Ext. 3108 md_Eq1_NVT.mdp Description: Binary data md_NPT.mdp Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-user

Re: [gmx-users] few doubts regarding 1-4 interaction

your response. Aswathy - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Tuesday, June 30, 2009 8:33:19 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] few doubts regarding 1-4 interaction Ms. A

[gmx-users] few doubts regarding 1-4 interaction

error(I have seen in the error section of gromacs that another possibility is to reduce the time step?) Can you please tell me your suggestion on these?? Thank you. Aswathy Dept. Biotechnology Ext. 3108 ___ gmx-users mailing listgmx-users

Re: [gmx-users] Coordinates change after minimization

3108 - Original Message - From: "XAvier Periole" To: "Discussion list for GROMACS users" Sent: Saturday, June 20, 2009 7:16:26 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] Coordinates change after minimization On Jun 20, 2009, at 15:3

Re: [gmx-users] Coordinates change after minimization

3108 - Original Message - From: "David van der Spoel" To: "Discussion list for GROMACS users" Sent: Saturday, June 20, 2009 6:07:20 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] Coordinates change after minimization Justin A. Lemkul wrote: > >

[gmx-users] Coordinates change after minimization

Hi, After minimizing the protein -ligand complex, the co-ordinates have changed drastically.My idea about minimization was the coordinates will have minute changes only. In this case my protein is completely transferring to a new co-ordinates.Is that reasonable.?? Thanks, Aswathy Dept

Re: [gmx-users] problem in ngmx

Ok. You meant I have to cross check these parameters before getting in to simulation.I will do that Thank you very much for your replies. Dept. Biotechnology Ext. 3108 - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Wednesday, June 17, 2009

Re: [gmx-users] problem in ngmx

hi Justin, I tried the NVT once with certain changes in the parameter file. Now its finished the 10 ps. But I have used the charge as the same from the antechamber program. Do you think the result will be reliable? Please check the mdp file attached for NVT. Thnaks for your help Aswathy Dept

Re: [gmx-users] problem in ngmx

rs' List" Sent: Tuesday, June 16, 2009 5:03:26 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Ms. Aswathy S wrote: > sorry..forgot to attach the file... > > After my NVT I have checked the PE of the system..It was stabilised..So I >

Re: [gmx-users] problem in ngmx

- From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Tuesday, June 16, 2009 4:44:47 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Ms. Aswathy S wrote: > Hi, > > In my NPT step I think there is

Re: [gmx-users] problem in ngmx

; (Captain Beefheart) OIn some pev Dept. Biotechnology Ext. 3108 - Original Message - From: "Ms. Aswathy S" To: "Discussion list for GROMACS users" Sent: Tuesday, June 16, 2009 12:40:04 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] pro

Re: [gmx-users] problem in ngmx

(checked in the xmgrace). Seems it works fine..Now started the NPT equilibration. Thank you very much for your support. Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Monday, June 15,

Re: [gmx-users] problem in ngmx

- From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Sunday, June 14, 2009 10:51:30 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Ms. Aswathy S wrote: > Hi Justin, > > I tried maximum to find ou

Re: [gmx-users] problem in ngmx

lease find some time to help me. Thank you very much, Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Saturday, June 13, 2009 6:23:04 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi

Re: [gmx-users] problem in ngmx

ps(1 steps).But the output coordinates file doesnt show any abnornmality as i checked in the viewer? My equilibration step was in NVT. whether nothing is happening or any other problem? Thanks & regards, Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From:

[gmx-users] problem in ngmx

help me, please??? Thanks, Aswathy ASBT Dept. Biotechnology Ext. 3108 ___ 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

Re: [gmx-users] Error in hdb file ffG43a1.hdb

Please ignore this post. I rectified the problem by using the GMXLIB export. Thank you very much for all the support Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: "Ms. Aswathy S" To: "gmx-users" Sent: Saturday, June 13, 2009 12:00:11 PM GMT +05

[gmx-users] Error in hdb file ffG43a1.hdb

??? --- Program pdb2gmx_mpi, VERSION 3.3.3 Source code file: h_db.c, line: 95 Fatal error: Error in hdb file ffG43a1.hdb: Wrong number of control atoms (2 iso 3) on line: 1 1 N -C CA Thanks in advance, Aswathy Dept

Re: [gmx-users] ERROR: pressure coupling not enough values (I need 1)

step 0 MPI process rank 0 (n0, p9393) caught a SIGSEGV. Thanks, Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Friday, June 12, 2009 4:31:28 PM GMT +05:30 Chennai, Kolkata, Mumbai, New

[gmx-users] ERROR: pressure coupling not enough values (I need 1)

Hi, thanks for the help till now.. Now I got a problem that an equilibration step of 20 ps shows an error as follows when i run grommp. ERROR: pressure coupling not enough values (I need 1) Please find the md.mdp file that I have used for this step. thanks, Aswathy Dept. Biotechnology Ext

[gmx-users] How can I create the OPLS-AA topology file for the liagnd

coreect me if my understanding is wrong. Thanks in advance, Aswathy ___ 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

[gmx-users] Fwd: Segmentation fault while running gromacs 4.0.4

Dept. Biotechnology Ext. 3108 - Forwarded Message - From: "Ms. Aswathy S" To: gmx-users@gromacs.org Sent: Tuesday, June 2, 2009 11:54:56 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Segmentation fault while running gromacs 4.0.4 Hi, I am working in GROMACS

[gmx-users] Re: Ligand is moving far away after energy minimization

Ms. Aswathy S wrote: > Dear Gromacs users, > > I am doing the MD of protein ligand complex. When I did the energy > minimization of this complex, in the result , the ligand molceule is moving > far away from the protein. > > What could be the possible reason? can any

[gmx-users] Ligand is moving far away after energy minimization

. Aswathy Amrita School of biotechnology Dept. Biotechnology Ext. 3108 ___ 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&#

[gmx-users] Re: IN4 molecule type error

Sorry for the mistake.. It worked well!!! Thank you... Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org Sent: Tuesday, February 3, 2009 1:47:57 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: gmx-users

[gmx-users] Re: IN4 molecule type error

fcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name TRYPSIN in water [ molecules ] ; Compound#mols Protein_A 1 IN4 1 SOL 8902 __

[gmx-users] Re: gmx-users Digest, Vol 58, Issue 2

p directory? Thanks, Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org Sent: Sunday, February 1, 2009 4:30:04 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: gmx-users Digest, Vol 58, Issue 2 Send gmx-users mailing

[gmx-users] IN4 molecule type error

the .mdp file processing topology... Generated 1284 of the 1485 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Cleaning up temporary file gromppVEFM2b Fatal error: No such moleculetype IN4 Can you please tell me what could be the reason for this? Please help me. T