I dont know what's wrong with your email but you should be very seriously check your email setting or whatever proper way to reply. This is the 3rd time you send identical question and you even quoted Ross' reply.
Hai
> On Mar 16, 2016, at 1:36 AM, necmettin pirinccioglu <pirincn.gmail.com> wrote:
>
> Dear All,
> I have been running MD for diphosphoric acid anion with the following input
> but I get the error message below. Helps will be welcomed!
>
> INPUT
> &cntrl
> imin=0, irest=1, ntx=5,
> nstlim=250000, dt=0.002,
> ntc=4, ntf=4,
> ntt=1, tautp=0.5,
> tempi=600.0, temp0=600.0,
> ntpr=500, ntwx=500,
> ntb=0, igb=0,
> cut=999
> /
>
> ERROR MESSAGE!!!
> ------------------------------
> ---------------------
> | Local SIZE OF NONBOND LIST = 1
> | TOTAL SIZE OF NONBOND LIST = 1
> vlimit exceeded for step 369; vmax = 22.0998
> vlimit exceeded for step 373; vmax = 54.3352
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 1 1 2
>
> --
> Necmettin Pirinccioglu (BSc, PhD)
> Department of Chemistry
> University of Dicle
> 21280 Diyarbakir
> TURKEY
>
>
> ------------------------------
>
> Message: 9
> Date: Thu, 25 Feb 2016 01:00:15 -0800
> From: Ross Walker <ross.rosswalker.co.uk>
> Subject: Re: [AMBER] problem running MD for diphosphoric acid anion
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <227AFD5C-E4F8-4D50-85CA-433B32C297B8.rosswalker.co.uk>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Necmettin,
>
> A few notes here. Firstly it is best to run a small number of steps say
> nstlim=500 with ntwx and ntpr = 1. That way you can see in detail what is
> going wrong and visualize the trajectory.
>
> Also, tempi=600 is hot - that may causes issues - especially if your system
> is not well equilibrated first.
>
> Finally ntc=4, ntf=4 - I have no idea if this works / gives you a stable
> potential function. I would not recommend going above ntf=2,ntc=2 for
> anything other than debugging.
>
> If changing to ntc=2,ntf=2 does not fix things then look carefully at your
> structure - it may not be well enough minimized, it may have structural
> deficiencies etc. Visualizing for and ntwx=1 run will help here.
>
> The parameters may also be suspect since this is not a regular amino /
> nucleic acid - where did you get the parameters from?
>
> All the best
> Ross
>
> Dear Ross, thanks for your kind reply. well firstly i did try with
> ntf=2,ntc=2 (the number 4 is for my last try) and secondly i have employed
> a shorter period. the trajectories indicate that the structure collapses
> and the mds are ended with the error after a while. please find the md
> trajectories as attached. I have done these calculations even at 700 K but
> it worked fine with other small molecules. but i have just got this with
> phosphoric acid. GAFF parameters were applied for the calculations... best
> wishes, necmettin
>
> --
> Necmettin Pirinccioglu (BSc, PhD)
> Department of Chemistry
> University of Dicle
> 21280 Diyarbakir
> TURKEY
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 5
> Date: Thu, 3 Mar 2016 01:22:43 -0800
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] problem running MD for diphosphoric acid anion
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <56D80263.7070907.cgl.ucsf.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Do you have a successful run previously where you warmed up your system
> to 600K? I would try setting ntpr and ntwx to 1 and look at the result.
> Apparently the bond between atoms 1 and 2 is being stressed too much.
> You may need a shorter time step for such a high temperature.
>
> Bill
>
>> On 3/3/16 12:49 AM, necmettin pirinccioglu wrote:
>> ---------- Forwarded message ----------
>> From: necmettin pirinccioglu <pirincn.gmail.com>
>> Date: Mon, Feb 29, 2016 at 9:56 AM
>> Subject: Re: problem running MD for diphosphoric acid anion
>> To: AMBER Mailing List <AMBER.ambermd.org>
>>
>>
>>
>> To: AMBER Mailing List <amber.ambermd.org>
>>
>>
>> Dear All,
>> I have been running MD for diphosphoric acid anion with the following
> input
>> but I get the error message below. Helps will be welcomed!
>>
>> INPUT
>> &cntrl
>> imin=0, irest=1, ntx=5,
>> nstlim=250000, dt=0.002,
>> ntc=4, ntf=4,
>> ntt=1, tautp=0.5,
>> tempi=600.0, temp0=600.0,
>> ntpr=500, ntwx=500,
>> ntb=0, igb=0,
>> cut=999
>> /
>>
>> ERROR MESSAGE!!!
>> ---------------------------------------------------
>> | Local SIZE OF NONBOND LIST = 1
>> | TOTAL SIZE OF NONBOND LIST = 1
>> vlimit exceeded for step 369; vmax = 22.0998
>> vlimit exceeded for step 373; vmax = 54.3352
>>
>> Coordinate resetting (SHAKE) cannot be accomplished,
>> deviation is too large
>> NITER, NIT, LL, I and J are : 0 0 1 1 2
>>
>> --
>> Necmettin Pirinccioglu (BSc, PhD)
>> Department of Chemistry
>> University of Dicle
>> 21280 Diyarbakir
>> TURKEY
>>
>>
>> ------------------------------
>>
>> Message: 9
>> Date: Thu, 25 Feb 2016 01:00:15 -0800
>> From: Ross Walker <ross.rosswalker.co.uk>
>> Subject: Re: [AMBER] problem running MD for diphosphoric acid anion
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <227AFD5C-E4F8-4D50-85CA-433B32C297B8.rosswalker.co.uk>
>> Content-Type: text/plain; charset=us-ascii
>>
>> Hi Necmettin,
>>
>> A few notes here. Firstly it is best to run a small number of steps say
>> nstlim=500 with ntwx and ntpr = 1. That way you can see in detail what is
>> going wrong and visualize the trajectory.
>>
>> Also, tempi=600 is hot - that may causes issues - especially if your
> system
>> is not well equilibrated first.
>>
>> Finally ntc=4, ntf=4 - I have no idea if this works / gives you a stable
>> potential function. I would not recommend going above ntf=2,ntc=2 for
>> anything other than debugging.
>>
>> If changing to ntc=2,ntf=2 does not fix things then look carefully at your
>> structure - it may not be well enough minimized, it may have structural
>> deficiencies etc. Visualizing for and ntwx=1 run will help here.
>>
>> The parameters may also be suspect since this is not a regular amino /
>> nucleic acid - where did you get the parameters from?
>>
>> All the best
>> Ross
>>
>> Dear Ross, thanks for your kind reply. well firstly i did try with
>> ntf=2,ntc=2 (the number 4 is for my last try) and secondly i have employed
>> a shorter period. the trajectories indicate that the structure collapses
>> and the mds are ended with the error after a while. please find the md
>> trajectories as attached. I have done these calculations even at 700 K but
>> it worked fine with other small molecules. but i have just got this with
>> phosphoric acid. GAFF parameters were applied for the calculations... best
>> wishes, necmettin
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 3 Mar 2016 16:37:13 +0530
> From: chandan patel <chandanz.gmail.com>
> Subject: Re: [AMBER] problem running MD for diphosphoric acid anion
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAOiU=0pM6NmzUL9kcb5Buwvmog_gnrZAT87S4CMwts_iivo1og.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hey,
> Smaller time step may help.
>> On Mar 3, 2016 2:52 PM, "Bill Ross" <ross.cgl.ucsf.edu> wrote:
>>
>> Do you have a successful run previously where you warmed up your system
>> to 600K? I would try setting ntpr and ntwx to 1 and look at the result.
>> Apparently the bond between atoms 1 and 2 is being stressed too much.
>> You may need a shorter time step for such a high temperature.
>>
>> Bill
>>
>>> On 3/3/16 12:49 AM, necmettin pirinccioglu wrote:
>>> ---------- Forwarded message ----------
>>> From: necmettin pirinccioglu <pirincn.gmail.com>
>>> Date: Mon, Feb 29, 2016 at 9:56 AM
>>> Subject: Re: problem running MD for diphosphoric acid anion
>>> To: AMBER Mailing List <AMBER.ambermd.org>
>>>
>>>
>>>
>>> To: AMBER Mailing List <amber.ambermd.org>
>>>
>>>
>>> Dear All,
>>> I have been running MD for diphosphoric acid anion with the following
>> input
>>> but I get the error message below. Helps will be welcomed!
>>>
>>> INPUT
>>> &cntrl
>>> imin=0, irest=1, ntx=5,
>>> nstlim=250000, dt=0.002,
>>> ntc=4, ntf=4,
>>> ntt=1, tautp=0.5,
>>> tempi=600.0, temp0=600.0,
>>> ntpr=500, ntwx=500,
>>> ntb=0, igb=0,
>>> cut=999
>>> /
>>>
>>> ERROR MESSAGE!!!
>>> ---------------------------------------------------
>>> | Local SIZE OF NONBOND LIST = 1
>>> | TOTAL SIZE OF NONBOND LIST = 1
>>> vlimit exceeded for step 369; vmax = 22.0998
>>> vlimit exceeded for step 373; vmax = 54.3352
>>>
>>> Coordinate resetting (SHAKE) cannot be accomplished,
>>> deviation is too large
>>> NITER, NIT, LL, I and J are : 0 0 1 1 2
>>>
>>> --
>>> Necmettin Pirinccioglu (BSc, PhD)
>>> Department of Chemistry
>>> University of Dicle
>>> 21280 Diyarbakir
>>> TURKEY
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 9
>>> Date: Thu, 25 Feb 2016 01:00:15 -0800
>>> From: Ross Walker <ross.rosswalker.co.uk>
>>> Subject: Re: [AMBER] problem running MD for diphosphoric acid anion
>>> To: AMBER Mailing List <amber.ambermd.org>
>>> Message-ID: <227AFD5C-E4F8-4D50-85CA-433B32C297B8.rosswalker.co.uk>
>>> Content-Type: text/plain; charset=us-ascii
>>>
>>> Hi Necmettin,
>>>
>>> A few notes here. Firstly it is best to run a small number of steps say
>>> nstlim=500 with ntwx and ntpr = 1. That way you can see in detail what
> is
>>> going wrong and visualize the trajectory.
>>>
>>> Also, tempi=600 is hot - that may causes issues - especially if your
>> system
>>> is not well equilibrated first.
>>>
>>> Finally ntc=4, ntf=4 - I have no idea if this works / gives you a stable
>>> potential function. I would not recommend going above ntf=2,ntc=2 for
>>> anything other than debugging.
>>>
>>> If changing to ntc=2,ntf=2 does not fix things then look carefully at
>> your
>>> structure - it may not be well enough minimized, it may have structural
>>> deficiencies etc. Visualizing for and ntwx=1 run will help here.
>>>
>>> The parameters may also be suspect since this is not a regular amino /
>>> nucleic acid - where did you get the parameters from?
>>>
>>> All the best
>>> Ross
>>>
>>> Dear Ross, thanks for your kind reply. well firstly i did try with
>>> ntf=2,ntc=2 (the number 4 is for my last try) and secondly i have
>> employed
>>> a shorter period. the trajectories indicate that the structure collapses
>>> and the mds are ended with the error after a while. please find the md
>>> trajectories as attached. I have done these calculations even at 700 K
>> but
>>> it worked fine with other small molecules. but i have just got this with
>>> phosphoric acid. GAFF parameters were applied for the calculations...
>> best
>>> wishes, necmettin
>
> Dear Bill, thank you for your advise... well I did it for shorter steps as
> also suggested by Ross... the structure eventually collapses. I did many
> calculations for small and medium size molecules at high temperatures using
> gaff but i did not get this error with these calculations. I think there is
> something wrong with phosphoric acid parameters...best wishes, necmettin
>
> PS. Dear Professor Case, thanks for your comment. yes indeed the previous
> message was seen as spam...np
> --
> Necmettin Pirinccioglu (BSc, PhD)
> Department of Chemistry
> University of Dicle
> 21280 Diyarbakir
> TURKEY
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Mar 16 2016 - 01:00:04 PDT
